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"GEO:GSE890" } ] }, "title" : "Gene expression profile at 3hr after common bile duct ligation", "dateAssigned" : "2003-12-12T00:00:00.000-06:00", "summary" : "Keywords: repeat sample", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE891" }, "primaryId" : "GEO:GSE891", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE891" } ] }, "title" : "Gene expression profile at 12hr after common bile duct ligation", "dateAssigned" : "2003-12-12T00:00:00.000-06:00", "summary" : "Keywords: repeat sample", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE892" }, "primaryId" : "GEO:GSE892", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE892" } ] }, "title" : "Gene expression profile at 12hr after ANIT administration", "dateAssigned" : "2003-12-12T00:00:00.000-06:00", "summary" : "Keywords: repeat 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"crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE898" } ] }, "title" : "Common bile duct ligation time-course", "dateAssigned" : "2003-12-12T00:00:00.000-06:00", "summary" : "Keywords: time-course", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE900" }, "primaryId" : "GEO:GSE900", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE900" } ] }, "title" : "Alpha-naphtylisothiocyanate administration time-course", "dateAssigned" : "2003-12-12T00:00:00.000-06:00", "summary" : "Keywords: time-course", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE903" }, "primaryId" : "GEO:GSE903", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE903" } ] }, "title" : "EOM and hindlimb muscle development", "dateAssigned" : "2003-12-12T00:00:00.000-06:00", "summary" : "Keywords: parallel 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"preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE924" }, "primaryId" : "GEO:GSE924", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE924" } ] }, "title" : "Cardiopulmonary bypass (CPB) vs sham-operated controls", "dateAssigned" : "2003-12-19T00:00:00.000-06:00", "summary" : "Keywords: other", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16077395" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE925" }, "primaryId" : "GEO:GSE925", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE925" } ] }, "title" : "A Comparison of Neonatal Rat Ventricular Myocytes Treated With Phenylephrine or PAMH", "dateAssigned" : "2003-12-19T00:00:00.000-06:00", "summary" : "Keywords: repeat sample", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16950785" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ 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"crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE1892" } ] }, "title" : "Gene Expression in Iron-Deficient Rat Duodenum", "dateAssigned" : "2004-10-26T00:00:00.000-05:00", "summary" : "Keywords: time-course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16629162" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE1911" }, "primaryId" : "GEO:GSE1911", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE1911" } ] }, "title" : "Hippocampal gene expression after brain injury", "dateAssigned" : "2004-11-01T00:00:00.000-06:00", "summary" : "Keywords: time-course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:11891777" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE1918" }, "primaryId" : "GEO:GSE1918", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE1918" } ] }, 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"htp/dataset" ], "id" : "GEO:GSE2982" } ] }, "title" : "Effect of inhaled anesthetic to cultured cortical neurons", "dateAssigned" : "2005-07-22T00:00:00.000-05:00", "summary" : "Keywords: DNA Oligonucleotide Array", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16495776" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3016" }, "primaryId" : "GEO:GSE3016", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3016" } ] }, "title" : "Gene expression evidence for remodeling of lateral hypothalamic circuitry in cocaine addiction", "dateAssigned" : "2005-07-27T00:00:00.000-05:00", "summary" : "Keywords: cocaine addiction ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16076954" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3068" }, "primaryId" : "GEO:GSE3068", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3068" } ] }, "title" : "normal and diabetic rat muscle treated and untreated with vanadyl sulfate", "dateAssigned" : "2005-08-05T00:00:00.000-05:00", "summary" : "Keywords: vanadium treatment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16684804" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3073" }, "primaryId" : "GEO:GSE3073", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3073" } ] }, "title" : "Stomach parietal cells expression analysis", "dateAssigned" : "2005-08-05T00:00:00.000-05:00", "summary" : "Keywords: other", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:15613615" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3110" }, "primaryId" : "GEO:GSE3110", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3110" } ] }, "title" : "Comprehensive description of the transcriptome of hypothalamo-neurohypophyseal system in euhydrated and dehydrated rat", "dateAssigned" : "2005-08-11T00:00:00.000-05:00", "summary" : "Keywords: Dehydration", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17329416" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3111" }, "primaryId" : "GEO:GSE3111", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3111" } ] }, "title" : "Comprehensive description of the transcriptome of PVN in euhydrated and dehydrated rat", "dateAssigned" : "2005-08-11T00:00:00.000-05:00", "summary" : "Keywords: DEHYDRATION, PVN", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16432224" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3125" }, "primaryId" : "GEO:GSE3125", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3125" } ] }, "title" : "Comprehensive description of the transcriptome of neurointermediate lobe in euhydrated and dehydrated rat", "dateAssigned" : "2005-08-13T00:00:00.000-05:00", "summary" : "Keywords: DEHYDRATED - NIL", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16432224" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3131" }, "primaryId" : "GEO:GSE3131", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3131" } ] }, "title" : "Microarray analysis of the dynamics of gene expression plasticity in the supraoptic nucleus following dehydration", "dateAssigned" : "2005-08-15T00:00:00.000-05:00", "summary" : "Keywords: SON, Dehydration, clone", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16432224" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3132" }, "primaryId" : "GEO:GSE3132", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3132" } ] }, "title" : "SSH-PCR dehydrated supraoptic nucleus", "dateAssigned" : "2005-08-15T00:00:00.000-05:00", "summary" : "Keywords: dehydrated, SON, clone", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16249312" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3133" }, "primaryId" : "GEO:GSE3133", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3133" } ] }, "title" : "NIA Neuroarray dehydration", "dateAssigned" : "2005-08-15T00:00:00.000-05:00", "summary" : "Keywords: dehydration, SON, NIA", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16249312" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3159" }, "primaryId" : "GEO:GSE3159", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3159" } ] }, "title" : "ICAT quantitative proteomic analysis of Myc-induced apoptosis", "dateAssigned" : "2005-08-17T00:00:00.000-05:00", "summary" : "Keywords: proteomic, apoptosis, cell fractions", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16316993" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3173" }, "primaryId" : "GEO:GSE3173", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3173" } ] }, "title" : "Identification of novel transcriptional networks in response to the treatment D3T (3H-1, 2-dithiole-3-thione) ", "dateAssigned" : "2005-08-22T00:00:00.000-05:00", "summary" : "Keywords: Response to antioxidant compound", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16317079" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3175" }, "primaryId" : "GEO:GSE3175", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3175" } ] }, "title" : " 3-Methylcholanthrene treated Rat", "dateAssigned" : "2005-08-22T00:00:00.000-05:00", "summary" : "Keywords: toxicity", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3210" }, "primaryId" : "GEO:GSE3210", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3210" } ] }, "title" : "A Gene Expression Signature that Predicts the Future Onset of Drug-Induced Renal Tubular Toxicity", "dateAssigned" : "2005-08-26T00:00:00.000-05:00", "summary" : "Keywords: time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16239200" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3215" }, "primaryId" : "GEO:GSE3215", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3215" } ] }, "title" : "Gene Expression for fetal kidneys of hyper insulinemia induced intrauterine growth restriction rat model", "dateAssigned" : "2005-08-29T00:00:00.000-05:00", "summary" : "Keywords: disease state analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16923994" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3219" }, "primaryId" : "GEO:GSE3219", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3219" } ] }, "title" : "Ischemic vs. nephrotoxic acute renal failure, early time points (2h and 8h)", "dateAssigned" : "2005-08-29T00:00:00.000-05:00", "summary" : "Keywords: Disease classification/time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16507785" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3221" }, "primaryId" : "GEO:GSE3221", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3221" } ] }, "title" : "reversible and irreversible Thy-1 nephritis", "dateAssigned" : "2005-08-29T00:00:00.000-05:00", "summary" : "Keywords: time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16528249" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3251" }, "primaryId" : "GEO:GSE3251", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3251" } ] }, "title" : "The gene expression profile of PDGF-treated neural stem cells corresponds to partially differentiated neurons and glia", "dateAssigned" : "2005-09-06T00:00:00.000-05:00", "summary" : "Keywords: treatment comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17079202" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3258" }, "primaryId" : "GEO:GSE3258", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3258" } ] }, "title" : "Comparison of three populations of OECs", "dateAssigned" : "2005-09-07T00:00:00.000-05:00", "summary" : "Keywords: OEC cells, adaptation to long-term culture, genetic immortalization", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16707787" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3290" }, "primaryId" : "GEO:GSE3290", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3290" } ] }, "title" : "Expression profiling in perinatal Ductus Arteriosus (DA) and Aorta (Ao).", "dateAssigned" : "2005-09-11T00:00:00.000-05:00", "summary" : "Keywords: Comparison gene expression ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16418320" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3298" }, "primaryId" : "GEO:GSE3298", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3298" } ] }, "title" : "mRNA expression in rat proximal femoral growthplate after mid-shaft fracture", "dateAssigned" : "2005-09-13T00:00:00.000-05:00", "summary" : "Keywords: time course, fracture, growthplate, rat", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17398174" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3299" }, "primaryId" : "GEO:GSE3299", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3299" } ] }, "title" : "Identification of biomarkers for tumor endothelial cell proliferation through gene expression profiling", "dateAssigned" : "2005-09-13T00:00:00.000-05:00", "summary" : "Keywords: Endothelial cell proliferation", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:15767550" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3302" }, "primaryId" : "GEO:GSE3302", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3302" } ] }, "title" : "Fetal lung development ", "dateAssigned" : "2005-09-13T00:00:00.000-05:00", "summary" : "Keywords: Time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16798779" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3304" }, "primaryId" : "GEO:GSE3304", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3304" } ] }, "title" : "Comparison of gene expression in conventional and germ-free intestine", "dateAssigned" : "2005-09-14T00:00:00.000-05:00", "summary" : "Keywords: comparative genomic hybridization", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3305" }, "primaryId" : "GEO:GSE3305", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3305" } ] }, "title" : "Age alters the gene expression profiles of rat oculomotor nucleus and spinal cord", 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"datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3311" }, "primaryId" : "GEO:GSE3311", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3311" } ] }, "title" : "Effect of chronic ethanol consumption on rat pancreas", "dateAssigned" : "2005-09-15T00:00:00.000-05:00", "summary" : "Keywords: stress response, disease state analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16804415" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3339" }, "primaryId" : "GEO:GSE3339", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3339" } ] }, "title" : "Response of young and aged Mesenchymal Stem Cells to Dexamethasone", "dateAssigned" : "2005-09-21T00:00:00.000-05:00", "summary" : "Keywords: age effect, treatment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16643645" } ] }, { "datasetId" : { 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"id" : "GEO:GSE3403" }, "primaryId" : "GEO:GSE3403", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3403" } ] }, "title" : "SHR-SP rats on Normal and High Salt+Fat diets, 2 vs. 8 weeks", "dateAssigned" : "2005-10-03T00:00:00.000-05:00", "summary" : "Keywords: timecourse, diet", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17438656" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3420" }, "primaryId" : "GEO:GSE3420", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3420" } ] }, "title" : "Effects of maternal vitamin A administration on the transcriptional profile of rat ductus arteriosus", "dateAssigned" : "2005-10-07T00:00:00.000-05:00", "summary" : "Keywords: time course, development, response to a nutritional agent", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17636115" } ] }, { "datasetId" : { "preferredCrossReference" 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"pages" : [ "htp/dataset" ], "id" : "GEO:GSE3518" }, "primaryId" : "GEO:GSE3518", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3518" } ] }, "title" : "Stomach ECL cell expression analysis", "dateAssigned" : "2005-10-26T00:00:00.000-05:00", "summary" : "Keywords: Gastric ECL cells, Subtractive Hybridization, Comparative genomic hybridization", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16403840" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3531" }, "primaryId" : "GEO:GSE3531", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3531" } ] }, "title" : "LTM in CA1 Aged versus young rats", "dateAssigned" : "2005-10-28T00:00:00.000-05:00", "summary" : "Keywords: behavior comparison, age comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16829144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ 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"publicationId" : "PMID:16550590" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3675" }, "primaryId" : "GEO:GSE3675", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3675" } ] }, "title" : "Gene expression profiles during the development of compensated or decompensated hypertrophy during pressure overload", "dateAssigned" : "2005-11-24T00:00:00.000-06:00", "summary" : "Keywords: dose response x time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:15728335" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3696" }, "primaryId" : "GEO:GSE3696", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3696" } ] }, "title" : "Rat brain microvessel SAGE", "dateAssigned" : "2005-11-29T00:00:00.000-06:00", "summary" : "Keywords: Novel gene identification", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16306934" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3740" }, "primaryId" : "GEO:GSE3740", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3740" } ] }, "title" : "Ethanol induced hepatic gene expression changes during gestation", "dateAssigned" : "2005-12-03T00:00:00.000-06:00", "summary" : "Keywords: Nutrition-gene interactions", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16946407" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3775" }, "primaryId" : "GEO:GSE3775", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3775" } ] }, "title" : "Global Gene Expression Profiles of Single-Cell Derived Fetal Rat Calvaria Cell Colonies with Adipocyte and Bone Markers", "dateAssigned" : "2005-12-07T00:00:00.000-06:00", "summary" : "Keywords: other", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3778" }, "primaryId" : "GEO:GSE3778", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3778" } ] }, "title" : "Gender dependent expression", "dateAssigned" : "2005-12-08T00:00:00.000-06:00", "summary" : "Keywords: repeat", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17620128" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3866" }, "primaryId" : "GEO:GSE3866", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3866" } ] }, "title" : "p38 MAPK overexpression in heart in vivo.", "dateAssigned" : "2005-12-19T00:00:00.000-06:00", "summary" : "Keywords: Gene transfer", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16873723" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3904" }, "primaryId" : "GEO:GSE3904", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3904" } ] }, "title" : "very moderate exercise training; variations in stress and toxicity gene expression in rat hearts.", "dateAssigned" : "2005-12-26T00:00:00.000-06:00", "summary" : "Keywords: exercise training-related stress response and cardioprotection", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3952" }, "primaryId" : "GEO:GSE3952", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE3952" } ] }, "title" : "Organ - specific expression profiles of rat treated with targretin, 9-cis retinoic acid, and 4-hydroxyphenylretinamide", "dateAssigned" : "2005-12-30T00:00:00.000-06:00", "summary" : "Keywords: parallel sample", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16648578" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4028" }, "primaryId" : "GEO:GSE4028", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4028" } ] }, "title" : "Effects of diethylstilbestrol (DES) on the anterior pituitary gland of the ACI, Copenhagen and Brown Norway Rat.", "dateAssigned" : "2006-01-13T00:00:00.000-06:00", "summary" : "Keywords: Estrogen Response", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4031" }, "primaryId" : "GEO:GSE4031", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4031" } ] }, "title" : "Ventral hippocampal lesion, tetrodotoxin disruption of the ventral hippocampus, and chronic administration of neuroleptics (colan-affy-rat-89421)", "dateAssigned" : "2006-01-13T00:00:00.000-06:00", "summary" : "Grand Total N=105", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4037" }, "primaryId" : "GEO:GSE4037", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4037" } ] }, "title" : "prosc-affy-rat-185420", "dateAssigned" : "2006-01-13T00:00:00.000-06:00", "summary" : "Keywords: other", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4038" }, "primaryId" : "GEO:GSE4038", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4038" } ] }, "title" : "sabba-affy-rat-168529", "dateAssigned" : "2006-01-13T00:00:00.000-06:00", "summary" : "Keywords: dose response", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4042" }, "primaryId" : "GEO:GSE4042", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4042" } ] }, "title" : "Gene expression profiling of a temperature-sensitive strain of Neospora caninum", "dateAssigned" : "2006-01-13T00:00:00.000-06:00", "summary" : "Keywords: mutant comparision, two class unpaired design", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21963790" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4080" }, "primaryId" : "GEO:GSE4080", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4080" } ] }, "title" : "Effect of DES-treated Ept congenic rat lines on gene expression in the anterior pituitary gland.", "dateAssigned" : "2006-01-23T00:00:00.000-06:00", "summary" : "Keywords: Estrogen Response", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4081" }, "primaryId" : "GEO:GSE4081", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4081" } ] }, "title" : "Expression QTL (eQTL) mapping in the anterior pituitary gland using DES-treated COPxACI F2 rats.", "dateAssigned" : "2006-01-23T00:00:00.000-06:00", "summary" : "Keywords: Estrogen Response", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4105" }, "primaryId" : "GEO:GSE4105", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4105" } ] }, "title" : "Rat LAD IR study", "dateAssigned" : "2006-01-26T00:00:00.000-06:00", "summary" : "Keywords: rat heart ventricles, LAD - left anterior descending coronary artery, IR - ischemia-reperfusion", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16554547" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4121" }, "primaryId" : "GEO:GSE4121", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4121" } ] }, "title" : "Limbal and Central Corneal Epithelia", "dateAssigned" : "2006-01-30T00:00:00.000-06:00", "summary" : "Keywords: gene expression SAGE-based, count", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16936091" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4206" }, "primaryId" : "GEO:GSE4206", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4206" } ] }, "title" : "Reduced inflammatory response under candesartan pre-treatment following transient focal ischemia in rats", "dateAssigned" : "2006-02-08T00:00:00.000-06:00", "summary" : "Keywords: disease state analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4242" }, "primaryId" : "GEO:GSE4242", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4242" } ] }, "title" : "devellis-5U24NS043562-02", "dateAssigned" : "2006-02-14T00:00:00.000-06:00", "summary" : "Keywords: time-course", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4254" }, "primaryId" : "GEO:GSE4254", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4254" } ] }, "title" : "Bis(2-chloroethoxy)methane-induced heart toxicity and recovery in male fisher rats", "dateAssigned" : "2006-02-16T00:00:00.000-06:00", "summary" : "Keywords: toxicity, recovery, cardiac, heart", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16844662" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4270" }, "primaryId" : "GEO:GSE4270", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4270" } ] }, "title" : "Aging Induced Alterations in Hepatic Gene Expression of the Male Fisher Rat", "dateAssigned" : "2006-02-17T00:00:00.000-06:00", "summary" : "Keywords: : Liver, rat, differential gene expression, microarray, transcriptome, aging, cytochrome P450, xenobiotic metabolism", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17366318" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4286" }, "primaryId" : "GEO:GSE4286", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4286" } ] }, "title" : "Making a predictive heart failure expression profile in Ren2 rat left ventricles", "dateAssigned" : "2006-02-21T00:00:00.000-06:00", "summary" : "Keywords: heart failure, comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17485520" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4327" }, "primaryId" : "GEO:GSE4327", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4327" } ] }, "title" : "Modulation of cardiomyocyte gene expression by n-3 PUFA supplementation", "dateAssigned" : "2006-03-03T00:00:00.000-06:00", "summary" : "Keywords: nutritional intervention, treatment response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17303130" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4340" }, "primaryId" : "GEO:GSE4340", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4340" } ] }, "title" : "Establishing a functional response of cardiomyocytes upon prorenin stimulation.", "dateAssigned" : "2006-03-05T00:00:00.000-06:00", "summary" : "Keywords: loop design", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16940215" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4418" }, "primaryId" : "GEO:GSE4418", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4418" } ] }, "title" : "Expression data from cerivastatin-treated rat skeletal muscle", "dateAssigned" : "2006-03-08T00:00:00.000-06:00", "summary" : "Keywords: dose response; exercise effect", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { 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"primaryId" : "GEO:GSE4441", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4441" } ] }, "title" : "Gene expression profiling in rat renal allografts after prolonged cold ischemia", "dateAssigned" : "2006-03-10T00:00:00.000-06:00", "summary" : "Keywords: transplantation, cold ischemia, inflammation, gene expression profiling", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17854277" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4458" }, "primaryId" : "GEO:GSE4458", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4458" } ] }, "title" : "Effer/Affer Interaction in Vestibular Caliceal vs. Dimorphic and Bouton Primary Afferent Neurons", "dateAssigned" : "2006-03-13T00:00:00.000-06:00", "summary" : "Keywords: expression profiling, neuropeptides, vestibular neuroepithelium, calretinin", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { 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"publications" : [ { "publicationId" : "PMID:16870687" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4551" }, "primaryId" : "GEO:GSE4551", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4551" } ] }, "title" : "experiment in midbrain primary cultures, enriched in dopaminergic neurons", "dateAssigned" : "2006-03-27T00:00:00.000-06:00", "summary" : "Keywords: depolarization, microarrays, time course.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17506860" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4552" }, "primaryId" : "GEO:GSE4552", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4552" } ] }, "title" : "Gene profiling of spleens of adult protected rats from Plasmodium berghei ANKA", "dateAssigned" : "2006-03-27T00:00:00.000-06:00", "summary" : "Keywords: age, malaria, protection, rat", "categoryTags" : 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"preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4653" }, "primaryId" : "GEO:GSE4653", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4653" } ] }, "title" : "Diaphragm in Diabetes", "dateAssigned" : "2006-04-11T00:00:00.000-05:00", "summary" : "Keywords: Disease state analysis (diabetes)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19915678" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4682" }, "primaryId" : "GEO:GSE4682", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4682" } ] }, "title" : "Gene expression analysis of peritoneal mesotheliomas following chemical treatment in F344 rats", "dateAssigned" : "2006-04-18T00:00:00.000-05:00", "summary" : "Keywords: Rat, Mesotheliomas, Bromochloractetic acid, o-Nitrotoluene, Carcinogenesis, Microarray", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16884916" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4702" }, "primaryId" : "GEO:GSE4702", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4702" } ] }, "title" : "The Spontaneously Hypertensive Rat: An Experimental Model of Sulfur Dioxide-induced Airways Disease", "dateAssigned" : "2006-04-21T00:00:00.000-05:00", "summary" : "Keywords: strain and treatment differences", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16929007" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4745" }, "primaryId" : "GEO:GSE4745", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4745" } ] }, "title" : "Expression data from Rat ventricles 3 days/28 days/42 days after STZ injection", "dateAssigned" : "2006-05-01T00:00:00.000-05:00", "summary" : "Keywords: disease state analysis, time course", "categoryTags" : [ 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"htp/dataset" ], "id" : "GEO:GSE4782" } ] }, "title" : "The effects of estrogen and testosterone on gene expression in the rat mesenteric arteries", "dateAssigned" : "2006-05-05T00:00:00.000-05:00", "summary" : "Keywords: hormone treatment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17652031" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4800" }, "primaryId" : "GEO:GSE4800", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4800" } ] }, "title" : "Gene expression in kidney from Lewis and Dahl(S) rat", "dateAssigned" : "2006-05-09T00:00:00.000-05:00", "summary" : "Keywords: animals with different genetic background comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17460389" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4821" }, "primaryId" : "GEO:GSE4821", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4821" } ] }, "title" : "Identification of putative learning and memory genes in the dentate gyrus of aged rats following the Morris Water Maze", "dateAssigned" : "2006-05-12T00:00:00.000-05:00", "summary" : "Keywords: behavior comparison, age comparison", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4865" }, "primaryId" : "GEO:GSE4865", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4865" } ] }, "title" : "Comparison of gene expression profiles between GnRH-treated and control rat pituitary organ cultures", "dateAssigned" : "2006-05-18T00:00:00.000-05:00", "summary" : "Keywords: rat pituitary organ culture treated vs control", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4959" }, "primaryId" : "GEO:GSE4959", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4959" } ] }, "title" : "Expression data from adult Rattus liver", "dateAssigned" : "2006-05-31T00:00:00.000-05:00", "summary" : "Keywords: a single ip injection of PCN (100 mg/kg), 8 h treatment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16997903" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4963" }, "primaryId" : "GEO:GSE4963", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4963" } ] }, "title" : "Heart Failure, DITPA and Captopril", "dateAssigned" : "2006-06-01T00:00:00.000-05:00", "summary" : "Keywords: Drug Effects on Heart Failure", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18030062" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4977" }, "primaryId" : "GEO:GSE4977", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4977" } ] }, "title" : "ALCAR supplementation to unloaded soleus muscle", "dateAssigned" : "2006-06-05T00:00:00.000-05:00", "summary" : "Keywords: ALCAR effect", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4990" }, "primaryId" : "GEO:GSE4990", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE4990" } ] }, "title" : "Expression profile between mast cells from diabetic prone and diabetic resistant rat strains", "dateAssigned" : "2006-06-06T00:00:00.000-05:00", "summary" : "Keywords: Expression profile between disease and control", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17082646" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5015" }, "primaryId" : "GEO:GSE5015", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5015" } ] }, "title" : "Sobel-1R01NS046414-01", "dateAssigned" : 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"categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17849278" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5026" }, "primaryId" : "GEO:GSE5026", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5026" } ] }, "title" : "Characterization of the piRNA Complex from Rat Testes", "dateAssigned" : "2006-06-08T00:00:00.000-05:00", "summary" : "Keywords: High-throughput pyrosequencing by the 454 Life Sciences Genome Sequencer 20™ System", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16778019" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5033" }, "primaryId" : "GEO:GSE5033", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5033" } ] }, "title" : "sabba-affy-rat-212007", "dateAssigned" : "2006-06-09T00:00:00.000-05:00", "summary" : "Keywords: dose response", "categoryTags" : [ 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"crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5085" } ] }, "title" : "Expression data from female SD rats with access to lifelong exercise", "dateAssigned" : "2006-06-15T00:00:00.000-05:00", "summary" : "Keywords: exercise dose reponse, sedentary, twice weekly physical activity, daily exercise", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5100" }, "primaryId" : "GEO:GSE5100", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5100" } ] }, "title" : "PPARalpha Agonists Induce a Fiber-Type Selective Transcriptional Response in Rat Skeletal Muscle", "dateAssigned" : "2006-06-19T00:00:00.000-05:00", "summary" : "Keywords: drug response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16707586" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5101" }, "primaryId" : "GEO:GSE5101", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5101" } ] }, "title" : "Response of multiple genes to a chronic dose of corticosteroids in rat muscles", "dateAssigned" : "2006-06-19T00:00:00.000-05:00", "summary" : "Keywords: Time-Series", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17473217" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5104" }, "primaryId" : "GEO:GSE5104", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5104" } ] }, "title" : "Genome-wide expression profile in rat model of renal isografts from brain dead donors", "dateAssigned" : "2006-06-19T00:00:00.000-05:00", "summary" : "Keywords: disease state analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:15808645" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5115" }, "primaryId" : "GEO:GSE5115", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5115" } ] }, "title" : "Time course analysis of TSH-stimulated rat thyroid cell lines", "dateAssigned" : "2006-06-21T00:00:00.000-05:00", "summary" : "Keywords: Time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16887886" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5131" }, "primaryId" : "GEO:GSE5131", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5131" } ] }, "title" : "Adjudin-induced germ cell loss from adult rat testes", "dateAssigned" : "2006-06-22T00:00:00.000-05:00", "summary" : "Keywords: Sertoli-germ cell adhesion regulation using an Adjudin model", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17332525" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5193" }, "primaryId" : "GEO:GSE5193", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5193" } ] }, "title" : "Neuronal differentiation-associated gene profiling of the CHB50 cell line", "dateAssigned" : "2006-06-29T00:00:00.000-05:00", "summary" : "Keywords: Compared differentiated (-tsTA/+p53 condition) CHB50 cells to proliferating (+tsTA/-p53 condition) CHB50 cells", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5215" }, "primaryId" : "GEO:GSE5215", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5215" } ] }, "title" : "Expression data from rat soleus during acute physical inactivity and walking", "dateAssigned" : "2006-07-03T00:00:00.000-05:00", "summary" : "Keywords: between group design", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5217" }, "primaryId" : "GEO:GSE5217", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5217" } ] }, "title" : "Expression data from rat soleus during chronic intermittent physical inactivity", "dateAssigned" : "2006-07-03T00:00:00.000-05:00", "summary" : "Keywords: between group design", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5266" }, "primaryId" : "GEO:GSE5266", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5266" } ] }, "title" : "Expression data from normal atria and ventricles", "dateAssigned" : "2006-07-07T00:00:00.000-05:00", "summary" : "Keywords: comparative genomic hybridization", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19486520" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5273" }, "primaryId" : "GEO:GSE5273", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5273" } ] }, "title" : "Clenbuterol, X-ray and 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"2006-07-10T00:00:00.000-05:00", "summary" : "Keywords: Disease-State Analysis (Salt-Sensitive Hypertension)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17481853" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5315" }, "primaryId" : "GEO:GSE5315", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5315" } ] }, "title" : "Estrogen response after stroke", "dateAssigned" : "2006-07-14T00:00:00.000-05:00", "summary" : "Keywords: treated vs control", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16971488" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5337" }, "primaryId" : "GEO:GSE5337", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5337" } ] }, "title" : "Gene Expression Profiling In Rat Smooth Muscle Cells Modulated by Rapamycin and Paclitaxel.", "dateAssigned" : "2006-07-18T00:00:00.000-05:00", "summary" : "Keywords: Cardiovascular disease, drug eluting stent, vascular smooth muscle, rapamycin, paclitaxel", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5350" }, "primaryId" : "GEO:GSE5350", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5350" } ] }, "title" : "MicroArray Quality Control (MAQC) Project", "dateAssigned" : "2006-07-19T00:00:00.000-05:00", "summary" : "Keywords: Cross-platform comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25633159" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5381" }, "primaryId" : "GEO:GSE5381", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5381" } ] }, "title" : "Gene expression analysis of liver and kidney following methapyrilene treatment in male Sprague-Dawley rats", "dateAssigned" : "2006-07-24T00:00:00.000-05:00", "summary" : "Keywords: Time course, tissue comparison, liver toxicity, hepatotoxicity", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5446" }, "primaryId" : "GEO:GSE5446", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5446" } ] }, "title" : "Gene expression of organ of Corti (OC), modiolus (MOD) and stria vascularis (SV) of newborn rats", "dateAssigned" : "2006-08-03T00:00:00.000-05:00", "summary" : "Keywords: Differential gene expression, stress response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17612509" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5478" }, "primaryId" : "GEO:GSE5478", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5478" } ] }, "title" : "Expression data from metanephric mesenchyme induced to convert into nephron epithelia", "dateAssigned" : "2006-08-08T00:00:00.000-05:00", "summary" : "Keywords: time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17693601" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5488" }, "primaryId" : "GEO:GSE5488", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5488" } ] }, "title" : " Salt Induced Hypertensive Disease Results in Over Expression of Matricellular Genes in Cerebral Arteries", "dateAssigned" : "2006-08-09T00:00:00.000-05:00", "summary" : "Keywords: Normotensive vs. Hypertensive Disease", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18156195" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5509" }, "primaryId" : "GEO:GSE5509", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5509" } ] }, "title" : "Expression data from Rat liver 48 hours after treated with different toxic compounds.", "dateAssigned" : "2006-08-11T00:00:00.000-05:00", "summary" : "Keywords: other", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18178960" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5516" }, "primaryId" : "GEO:GSE5516", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5516" } ] }, "title" : "Activity- and mTOR-Dependent Suppression of Kv1.1 Channel mRNA Translation in Dendrites", "dateAssigned" : "2006-08-14T00:00:00.000-05:00", "summary" : "Keywords: comparison of synaptosomal mRNA to total hippocampal mRNA", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17023663" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5545" }, "primaryId" : "GEO:GSE5545", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5545" } ] }, "title" : "Platelet Activating Factor Receptor and Innate Immunity", "dateAssigned" : "2006-08-15T00:00:00.000-05:00", "summary" : "Keywords: Competitive hybridizations", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17056547" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5593" }, "primaryId" : "GEO:GSE5593", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5593" } ] }, "title" : "Acetaminophen (APAP) Rat Blood Training Gene Expression Data Set", "dateAssigned" : "2006-08-24T00:00:00.000-05:00", "summary" : "Keywords: Dose response, Time course, Microarray, Gene expression", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17984051" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5594" }, "primaryId" : "GEO:GSE5594", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5594" } ] }, "title" : "Acetaminophen (APAP) Rat Blood Test Gene Expression Data Set", "dateAssigned" : "2006-08-24T00:00:00.000-05:00", "summary" : "Keywords: Dose response, Time course, Microarray, Gene expression", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17984051" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5595" }, "primaryId" : "GEO:GSE5595", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5595" } ] }, "title" : "Acetaminophen (APAP) Rat Liver Test Gene Expression Data Set", "dateAssigned" : "2006-08-24T00:00:00.000-05:00", "summary" : "Keywords: Dose response, Time course, Microarray, Gene expression", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17984051" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5606" }, "primaryId" : "GEO:GSE5606", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5606" } ] }, "title" : "Expression data from Normal (control) and Diabetic animals LV heart tissue (At 16wks)", "dateAssigned" : "2006-08-25T00:00:00.000-05:00", "summary" : "Keywords: single time point, comparison control animal v. diabetic animal", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17062650" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5647" }, "primaryId" : "GEO:GSE5647", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5647" } ] }, "title" : "Long Term Thermal Injury Analysis", "dateAssigned" : "2006-08-28T00:00:00.000-05:00", "summary" : "Keywords: Time Course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18755477" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5664" }, "primaryId" : "GEO:GSE5664", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5664" } ] }, "title" : "gene profiling in carcinoma cell during EMT", "dateAssigned" : "2006-08-29T00:00:00.000-05:00", "summary" : "Keywords: time course ; EMT ; cancer cell line ; FGF-1", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18189245" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5666" }, "primaryId" : "GEO:GSE5666", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5666" } ] }, "title" : "Hippocampal pathways in cognitive impairment", "dateAssigned" : "2006-08-29T00:00:00.000-05:00", "summary" : "Keywords: Immediate Early Genes, Insulin Signaling, Cholesterol, Myelination, Glia, Inflammation, Young and Old comparaison, behavioral-characterization, Aging-related cognitive impairment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17376971" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5680" }, "primaryId" : "GEO:GSE5680", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5680" } ] }, "title" : "Expression data for an eQTL experiment in rat eye", "dateAssigned" : "2006-08-31T00:00:00.000-05:00", "summary" : "Keywords: eQTL, F2 cross", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16983098" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5762" }, "primaryId" : "GEO:GSE5762", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5762" } ] }, "title" : "High resolution time-course data of regenerating Dorsal Root Ganglion neurons", "dateAssigned" : "2006-09-05T00:00:00.000-05:00", "summary" : "Keywords: time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17610582" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5789" }, "primaryId" : "GEO:GSE5789", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5789" } ] }, "title" : "Effect of 13 weeks of subchronic exposure to TCDD, PeCDF, PCB126, PCB153 and PCB126/PCB153 on hepatic gene expression", "dateAssigned" : "2006-09-07T00:00:00.000-05:00", "summary" : "Keywords: Environmental pollutant toxicity comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20959002" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5849" }, "primaryId" : "GEO:GSE5849", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5849" } ] }, "title" : "Identification of Candidate Genes for Alcohol Preference by Expression Profiling of Congenic Strains", "dateAssigned" : "2006-09-15T00:00:00.000-05:00", "summary" : "Keywords: alcohol, congenic, rat, gene expression, brain, nucleus accumbens, amygdala, frontal cortex, hippocampus, striatum", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17451403" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5860" }, "primaryId" : "GEO:GSE5860", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5860" } ] }, "title" : "Gene expression analysis of rat livers after exposure to acetaminophen", "dateAssigned" : "2006-09-18T00:00:00.000-05:00", "summary" : "Keywords: Competitive hybridization", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17366322" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5910" }, "primaryId" : "GEO:GSE5910", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5910" } ] }, "title" : "Octreotide LAR and the oxyntic mucosa", "dateAssigned" : "2006-09-26T00:00:00.000-05:00", "summary" : "Keywords: regulation, proliferation, Affymetrix GeneChip, qRT-PCR, immunohistochemistry.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:10700043" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5923" }, "primaryId" : "GEO:GSE5923", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5923" } ] }, "title" : "Expression data from Aristolochic Acid and Ochratoxin A treated Tsc2 mutant (Eker) and corresponding wild type rats", "dateAssigned" : "2006-09-27T00:00:00.000-05:00", "summary" : "Keywords: time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17483316" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5940" }, "primaryId" : "GEO:GSE5940", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5940" } ] }, "title" : "Gene Expression Profiling of Primary Rat Oligodendrocytes", "dateAssigned" : "2006-09-28T00:00:00.000-05:00", "summary" : "Keywords: develepmental stage, oligodendrocyte differentiation", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17005852" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5943" }, "primaryId" : "GEO:GSE5943", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5943" } ] }, "title" : "Colonic gene expression upon dietary treatment", "dateAssigned" : "2006-09-29T00:00:00.000-05:00", "summary" : "Keywords: Dietary treatment, colon mucosa, Rat ", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5996" }, "primaryId" : "GEO:GSE5996", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE5996" } ] }, "title" : "Distinct Gene Expression Patterns in Biomechanically Stretched Cardiomyocytes", "dateAssigned" : "2006-10-09T00:00:00.000-05:00", "summary" : "Keywords: stress response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18158353" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6093" }, "primaryId" : "GEO:GSE6093", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6093" } ] }, "title" : "Expression data from rat mammary tumors with varying invasive phenotyes", "dateAssigned" : "2006-10-20T00:00:00.000-05:00", "summary" : "Keywords: tumor progression", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17405122" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6102" }, "primaryId" : "GEO:GSE6102", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6102" } ] }, "title" : "Dietary exposure to soy or whey proteins alters colonic global gene expression profiles during rat colon tumorigenesis", "dateAssigned" : "2006-10-23T00:00:00.000-05:00", "summary" : "Keywords: Comarative genomic hybridization", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:15644144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6104" }, "primaryId" : "GEO:GSE6104", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6104" } ] }, "title" : "Rat right heart pulmonary embolism microarray", "dateAssigned" : "2006-10-23T00:00:00.000-05:00", "summary" : "Keywords: Time course and dose response in experimental PE", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18430806" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6110" }, "primaryId" : "GEO:GSE6110", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6110" } ] }, "title" : "Increased Susceptibility of Aging Kidney to Ischemic Injury: Identification of Molecular Pathways using Microarray", "dateAssigned" : "2006-10-23T00:00:00.000-05:00", "summary" : "Keywords: aging, caloric-restriction, kidney", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17670906" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6119" }, "primaryId" : "GEO:GSE6119", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6119" } ] }, "title" : "Exogenous Glucosamine Globally Protects Chondrocytes from the Arthritogenic Effects of IL-1beta", "dateAssigned" : "2006-10-24T00:00:00.000-05:00", "summary" : "Keywords: treatment response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17109745" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6189" }, "primaryId" : "GEO:GSE6189", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6189" } ] }, "title" : "Molecular Mechanisms of Early Response in Adaptive Cerebral Arteriogenesis", "dateAssigned" : "2006-10-30T00:00:00.000-06:00", "summary" : "Keywords: early response time course, selective collateral growth, brain", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18594555" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6197" }, "primaryId" : "GEO:GSE6197", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6197" } ] }, "title" : "Rat Semi-Circular Canal Duct Gene Expression Studies", "dateAssigned" : "2006-10-30T00:00:00.000-06:00", "summary" : "Keywords: drug response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20398257" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6204" }, "primaryId" : "GEO:GSE6204", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6204" } ] }, "title" : "Rat gastric ECL cell transcriptomes: Change of gene expression during 24 hrs fasting", "dateAssigned" : "2006-10-31T00:00:00.000-06:00", "summary" : "Keywords: rat whole genome expression microarray analysis (transcriptome)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17536021" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6208" }, "primaryId" : "GEO:GSE6208", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6208" } ] }, "title" : "Comparison of Renal Gene Expression from Dahl Salt-Sensitive (S) and the Renal Protective S.SHR(2) Congenic Strain", "dateAssigned" : "2006-11-01T00:00:00.000-06:00", "summary" : "Keywords: time course", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6215" }, "primaryId" : "GEO:GSE6215", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6215" } ] }, "title" : "Genetic basis of rare arterial and renal phenotypes in the Brown Norway rat", "dateAssigned" : "2006-11-02T00:00:00.000-06:00", "summary" : "Keywords: strain effect", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17356016" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6216" }, "primaryId" : "GEO:GSE6216", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6216" } ] }, "title" : "Effects of ACTH and DEX on gene expression in rat kidneys", "dateAssigned" : "2006-11-02T00:00:00.000-06:00", "summary" : "Keywords: repeat", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6229" }, "primaryId" : "GEO:GSE6229", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6229" } ] }, "title" : "Genomic profiling of aged rat skeletal muscle", "dateAssigned" : "2006-11-06T00:00:00.000-06:00", "summary" : "Keywords: age skeletal muscle sensorimotor disturbances", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17503500" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6249" }, "primaryId" : "GEO:GSE6249", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6249" } ] }, "title" : "Expression data from adrenal glands from normoxic and hypoxic neonatal rats", "dateAssigned" : "2006-11-08T00:00:00.000-06:00", "summary" : "Keywords: effects of hypoxia on adrenal steroidogenesis in the neonatal rat", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17213367" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6254" }, "primaryId" : "GEO:GSE6254", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6254" } ] }, "title" : "Identification of activity-dependent gene expression profiles in cultured rat cortical neurons", "dateAssigned" : "2006-11-09T00:00:00.000-06:00", "summary" : "Keywords: pharmacological agents, cortical neurons", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17443680" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6299" }, "primaryId" : "GEO:GSE6299", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6299" } ] }, "title" : "Gene expression and cell cycle arrest in a rat keratinocyte cell line exposed to 56 Fe Ions", "dateAssigned" : "2006-11-16T00:00:00.000-06:00", "summary" : "Keywords: Dose response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17392591" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6332" }, "primaryId" : "GEO:GSE6332", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6332" } ] }, "title" : "Molecular Signatures of Trauma Hemorrhagic Shock-Induced Lung Injury: Hemorrhage- and Injury-Associated Genes", "dateAssigned" : "2006-11-20T00:00:00.000-06:00", "summary" : "Keywords: Treatment response to shock", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17545943" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6342" }, "primaryId" : "GEO:GSE6342", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6342" } ] }, "title" : "Impact of Animal Strain on Gene Expression in a Rat Model of Acute Cardiac Rejection", "dateAssigned" : "2006-11-21T00:00:00.000-06:00", "summary" : "The expression levels of many genes show wide natural variation among strains or populations. This study investigated the potential for animal strain-related genotypic differences to confound gene expression profiles in acute cellular rejection (ACR). Additional analysis allowed for selection of 49 candidate genes uniquely associated with ACR, but only after accounting for the unexpectedly large effect of animal strain. Studies of ACR that examine gene expression in peripheral blood may be confounded by strain differences. These results indicate the need for study designs that eliminate or control for the large effect of genetic background on the transcriptome of immune cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19552812" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6353" }, "primaryId" : "GEO:GSE6353", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6353" } ] }, "title" : "IFN-gamma activation of cultured neonatal rat microglia", "dateAssigned" : "2006-11-22T00:00:00.000-06:00", "summary" : "Keywords: Microglia activation", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17188367" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6497" }, "primaryId" : "GEO:GSE6497", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6497" } ] }, "title" : "Expression profile of syngeneic (sTX) and allogeneic kidney (aTX) transplantation compared to control (ctr) kidneys", "dateAssigned" : "2006-12-11T00:00:00.000-06:00", "summary" : "Keywords: gene expression changes due to acute rejection", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18261221" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6499" }, "primaryId" : "GEO:GSE6499", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6499" } ] }, "title" : "Microarray analyses that reveal the population of dendritic RNAs and their redistribution by neural activity", "dateAssigned" : "2006-12-11T00:00:00.000-06:00", "summary" : "Keywords: Comparisons of RNAs that are presumed to be derived from neuronal dendritic parts (HP and D4) with those from somas (LP and C2).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17207874" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6541" }, "primaryId" : "GEO:GSE6541", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6541" } ] }, "title" : "Paradoxical role of zinc in cardiac injury: a potential link to air pollution mortality?", "dateAssigned" : "2006-12-15T00:00:00.000-06:00", "summary" : "Keywords: Pulmonary exposure, Cardiac gene expression", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18197293" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6693" }, "primaryId" : "GEO:GSE6693", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6693" } ] }, "title" : "Time-dependent response of hippocampal CA1 and CA3 to oxidative stress", "dateAssigned" : "2007-01-09T00:00:00.000-06:00", "summary" : "Keywords: Time course stress response study", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17553663" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6699" }, "primaryId" : "GEO:GSE6699", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6699" } ] }, "title" : "Perirenal and epididymal preadipocytes from young and old rats.", "dateAssigned" : "2007-01-10T00:00:00.000-06:00", "summary" : "Keywords: cell type and age comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20106964" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6701" }, "primaryId" : "GEO:GSE6701", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6701" } ] }, "title" : "Expression data from ischemia and reperfusion events in NRVMs using Coverslip Hypoxia", "dateAssigned" : "2007-01-10T00:00:00.000-06:00", "summary" : "Keywords: time course", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6718" }, "primaryId" : "GEO:GSE6718", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6718" } ] }, "title" : "Transcriptional Response to Aging and Caloric Restriction in Heart and Adipose Tissue", "dateAssigned" : "2007-01-11T00:00:00.000-06:00", "summary" : "Keywords: Aging Caloric Restriction", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17874999" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6748" }, "primaryId" : "GEO:GSE6748", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6748" } ] }, "title" : "renal ischemia vs sham - 24h", "dateAssigned" : "2007-01-16T00:00:00.000-06:00", "summary" : "Keywords: disease state", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18272597" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6749" }, "primaryId" : "GEO:GSE6749", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6749" } ] }, "title" : "renal ischemia vs sham - 7d", "dateAssigned" : "2007-01-16T00:00:00.000-06:00", "summary" : "Keywords: disease state", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18272597" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6879" }, "primaryId" : "GEO:GSE6879", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6879" } ] }, "title" : "Dietary effect of SPI or Genistein alters rat mammary epithelial global gene expression profiles ", "dateAssigned" : "2007-01-26T00:00:00.000-06:00", "summary" : "Keywords: Comarative genomic hybridization", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17341692" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6880" }, "primaryId" : "GEO:GSE6880", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6880" } ] }, "title" : "Heart in Diabetes", "dateAssigned" : "2007-01-26T00:00:00.000-06:00", "summary" : "Keywords: Disease state analysis (diabetes)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17566115" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6917" }, "primaryId" : "GEO:GSE6917", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6917" } ] }, "title" : "Effects of Phenylethyl Isothiocyanate on N-Nitrosomethylbenzylamine-induced Cytotoxicity in Rat Esophagus", "dateAssigned" : "2007-01-30T00:00:00.000-06:00", "summary" : "Keywords: Toxicogenomics,reference design", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17616710" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6929" }, "primaryId" : "GEO:GSE6929", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6929" } ] }, "title" : "Angiogenesis inhibitors ameliorates inflammatory infiltrate, fibrosis and portal pressure in cirrhotic rats", "dateAssigned" : "2007-02-01T00:00:00.000-06:00", "summary" : "Keywords: angiogenesis, cirrhosis, liver, Affymetrix, fibrosis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17935226" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6933" }, "primaryId" : "GEO:GSE6933", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6933" } ] }, "title" : "Unique Molecular Signature of Multipotent Adult Progenitor Cells (Affy)", "dateAssigned" : "2007-02-01T00:00:00.000-06:00", "summary" : "Keywords: mRNA expression profiling, oligonucleotide microarrays, stem cells", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17683608" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6943" }, "primaryId" : "GEO:GSE6943", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE6943" } ] }, "title" : "Normal Heart vs Normal Diaphragm", "dateAssigned" : "2007-02-02T00:00:00.000-06:00", "summary" : "Keywords: Cell type comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18207466" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7002" }, "primaryId" : "GEO:GSE7002", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7002" } ] }, "title" : "Gene Expression Changes in the Rat Nasal Epithelium Following Formaldehyde Exposure", "dateAssigned" : "2007-02-09T00:00:00.000-06:00", "summary" : "Keywords: time course, dose response, gene expression", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17449896" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7041" }, "primaryId" : "GEO:GSE7041", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7041" } ] }, "title" : "Expression data from Rat lungs", "dateAssigned" : "2007-02-15T00:00:00.000-06:00", "summary" : "Keywords: strain-condition analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17468131" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7079" }, "primaryId" : "GEO:GSE7079", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7079" } ] }, "title" : "Chronic rat exposure to cigarette smoke", "dateAssigned" : "2007-02-20T00:00:00.000-06:00", "summary" : "Keywords: Timecourse", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17720875" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7087" }, "primaryId" : "GEO:GSE7087", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7087" } ] }, "title" : "Global gene expression profiling on renal scarring in rat model of pyelonephritis", "dateAssigned" : "2007-02-21T00:00:00.000-06:00", "summary" : "Keywords: renal scarring, TGF-ß , IL-1ß", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7139" }, "primaryId" : "GEO:GSE7139", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7139" } ] }, "title" : "Comparative GeneChip expression profiling of four brain regions", "dateAssigned" : "2007-02-26T00:00:00.000-06:00", "summary" : "Keywords: Comparative analysis of different regions of the brain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19228403" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7171" }, "primaryId" : "GEO:GSE7171", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7171" } ] }, "title" : "Pain microarray analysis 1", "dateAssigned" : "2007-03-01T00:00:00.000-06:00", "summary" : "Keywords: gene expression analysis via microarray", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:15730869" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7174" }, "primaryId" : "GEO:GSE7174", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7174" } ] }, "title" : "Differential gene expression analysis of iodide treated rat thyroid follicular cell line PCCl3", "dateAssigned" : "2007-03-02T00:00:00.000-06:00", "summary" : "Keywords: comparative genomic analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18272324" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7193" }, "primaryId" : "GEO:GSE7193", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7193" } ] }, "title" : "Rosiglitazone effects on kidney gene expression", "dateAssigned" : "2007-03-05T00:00:00.000-06:00", "summary" : "Keywords: Thiazolidinediones, PPAR-gamma agonists, renal, type II diabetes, obesity", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18700276" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7221" }, "primaryId" : "GEO:GSE7221", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7221" } ] }, "title" : "Comparison of rat thoracic duct to vena cava", "dateAssigned" : "2007-03-07T00:00:00.000-06:00", "summary" : "Keywords: Thoracic duct, lymphatics, microarray", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7222" }, "primaryId" : "GEO:GSE7222", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7222" } ] }, "title" : "Global gene expression analysis of quercetin bioactivity in cultured rat cardiomyocytes", "dateAssigned" : "2007-03-08T00:00:00.000-06:00", "summary" : "Keywords: nutritional intervention, dose response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18178720" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7253" }, "primaryId" : "GEO:GSE7253", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7253" } ] }, "title" : "Puberty and Diabetes in the Kidney", "dateAssigned" : "2007-03-13T00:00:00.000-05:00", "summary" : "Keywords: Age-Disease State Interaction Analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18030501" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7267" }, "primaryId" : "GEO:GSE7267", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7267" } ] }, "title" : "Belgrade +/b and b/b Duodenum and Jejunum", "dateAssigned" : "2007-03-14T00:00:00.000-05:00", "summary" : "Keywords: Belgrade, iron deficiency, intestine, microarray", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18258795" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7271" }, "primaryId" : "GEO:GSE7271", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7271" } ] }, "title" : "Sex differences in gene expression profiles during hantavirus infection of rats", "dateAssigned" : "2007-03-14T00:00:00.000-05:00", "summary" : "Keywords: time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18053684" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7281" }, "primaryId" : "GEO:GSE7281", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7281" } ] }, "title" : "Development of Progressive Aortic Vasculopathy in a Rat Model of Aging", "dateAssigned" : "2007-03-15T00:00:00.000-05:00", "summary" : "Keywords: time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17873024" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7323" }, "primaryId" : "GEO:GSE7323", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7323" } ] }, "title" : "Hippocampus response to ketone bodies (maalo-affy-rat-387180)", "dateAssigned" : "2007-03-20T00:00:00.000-05:00", "summary" : "Keywords: dose response", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7328" }, "primaryId" : "GEO:GSE7328", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7328" } ] }, "title" : "Pain microarray analysis 2", "dateAssigned" : "2007-03-20T00:00:00.000-05:00", "summary" : "Keywords: neonatally injured paw, inflammation, carrageenan injection", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:15730869" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7397" }, "primaryId" : "GEO:GSE7397", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7397" } ] }, "title" : "Adult cardiomyocytes treated with fractalkine (CX3CL1)", "dateAssigned" : "2007-03-29T00:00:00.000-05:00", "summary" : "Keywords: Fractalkines effect on cardiomyocytes", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7441" }, "primaryId" : "GEO:GSE7441", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7441" } ] }, "title" : "Transcriptional profile of primary astrocytes expressing ALS-linked mutant SOD1.", "dateAssigned" : "2007-04-03T00:00:00.000-05:00", "summary" : "Keywords: Cell type comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18683239" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7472" }, "primaryId" : "GEO:GSE7472", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7472" } ] }, "title" : "Colonic gene expression upon Salmonella infection and dietary treatment", "dateAssigned" : "2007-04-06T00:00:00.000-05:00", "summary" : "Keywords: Dietary infection study, colon mucosa, Rat", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17850650" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7479" }, "primaryId" : "GEO:GSE7479", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7479" } ] }, "title" : "Transcriptomics and proteomics in colon mucosa from rats fed quercetin", "dateAssigned" : "2007-04-09T00:00:00.000-05:00", "summary" : "Keywords: Transscriptomics, proteomics, quercetin-exposed and control rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18095365" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7483" }, "primaryId" : "GEO:GSE7483", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7483" } ] }, "title" : "Microarray analysis of aortic tissue from different rat hypertensive models", "dateAssigned" : "2007-04-09T00:00:00.000-05:00", "summary" : "Keywords: strain comparison, treatment vs control", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7491" }, "primaryId" : "GEO:GSE7491", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7491" } ] }, "title" : "Expression data from rat lung alveolar development", "dateAssigned" : "2007-04-10T00:00:00.000-05:00", "summary" : "Keywords: Time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17911382" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7493" }, "primaryId" : "GEO:GSE7493", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7493" } ] }, "title" : "Mutant SOD1 rats (lobsi-affy-rat-194438)", "dateAssigned" : "2007-04-10T00:00:00.000-05:00", "summary" : "Keywords: time-course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17463094" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7496" }, "primaryId" : "GEO:GSE7496", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7496" } ] }, "title" : "Transcription profiling of rat colonic mucosa at different time points following Salmonella infection", "dateAssigned" : "2007-04-11T00:00:00.000-05:00", "summary" : "Keywords: Time point infection study, colon mucosa, Rat", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17850650" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7501" }, "primaryId" : "GEO:GSE7501", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7501" } ] }, "title" : "Genes in nonpermissive temperature-induced cell growth arrest and differentiation of astrocyte RCG-12 cells", "dateAssigned" : "2007-04-12T00:00:00.000-05:00", "summary" : "Keywords: Astrocyte cell; growth arrest; differentiation; temperature-sensitive simian virus 40 large T-antigen; nonpermissive temperature", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17440958" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7550" }, "primaryId" : "GEO:GSE7550", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7550" } ] }, "title" : "ACTH-treated rats: a model to study IGFR-PI3K regulon", "dateAssigned" : "2007-04-19T00:00:00.000-05:00", "summary" : "Keywords: disease state comparison", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7584" }, "primaryId" : "GEO:GSE7584", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7584" } ] }, "title" : "Gene expression studies in IEC-6 cells induced by non-steroidal anti-inflammatory agents", "dateAssigned" : "2007-04-23T00:00:00.000-05:00", "summary" : "Keywords: dose response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18281595" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7623" }, "primaryId" : "GEO:GSE7623", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7623" } ] }, "title" : "24 h-fasting effects on the brown and white adipose tissue and liver", "dateAssigned" : "2007-04-25T00:00:00.000-05:00", "summary" : "Keywords: treatment comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18175912" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7625" }, "primaryId" : "GEO:GSE7625", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7625" } ] }, "title" : "Transcriptome analysis of an oxidative stress-induced rat renal carcinogenesis model", "dateAssigned" : "2007-04-26T00:00:00.000-05:00", "summary" : "Keywords: dose response, disease state analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25008760" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7628" }, "primaryId" : "GEO:GSE7628", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7628" } ] }, "title" : "Evaluation of expression quantitative trait loci within two interacting blood pressure quantitative trait loci", "dateAssigned" : "2007-04-26T00:00:00.000-05:00", "summary" : "Keywords: rat, hypertension, genetics, polygenic trait, microarray, gene expression", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17938377" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7640" }, "primaryId" : "GEO:GSE7640", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7640" } ] }, "title" : "Gene expression profile induced by moderate physical exercise in heart left ventricles in rats", "dateAssigned" : "2007-04-26T00:00:00.000-05:00", "summary" : "Keywords: Case-Control: Response to physical exsercise", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19643001" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7654" }, "primaryId" : "GEO:GSE7654", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7654" } ] }, "title" : "Gene expression profiling of hepatitis development and hepatocarcinogenesis initiation in LEC rats.", "dateAssigned" : "2007-04-27T00:00:00.000-05:00", "summary" : "Keywords: disease state analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7697" }, "primaryId" : "GEO:GSE7697", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7697" } ] }, "title" : "Granulosa cell gene expression associated with oocyte developmental competence", "dateAssigned" : "2007-05-03T00:00:00.000-05:00", "summary" : "Keywords: Dose response", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7703" }, "primaryId" : "GEO:GSE7703", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7703" } ] }, "title" : "Mat-Lylu cell line compared to G cell line", "dateAssigned" : "2007-05-03T00:00:00.000-05:00", "summary" : "Keywords: cell line comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17713630" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7755" }, "primaryId" : "GEO:GSE7755", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7755" } ] }, "title" : "Gene expression in fetal gubernaculum and testis of wildtype (LE/wt) and cryptorchid (LE/orl) rats", "dateAssigned" : "2007-05-07T00:00:00.000-05:00", "summary" : "Keywords: strain/condition predisposition, disease state analysis, developmental", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18222913" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7799" }, "primaryId" : "GEO:GSE7799", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7799" } ] }, "title" : "Cardiac and Soleus muscles following exposure of rats to heat acclimation and exercise training", "dateAssigned" : "2007-05-15T00:00:00.000-05:00", "summary" : "Keywords: stress response", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7826" }, "primaryId" : "GEO:GSE7826", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7826" } ] }, "title" : "Gene expression affected by TNFa and SB203580", "dateAssigned" : "2007-05-17T00:00:00.000-05:00", "summary" : "Keywords: p38 signal response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17652167" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7836" }, "primaryId" : "GEO:GSE7836", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7836" } ] }, "title" : "Global analysis of gene expression in REF52 cells expressing SV40 T antigens", "dateAssigned" : "2007-05-17T00:00:00.000-05:00", "summary" : "SV40 transforms cells through the action of two oncoproteins, large T antigen and small t antigen. Small t antigen targets phosphatase PP2A, while large T antigen stimulates cell proliferation and survival by action on multiple proteins, including the tumor suppressors Rb and p53. Large T antigen also binds components of the transcription initiation complex and several transcription factors. We examine global gene expression in SV40-transformed REF52 cells. SV40 transformation alters the expression of approximately 480 cellular genes. Much of this regulation is consistent with T antigen action on the Rb-E2F pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19201438" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7891" }, "primaryId" : "GEO:GSE7891", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7891" } ] }, "title" : "Trancriptome profiling of rat inner medullary collecting duct", "dateAssigned" : "2007-05-24T00:00:00.000-05:00", "summary" : "Keywords: gene expression comparision between cell type", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17956998" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7899" }, "primaryId" : "GEO:GSE7899", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7899" } ] }, "title" : "Transcriptional profiling of inductive prostatic mesenchyme", "dateAssigned" : "2007-05-25T00:00:00.000-05:00", "summary" : "Keywords: SAGE, gene profiling", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17922897" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7906" }, "primaryId" : "GEO:GSE7906", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7906" } ] }, "title" : "Cell-type Specific Regulation of Gene Expression by Simian Virus 40 T antigens", "dateAssigned" : "2007-05-25T00:00:00.000-05:00", "summary" : "SV40 transforms cells through the action of two oncoproteins, large T antigen and small t antigen. Small t antigen targets phosphatase PP2A, while large T antigen stimulates cell proliferation and survival by action on multiple proteins, including the tumor suppressors Rb and p53. Large T antigen also binds components of the transcription initiation complex and several transcription factors. We examined global gene expression in SV40-transformed mouse embryo fibroblasts, and in enterocytes obtained from transgenic mice. SV40 transformation alters the expression of approximately 800 cellular genes in both systems. Much of this regulation is observed in both MEFs and enterocytes and is consistent with T antigen action on the Rb-E2F pathway. However, the regulation of many genes is cell-type specific, suggesting that unique signaling pathways are activated in different cell types upon transformation, and that the consequences of SV40 transformation depends on the type of cell targeted.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19201438" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7955" }, "primaryId" : "GEO:GSE7955", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7955" } ] }, "title" : "Transcriptional response of rat cerebrocortical tissue following acute exposure to permethrin or deltamethrin.", "dateAssigned" : "2007-05-30T00:00:00.000-05:00", "summary" : "Keywords: dose response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19017407" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7970" }, "primaryId" : "GEO:GSE7970", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7970" } ] }, "title" : "Wistar rats with iron deficiency and repletion and Belgrade rats normally fed or fed iron in drinking water: villus", "dateAssigned" : "2007-05-31T00:00:00.000-05:00", "summary" : "Keywords: iron stress response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21436314" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7999" }, "primaryId" : "GEO:GSE7999", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE7999" } ] }, "title" : "Gene profiling of the heart myocardium after a single dose administration of Isoproterenol hydrochloride", "dateAssigned" : "2007-06-01T00:00:00.000-05:00", "summary" : "Keywords: time course study of Isoproternol hydrochloride", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8013" }, "primaryId" : "GEO:GSE8013", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8013" } ] }, "title" : "Gene expression profiling under low dose and short incubation time of cadmium in primary rat hepatocyte in culture", "dateAssigned" : "2007-06-04T00:00:00.000-05:00", "summary" : "Keywords: early protective responses", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19010381" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8051" }, "primaryId" : "GEO:GSE8051", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8051" } ] }, "title" : "Gene expression in a resistance artery in 2 models of hypertension in the rat", "dateAssigned" : "2007-06-07T00:00:00.000-05:00", "summary" : "Keywords: Comparison of global gene expression in resistance arteries of normotensive and genetically hypertensive rats and ACTH-treated rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17986358" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8077" }, "primaryId" : "GEO:GSE8077", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8077" } ] }, "title" : "Global analyses of gene expression in early experimental knee osteoarthritis", "dateAssigned" : "2007-06-11T00:00:00.000-05:00", "summary" : "Keywords: disease state analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17530714" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8078" }, "primaryId" : "GEO:GSE8078", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8078" } ] }, "title" : "A Multi- Kinase Inhibitor Modulates Pulmonary Hypertension in a Rodent Model 1", "dateAssigned" : "2007-06-11T00:00:00.000-05:00", "summary" : "Keywords: Drug Effect", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18303084" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8132" }, "primaryId" : "GEO:GSE8132", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8132" } ] }, "title" : "A Multi- Kinase Inhibitor Modulates Pulmonary Hypertension in a Rodent Model 2", "dateAssigned" : "2007-06-14T00:00:00.000-05:00", "summary" : "Keywords: Drug Effect", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18303084" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8184" }, "primaryId" : "GEO:GSE8184", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8184" } ] }, "title" : "Profiling Single and Repeated Immobilization Stress Responses in Gene Expression", "dateAssigned" : "2007-06-19T00:00:00.000-05:00", "summary" : "Keywords: Stress responses", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8201" }, "primaryId" : "GEO:GSE8201", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8201" } ] }, "title" : "Expression Profiling of Genes Concerning to Protective Effect in Heart by Benidipine Hydrochloride.", "dateAssigned" : "2007-06-21T00:00:00.000-05:00", "summary" : "Keywords: Diseased state and drug effect analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8238" }, "primaryId" : "GEO:GSE8238", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8238" } ] }, "title" : "Interactions Between Progesterone and Tumor Necrosis Factor-alpha in the Regulation of Primordial Follicle Assembly", "dateAssigned" : "2007-06-22T00:00:00.000-05:00", "summary" : "Keywords: expression analysis, progesterone, TNFa, follicle assembly, ovary", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17127748" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8251" }, "primaryId" : "GEO:GSE8251", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8251" } ] }, "title" : "Non-genotoxic Hepatocarcinogens", "dateAssigned" : "2007-06-22T00:00:00.000-05:00", "summary" : "Keywords: dose response, time course, compound treatment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17557906" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8252" }, "primaryId" : "GEO:GSE8252", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8252" } ] }, "title" : "Acute Gene Induction by Tienilic Acid in the Male Sprague Dawley Rat: Possible Role for Danger", "dateAssigned" : "2007-06-22T00:00:00.000-05:00", "summary" : "Keywords: time course, stress response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18958736" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8253" }, "primaryId" : "GEO:GSE8253", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8253" } ] }, "title" : "Non-alcoholic Steatohepatitis following feeding of high polyunsaturated fat diets", "dateAssigned" : "2007-06-22T00:00:00.000-05:00", "summary" : "Keywords: Steatosis and unsaturated fat", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17947452" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8302" }, "primaryId" : "GEO:GSE8302", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8302" } ] }, "title" : "Comprehensive analysis of PPARa-dependent regulation of hepatic lipid metabolism by expression profiling - 5", "dateAssigned" : "2007-06-26T00:00:00.000-05:00", "summary" : "Keywords: identification of target genes", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18288265" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8310" }, "primaryId" : "GEO:GSE8310", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8310" } ] }, "title" : "Gene expression data from hypothalamus of normal sexual development of the female rat", "dateAssigned" : "2007-06-27T00:00:00.000-05:00", "summary" : "Keywords: comparison between Early pubertal and Juvenile or Late pubertal and Juvenile stages of sexual development in the female rat", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8314" }, "primaryId" : "GEO:GSE8314", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8314" } ] }, "title" : "Characterization of weight loss and weight regain mechanisms after Roux-en-Y gastric bypass in rats", "dateAssigned" : "2007-06-27T00:00:00.000-05:00", "summary" : "Keywords: gene expression analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17626126" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8318" }, "primaryId" : "GEO:GSE8318", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8318" } ] }, "title" : "Expression from control subplate neurons with few synapses and cocultured subplate neurons with induced synaptogenesis", "dateAssigned" : "2007-06-28T00:00:00.000-05:00", "summary" : "Keywords: treatment type comparison, time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19029062" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8321" }, "primaryId" : "GEO:GSE8321", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8321" } ] }, "title" : "Soleus muscle response to level running", "dateAssigned" : "2007-06-28T00:00:00.000-05:00", "summary" : "Keywords: Exercise response; pre versus 24-hr post", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8329" }, "primaryId" : "GEO:GSE8329", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8329" } ] }, "title" : "Gene expression profiling in the heart following exposure of rats to heat acclimation, its loss and re-induction.", "dateAssigned" : "2007-06-29T00:00:00.000-05:00", "summary" : "Keywords: heart, Left ventricle", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8341" }, "primaryId" : "GEO:GSE8341", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8341" } ] }, "title" : "ChIP-on-chip experiments of normal and failed hearts of Dahl rat", "dateAssigned" : "2007-06-30T00:00:00.000-05:00", "summary" : "Keywords: ChIP-chip", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19077033" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8390" }, "primaryId" : "GEO:GSE8390", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8390" } ] }, "title" : "Added effects of acute heat-stress on the clinical signs associated with fescue toxicosis", "dateAssigned" : "2007-07-05T00:00:00.000-05:00", "summary" : "Keywords: Stress response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19574562" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8393" }, "primaryId" : "GEO:GSE8393", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8393" } ] }, "title" : "Patterns of gene expression following contact of sympathetic neurons with their myocyte targets", "dateAssigned" : "2007-07-05T00:00:00.000-05:00", "summary" : "Keywords: Patterns of gene expression by neuron-target interaction", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8421" }, "primaryId" : "GEO:GSE8421", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8421" } ] }, "title" : "Gene Expression Profile in Rat Adrenal Zona Glomerulosa Cells Stimulated with Aldosterone Secretagogues", "dateAssigned" : "2007-07-09T00:00:00.000-05:00", "summary" : "Keywords: agent response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17895393" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8423" }, "primaryId" : "GEO:GSE8423", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8423" } ] }, "title" : "Gene Expression Analysis of the Rat Retina during Maturation ", "dateAssigned" : "2007-07-10T00:00:00.000-05:00", "summary" : "Keywords: Dye-swap, 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cells", "dateAssigned" : "2007-07-11T00:00:00.000-05:00", "summary" : "Keywords: rat tracheal epithelial RTEC11; growth arrest; differentiation; gene expression", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18725308" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8467" }, "primaryId" : "GEO:GSE8467", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8467" } ] }, "title" : "Micro-RNAs in Adult Rat Liver are Refractory to 19 Hours Dioxin Exposure", "dateAssigned" : "2007-07-13T00:00:00.000-05:00", "summary" : "Keywords: miRNA expression, response to xenobiotics, genetic modification, comparative genome hybridization", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17698510" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8469" }, "primaryId" : "GEO:GSE8469", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8469" } ] }, "title" : "Micro-RNAs in Adult Long-Evans (Turku/AB) Rat Liver are Refractory to 96 Hours Dioxin Treatment", "dateAssigned" : "2007-07-13T00:00:00.000-05:00", "summary" : "Keywords: miRNA expression, response to xenobiotics, feed restriction response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17698510" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8470" }, "primaryId" : "GEO:GSE8470", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8470" } ] }, "title" : "Micro-RNAs in Adult Rat Liver are Refractory to Dioxin Treatment", "dateAssigned" : "2007-07-13T00:00:00.000-05:00", "summary" : "Keywords: miRNA expression, Time course, response to xenobiotics, genetic modification, comparative genome hybridization", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17698510" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8491" }, "primaryId" : "GEO:GSE8491", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8491" } ] }, "title" : "The Transcriptome of the rat hypothalamo-neurohypophyseal system is highly strain-dependant", "dateAssigned" : "2007-07-16T00:00:00.000-05:00", "summary" : "Keywords: Transcriptome, Hypothalamo-neurohypophyseal system, Genetic", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18001331" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8538" }, "primaryId" : "GEO:GSE8538", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8538" } ] }, "title" : "Mesenteric adipose tissue of rats treated with oleoyl-estrone", "dateAssigned" : "2007-07-20T00:00:00.000-05:00", "summary" : "Keywords: Effects of a drug on gene expression", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17725831" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8587" }, "primaryId" : "GEO:GSE8587", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8587" } ] }, "title" : "Gene expression changes in cecum mucosa upon dietary treatment ", "dateAssigned" : "2007-07-26T00:00:00.000-05:00", "summary" : "Keywords: Dietary treatment, cecum mucosa, Rat", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8700" }, "primaryId" : "GEO:GSE8700", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE8700" } ] }, "title" : "Expression data from epididymal fat tissues of diet induced obese rats", "dateAssigned" : "2007-08-06T00:00:00.000-05:00", "summary" : "Keywords: single time point, comparison control animal vs. diet induced obese animal", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : 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"PMID:18579462" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE9570" }, "primaryId" : "GEO:GSE9570", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE9570" } ] }, "title" : "Expression data from embryonic rat kidney timepoints and a budded WD-MM recombination tissue", "dateAssigned" : "2007-11-08T00:00:00.000-06:00", "summary" : "Keywords: time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18087037" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE9634" }, "primaryId" : "GEO:GSE9634", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE9634" } ] }, "title" : "Gene Expression Changes due to Rat Lung Ischemia-Reperfusion Injury", "dateAssigned" : "2007-11-16T00:00:00.000-06:00", "summary" : "Keywords: time course", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" 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"2008-02-22T00:00:00.000-06:00", "summary" : "Keywords: gene expression study, preneoplasic lesion vs. microdissected normal renal tubules", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19717638" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10623" }, "primaryId" : "GEO:GSE10623", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10623" } ] }, "title" : "Effects of Black Raspberry diet on N-Nitrosomethylbenzylamine-altered gene expression in Rat Esophagus", "dateAssigned" : "2008-02-24T00:00:00.000-06:00", "summary" : "Keywords: Toxicogenomics, reference design.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19003582" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10641" }, "primaryId" : "GEO:GSE10641", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10641" } ] }, "title" : "Mammary gland gene expression timecourse with or without NMU treatment between Cop and F344 rat", "dateAssigned" : "2008-02-26T00:00:00.000-06:00", "summary" : "Keywords: Different rat strains and Timecourse", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10649" }, "primaryId" : "GEO:GSE10649", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10649" } ] }, "title" : "Sex-differences in the control of gluconeogenesis and hepatic glucose output in rats", "dateAssigned" : "2008-02-27T00:00:00.000-06:00", "summary" : "Keywords: Hepatic glucose output, gluconeogenesis, gene expression, respons to insulin treatment and mild starvation", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10669" }, "primaryId" : "GEO:GSE10669", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10669" } ] }, "title" : "Different gene expression between Contol group, Model group and Drup(7-P) group", "dateAssigned" : "2008-02-29T00:00:00.000-06:00", "summary" : "Keywords: comparative genomic hybridization", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10720" }, "primaryId" : "GEO:GSE10720", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10720" } ] }, "title" : "Expression Profiling of Severed Rat Medial Collateral Ligament Following Injury", "dateAssigned" : "2008-03-04T00:00:00.000-06:00", "summary" : "Keywords: Time course of changes in gene expression in the healing of the rat medial collateral ligament.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10748" }, "primaryId" : "GEO:GSE10748", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10748" } ] }, "title" : "Expression data from brain tissue of Rattus norvegicus treated with D-Serine", "dateAssigned" : "2008-03-06T00:00:00.000-06:00", "summary" : "Keywords: Dose course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19212759" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10770" }, "primaryId" : "GEO:GSE10770", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10770" } ] }, "title" : "Conserved Transcriptional Response of Rodent Liver to TCDD: Rat", "dateAssigned" : "2008-03-09T00:00:00.000-06:00", "summary" : "Our results suggest that a small core of genes is responsible for mediating the similar features of dioxin hepatotoxicity in rats and mice but non-overlapping pathways are simultaneously at play to result in distinctive histopathological outcomes. The extreme divergence between mouse and rat transcriptomic responses appears to reflect divergent transcriptional-regulatory networks. Taken together, these data suggest that both rat and mouse models should be used to screen the acute hepatotoxic effects of drugs and toxic compounds.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18796159" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10775" }, "primaryId" : "GEO:GSE10775", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10775" } ] }, "title" : " Expression profiling of mammalian Schwann cells in response to treatment with NRG and/or IGF", "dateAssigned" : "2008-03-11T00:00:00.000-05:00", "summary" : "Keywords: Input of growth and mitogenic pathways in mitochondria biogenesis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19920079" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10823" }, "primaryId" : "GEO:GSE10823", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10823" } ] }, "title" : "Species difference in gene expression effect of trichloroethylene (TCE) between mouse and rat (rat)", "dateAssigned" : "2008-03-14T00:00:00.000-05:00", "summary" : "Keywords: Response to chemical", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10854" }, "primaryId" : "GEO:GSE10854", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10854" } ] }, "title" : "The anti-angiogenic and anti-tumor cell signaling networks of the kringle 1 domain of hepatocyte growth factor (HGFK1) ", "dateAssigned" : "2008-03-17T00:00:00.000-05:00", "summary" : "Keywords: HGFK1, anti-angiogenic signaling network, anti-tumor cell signaling network", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10919" }, "primaryId" : "GEO:GSE10919", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10919" } ] }, "title" : "Transgenerational epigenetic programming of the embryonic testis transcriptome", "dateAssigned" : "2008-03-21T00:00:00.000-05:00", "summary" : "Keywords: expression analysis, transgenerational changes due to Vinclozolin", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18042343" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10923" }, "primaryId" : "GEO:GSE10923", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10923" } ] }, "title" : "NAP provides neuroprotection against kainic acid-induced cell death", "dateAssigned" : "2008-03-24T00:00:00.000-05:00", "summary" : "Keywords: stress response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19799711" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10949" }, "primaryId" : "GEO:GSE10949", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE10949" } ] }, "title" : "Kidney-specific Dysfunction of the Organic Anion Transporter MRP2 (ABCC2): Functional Consequences for Renal Grafts", "dateAssigned" : "2008-03-26T00:00:00.000-05:00", "summary" : "Keywords: dysfunction of organic anion transporter MRP2 (ABCC2)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19214140" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11022" }, "primaryId" : "GEO:GSE11022", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11022" } ] }, "title" : "Dietary calcium inhibits colitis development in HLA-B27 transgenic rats", "dateAssigned" : "2008-04-02T00:00:00.000-05:00", "summary" : "Keywords: nutritional intervention", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19535420" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11091" }, "primaryId" : "GEO:GSE11091", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11091" } ] }, "title" : "Subchronic inhalation of zinc sulfate induces cardiac changes in healthy rats", "dateAssigned" : "2008-04-08T00:00:00.000-05:00", "summary" : "Keywords: dose response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18601943" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11097" }, "primaryId" : "GEO:GSE11097", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11097" } ] }, "title" : "Coordinated Changes in Xenobiotic Metabolizing Enzyme Gene Expression in Aging Male Rats: Brown Norway and F344", "dateAssigned" : "2008-04-08T00:00:00.000-05:00", "summary" : "Keywords: age effect on toxin susceptibility", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18653662" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11133" }, "primaryId" : "GEO:GSE11133", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11133" } ] }, "title" : "Glial derived neurotrophic factor promotes ovarian primordial follicle development during folliculogenesis", "dateAssigned" : "2008-04-10T00:00:00.000-05:00", "summary" : "Keywords: expression analysis, glial derived neurotrophic factor, follicle transition, ovary", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18304989" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11180" }, "primaryId" : "GEO:GSE11180", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11180" } ] }, "title" : "Genomic expression analysis of rat chromosome 4 for skeletal traits at femoral neck", "dateAssigned" : "2008-04-15T00:00:00.000-05:00", "summary" : "Keywords: Comparison of gene expression profiles between F344, LEW, COP and DA rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18728226" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11218" }, "primaryId" : "GEO:GSE11218", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11218" } ] }, "title" : "Identification of Dynamically Regulated MicroRNA and mRNA Networks in Oligodendrocytes", "dateAssigned" : "2008-04-20T00:00:00.000-05:00", "summary" : "Keywords: developmental stage", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18987208" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11267" }, "primaryId" : "GEO:GSE11267", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11267" } ] }, "title" : "Positive emotion-specific changes in gene expression profile in hypothalamus of the tickled rats", "dateAssigned" : "2008-04-25T00:00:00.000-05:00", "summary" : "Keywords: Stress response", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11277" }, "primaryId" : "GEO:GSE11277", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11277" } ] }, "title" : "A2B5/OTMP+ rat perineuronal oligodendrocytes ", "dateAssigned" : "2008-04-27T00:00:00.000-05:00", "summary" : "Keywords: developmental", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11283" }, "primaryId" : "GEO:GSE11283", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11283" } ] }, "title" : "Transcriptional gene profile of peripheral blood derived mesenchymal stromal cells from GFP transgenic rat", "dateAssigned" : "2008-04-28T00:00:00.000-05:00", "summary" : "Keywords: mesenchymal stromal cells (MSCs), peripheral blood (PB), bone marrow (BM), green fluorescent protein (GFP) transgenic rat, microarray", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11334" }, "primaryId" : "GEO:GSE11334", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11334" } ] }, "title" : "Identification of a miRNA Regulatory Network in FACS-Purified Neuronal Progenitors at the Onset of Rat Neurogenesis", "dateAssigned" : "2008-05-04T00:00:00.000-05:00", "summary" : "Keywords: Developmental", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19689821" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11465" }, "primaryId" : "GEO:GSE11465", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11465" } ] }, "title" : "Myasthenia gravis model: gene expression profile in diaphragm, extensor digitorum longus and extraocular muscles of rats", "dateAssigned" : "2008-05-15T00:00:00.000-05:00", "summary" : "Keywords: myasthenia gravis (MG), rats with actively induced experimentally acquired MG (EAMG)", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11468" }, "primaryId" : "GEO:GSE11468", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11468" } ] }, "title" : "Molecular Profiling of Small and Large Retinal Ganglion Cells", "dateAssigned" : "2008-05-15T00:00:00.000-05:00", "summary" : "Keywords: comparative hybridization", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18640154" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11473" }, "primaryId" : "GEO:GSE11473", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11473" } ] }, "title" : "Rapid encoding of information alters the profile of plasticity related mRNA transcripts in the hippocampal CA3 region", "dateAssigned" : "2008-05-16T00:00:00.000-05:00", "summary" : "Keywords:behavioral intervention: spatial learning paradigm ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18650386" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11474" }, "primaryId" : "GEO:GSE11474", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11474" } ] }, "title" : "Rapid encoding of information alters the profile of plasticity related mRNA transcripts in the hippocampal CA1 region.", "dateAssigned" : "2008-05-16T00:00:00.000-05:00", "summary" : "Keywords: behavioral intervention: spatial learning paradigm", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18650386" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11475" }, "primaryId" : "GEO:GSE11475", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11475" } ] }, "title" : "Rapid encoding of information alters the profile of plasticity related mRNA transcripts in the hippocampal DG region.", "dateAssigned" : "2008-05-16T00:00:00.000-05:00", "summary" : "Keywords: behavioral intervention: spatial learning paradigm", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18650386" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11478" }, "primaryId" : "GEO:GSE11478", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11478" } ] }, "title" : "Effect of corticosterone treatment on rat neuronal progenitor cells", "dateAssigned" : "2008-05-16T00:00:00.000-05:00", "summary" : "Keywords: expression analysis, corticosterone, neuronal progenitor, cortex", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11492" }, "primaryId" : "GEO:GSE11492", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11492" } ] }, "title" : "Transcript Profiling of High Fat Diet induced Obesity-prone and Obesity-resistant Rats", "dateAssigned" : "2008-05-19T00:00:00.000-05:00", "summary" : "Rodents respond to chronic high fat diet in at least two ways: some of them may readily gain body weight and become obese (termed obesity-prone), and others may not (termed obesity-resistant). An integrated approach of transcript and metabolic profiling of obesity-prone and obesity-resistant rats has been conducted, showing significantly different transcript and metabolic profiles in the two phenotypes. The major transcriptional differences involved hepatic fatty acid metabolism and ketogenesis in response to 16 weeks of high fat diet. At the same time, the different metabolic profiles (in liver tissue extracts, serum, and urine) between the two phenotypes could be ascribed to the corresponding pathways identified with multivariate statistical analysis, including fatty acid metabolism, Krebs cycle, and amino acid metabolism. The integration of results from both transcript and metabolic profiling revealed the different responses to dietary intervention of the two phenotypes and the physiological basis of susceptibility to metabolic disease in obesity-prone rats from a systematic view.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19913842" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11500" }, "primaryId" : "GEO:GSE11500", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11500" } ] }, "title" : "Expression data from renal primary epithelial cells", "dateAssigned" : "2008-05-19T00:00:00.000-05:00", "summary" : "Keywords: transgene", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18721488" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11520" }, "primaryId" : "GEO:GSE11520", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11520" } ] }, "title" : "Identification of flap structure specific endonuclease 1 as a factor involved in LTM formation of aversive learning", "dateAssigned" : "2008-05-20T00:00:00.000-05:00", "summary" : "We proposed that DNA recombination/repair processes play a role in memory formation. Here, we used microarray analysis of rat amygdala genes to identify possible DNA recombination/repair factors involved in memory consolidation of conditioned taste aversion (CTA). Among the genes that showed statistically significant differential expression, we identified fen-1, encoding a flap-structure specific DNA endonuclease. Amygdalar fen-1 mRNA induction was associated to the illness component of CTA, since it could be observed by the pairing of a flavor and gastrointestinal illness, by the illness itself, but not by the presentation of the flavor alone. No CTA related induction of fen-1 expression was observed in the insular cortex. Importantly, functional validation studies demonstrated that amygdalar suppression of fen-1 expression impaired memory consolidation of CTA. Overall, our studies helped identify a new DNA recombination/repair candidate factor involved in memory formation of aversive experiences. ", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11529" }, "primaryId" : "GEO:GSE11529", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11529" } ] }, "title" : "Sex-specific early growth hormone response genes in rat liver (Rattus norvegicus)", "dateAssigned" : "2008-05-21T00:00:00.000-05:00", "summary" : "A series of two color gene expression profiles obtained using Agilent 44K expression microarrays was used to examine sex-dependent and growth hormone-dependent differences in gene expression in rat liver. This series is comprised of pools of RNA prepared from untreated male and female rat liver, hypophysectomized (‘Hypox’) male and female rat liver, and from livers of Hypox male rats treated with either a single injection of growth hormone and then killed 30, 60, or 90 min later, or from livers of Hypox male rats treated with two growth hormone injections spaced 3 or 4 hr apart and killed 30 min after the second injection. The pools were paired to generate the following 6 direct microarray comparisons: 1) untreated male liver vs. untreated female liver; 2) Hypox male liver vs. untreated male liver; 3) Hypox female liver vs. untreated female liver; 4) Hypox male liver vs. Hypox female liver; 5) Hypox male liver + 1 growth hormone injection vs. Hypox male liver; and 6) Hypox male liver + 2 growth hormone injections vs. Hypox male liver. A comparison of untreated male liver and untreated female liver liver gene expression profiles showed that of the genes that showed significant expression differences in at least one of the 6 data sets, 25% were sex-specific. Moreover, sex specificity was lost for 88% of the male-specific genes and 94% of the female-specific genes following hypophysectomy. 25-31% of the sex-specific genes whose expression is altered by hypophysectomy responded to short-term growth hormone treatment in hypox male liver. 18-19% of the sex-specific genes whose expression decreased following hypophysectomy were up-regulated after either one or two growth hormone injections. Finally, growth hormone suppressed 24-36% of the sex-specific genes whose expression was up-regulated following hypophysectomy, indicating that growth hormone acts via both positive and negative regulatory mechanisms to establish and maintain the sex specificity of liver gene expression. For full details, see V. Wauthier and D.J. Waxman, Molecular Endocrinology (2008)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18483176" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11542" }, "primaryId" : "GEO:GSE11542", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11542" } ] }, "title" : "Expression data from rat mixed tissues samples", "dateAssigned" : "2008-05-23T00:00:00.000-05:00", "summary" : "Keywords: process control", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18778252" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11574" }, "primaryId" : "GEO:GSE11574", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11574" } ] }, "title" : "The responses of astrocytes stimulated by extracellular a-synuclein", "dateAssigned" : "2008-05-28T00:00:00.000-05:00", "summary" : "Abnormal neuronal aggregation of a-synuclein is implicated in the development of Parkinson’s disease. Glial cells also show extensive a-synuclein pathology and are thought to contribute to disease progression. However, the mechanism that produces the glial a-synuclein pathology and the interaction between neurons and glia in the disease-inflicted microenvironment remain unknown. Here, we show that in neuronal cells misfolded a-synuclein proteins are selectively translocated into vesicles, leading to exocytosis of the aggregated forms. More importantly, our data demonstrate that astrocytes take up the neuron-derived a-synuclein aggregates and produce a-synuclein inclusions similar to the ones found in human brains. This uptake is paralleled by changes in the gene expression profile reflecting an inflammatory response. These results suggest that astroglial a-synuclein pathology is produced by cell-to-cell transmission of neuronal a-synuclein aggregates. This transmission step is thus an important mediator of pathogenic glial responses and could qualify as a new therapeutic target.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20071342" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11617" }, "primaryId" : "GEO:GSE11617", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11617" } ] }, "title" : "Percutaneous Collagen Induction (PCI) in rat", "dateAssigned" : "2008-05-30T00:00:00.000-05:00", "summary" : "The purpose of the present study is to determine the effect of Percutaneous Collagen Induction (PCI) on the epidermis and dermis, including the systemic inflammatory response on gene expression level using microarray analysis. PCI Therapy is an alternative for safely treating wrinkles and scars and smoothening the skin. Therefore animal experiments were performed using 31 male Sprague-Dawley rats (350–375 g), age 4 month, randomly assigned into three groups: group (A) (n=24: needling plus skin care), group (B) (n=6: skincare only, controls after 24 h) and group (C) (n=1: negative control). Rats were anesthetized, shaved, and received a 30% total body surface area (TBSA) scald needling (10min) to induce percutaneous collagen, using a medical needling instrument (Environ® Medical Roll-CITTM, Vivida SA cc, Cape Town, South Africa). After needling surgery, the rats were immediately prepared with high levels of vitamin A cream and vitamin C cream, applied topically after cleaning once per day. The control group (C) rats received no injury, no skin care, no treatment, no anesthesia, and no analgesia. Gene expression analyses were performed 1 h, 24 h, 2, 4, and 8 weeks after PCI surgery. To confirm RNA expression in rat skin, self developed microarrays including genes like cytokines, such as vascular endothelial growth factor (VEGF), fibroblast growth factor (FGF 2), keratinocyte growth factor (KGF), epidermal growth factor (EGF), and transforming growth factors (TGF ß1, ß2, ß3) were used. ", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11622" }, "primaryId" : "GEO:GSE11622", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11622" } ] }, "title" : "Molecular Analysis of the Vaginal Response to Estrogens in the Ovariectomized Rat and Postmenopausal Woman", "dateAssigned" : "2008-05-30T00:00:00.000-05:00", "summary" : "Keywords: Disease State Analysis: Animal Model Validation", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18578861" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11722" }, "primaryId" : "GEO:GSE11722", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11722" } ] }, "title" : "Irinotecan-induced gene expression changes in the rat intestine", "dateAssigned" : "2008-06-09T00:00:00.000-05:00", "summary" : "Keywords: Time course and tissue comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:17594691" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11730" }, "primaryId" : "GEO:GSE11730", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11730" } ] }, "title" : "mRNAs in un-injured and injured rat cortical axons isolated after 13 days in culture", "dateAssigned" : "2008-06-10T00:00:00.000-05:00", "summary" : "Keywords: axonal expression analysis; injury state analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19369540" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11733" }, "primaryId" : "GEO:GSE11733", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11733" } ] }, "title" : "Whole genome microarray of the retina reveals a progressive response with increasing duration of diabetes.", "dateAssigned" : "2008-06-10T00:00:00.000-05:00", "summary" : "Gene expression changes were identified by whole genome microarray and confirmed by qPCR in the same set of animals as used in the microarray analyses and subsequently validated in independent sets of animals. Significantly more and larger magnitude gene expression changes were observed after 3 months than after 1 month of diabetes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18554398" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11829" }, "primaryId" : "GEO:GSE11829", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11829" } ] }, "title" : "Prg1 is regulated by the basic helix-loop-helix transcription factor Math2", "dateAssigned" : "2008-06-19T00:00:00.000-05:00", "summary" : "Math2 (NEX-1/NeuroD6) is a member of the bHLH transcription factor family and is involved in neuronal differentiation and maturation. In the present study, we identified the genes targeted by Math2 using DNA microarrays and cultured rat cortical cells transfected with Math2. Of the genes regulated by Math2, we focused on plasticity-related gene 1 (Prg1). Prg1 expression induced by Math2 was confirmed in cultured rat cortical cells and PC12 cells analyzed by real-time quantitative PCR. Examining the promoter region of rat Prg1, we found four E-boxes designated -E1 to -E4 (CANNTG) which were recognized by the bHLH transcription factor. Using chromatin immunoprecipitation (ChIP) assays, we found that Math2 directly bound to the E-box(es) in the Prg1 promoter. The reporter assay of Prg1 showed that -E1 was critical for the regulation of the Prg1 expression by Math2. Then, the functional role of Math2 and Prg1 was investigated in PC12 cells. Seventy-two hours after transfection of Math2 or Prg1, neurite length and number was significantly induced in PC12 cells. Co-transfection with Prg1-siRNA completely inhibited Math2-mediated morphological changes. Our results suggest that Math2 directly regulates Prg1 expression and Math2-Prg1 cascade plays an important role in neurite outgrowth in PC12 cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18643870" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11842" }, "primaryId" : "GEO:GSE11842", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11842" } ] }, "title" : "Transgenerational effects of the endocrine disruptor Vinclozolin on the prostate transcriptome and adult onset disease", "dateAssigned" : "2008-06-20T00:00:00.000-05:00", "summary" : "Keywords: expression analysis, transgenerational changes due to Vinclozolin", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18220299" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11851" }, "primaryId" : "GEO:GSE11851", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11851" } ] }, "title" : "Gene expression in rat right ventricles during chronic pulmonary embolism", "dateAssigned" : "2008-06-20T00:00:00.000-05:00", "summary" : "Pulmonary vascular occlusions due to thromboemboli can result in pulmonary hypertension and right heart damage. Treatments to clear the vascular obstructions such as i.v. heparain or thrombolytics can resolve the hypertension but right ventricular damage often occurs first. Methods of protecting the right ventricle from hypertensive damage during the course of acute treatment to clear the thromboemboli are needed. Monocyte- and neutrophil-mediated inflammation and fibrosis are associated with chronic right ventricular damage but the pathways involved are not understood. A comprehesive survey of gene expression during chronic pulmonary embolism verses control rats has been conducted in this study.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19602618" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11987" }, "primaryId" : "GEO:GSE11987", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE11987" } ] }, "title" : "Expression data from GLI1-transformed RK3E cells", "dateAssigned" : "2008-07-03T00:00:00.000-05:00", "summary" : "We used microarrays to obtain the global gene expression profiles in cells transformed by GLI1 and identified distinct classes of genes by comparing with those of desmoplastic medulloblastomas", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18924150" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12007" }, "primaryId" : "GEO:GSE12007", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12007" } ] }, "title" : "Identification of Sox10 target genes by comparative expression profiling", "dateAssigned" : "2008-07-04T00:00:00.000-05:00", "summary" : "RT4D6 Schwannoma cells were treated with siRNA specific for Sox10 and a mutant siRNA. Total RNA from the cells were used to screen for differentially expressed genes. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18786246" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12018" }, "primaryId" : "GEO:GSE12018", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12018" } ] }, "title" : "Gene Expression Analysis of Carbonyl Sulfide Neurotoxicity", "dateAssigned" : "2008-07-07T00:00:00.000-05:00", "summary" : "To gain insight into the pathogenesis of carbonyl sulfide induced neurotoxicity, we examined the gene expression profile of exposed rats before the onset of morphological changes (days 1 and 2) using the most consistently affected brain region, the posterior colliculus.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19395590" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12030" }, "primaryId" : "GEO:GSE12030", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12030" } ] }, "title" : "Gene expression profiling of hepatocarcinogenesis initiation in Fischer-344 rats.", "dateAssigned" : "2008-07-08T00:00:00.000-05:00", "summary" : "Diethylnitrosamine is used as initiator carcinogen in the modiffied resistan model but is not known its effect on gene expression profile on this stage. In other way, CAPE is compound with anticarcinogenic propertie when is administered 12 h before DEN and with the aim to characterize its effect on gene expression profile when is administered alone and in combination with diethylnitrosamine, these analysis were made. Male Fischer-344 rats were we used 4 animal per each treatment and all treatments are compared with not treated rats. Were identified groups of genes related with Carcinogens metabolism, oxidative stress and cell regulation with important differences between treatments.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20360939" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12066" }, "primaryId" : "GEO:GSE12066", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12066" } ] }, "title" : "Segregation of genes influencing skeletal phenotypes in congenic P/NP rats", "dateAssigned" : "2008-07-10T00:00:00.000-05:00", "summary" : "Keywords: Comparison of gene expression profiles between NP, P, NP.P and P.NP rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20200994" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12087" }, "primaryId" : "GEO:GSE12087", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12087" } ] }, "title" : "Identification of cold-shock protein RBM3 as a possible regulator of skeletal muscle size", "dateAssigned" : "2008-07-11T00:00:00.000-05:00", "summary" : "The goal of this study was to identify changes in muscle gene expression that may contribute to loss of adaptability of old muscle. Muscle atrophy was induced in young adult (6-month) and old (32-month) male Brown Norway/F344 rats by two weeks of hind limb suspension (HS) and soleus muscles were analyzed by cDNA microarrays. We conclude that a cold shock response may be part of a compensatory mechanism in muscles undergoing atrophy to preserve remaining muscle mass and that RBM3 may be a therapeutic target to prevent muscle loss.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18753264" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12112" }, "primaryId" : "GEO:GSE12112", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12112" } ] }, "title" : "Chemoprevention of the hepatocarcinogenesis by celecoxib", "dateAssigned" : "2008-07-15T00:00:00.000-05:00", "summary" : "Microarray analysis is a useful methodology to identify target genes modulated by anticancer drugs. Here, celecoxib effect on gene expression profiles was evaluated in the modified resistant hepatocyte model. Animals subjected to carcinogenic treatment were fed with diet containing 1500 ppm of celecoxib. Two schemes of celecoxib administration were designed. In the progression protocol, celecoxib was administrated between days 18 and 25 post-cancer initiation, a total of 8 celecoxib treatment days, when well established preneoplastic lesions starts to appear. In the initiation protocol, celecoxib was administrated from one week before until 25 days after of cancer initiation, a total of 32 celecoxib treatment days. A rat group was subjected only to the carcinogenic treatment as cancer positive control. Gene expression profiles of all groups were compared to a negative untreated control. The evaluation of gene expression profiles permitted us to identify new target genes that are modulated by celecoxib treatment. A possible mechanism of celecoxib chemoprevention of hepatocarcinogenesis is proposed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20145537" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12132" }, "primaryId" : "GEO:GSE12132", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12132" } ] }, "title" : "Rat response to changes in developmental stage - 3 types of tissue, 3 gravity conditions, 2 developmental conditions", "dateAssigned" : "2008-07-16T00:00:00.000-05:00", "summary" : "Keywords: Gene Expression experiment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25649141" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12153" }, "primaryId" : "GEO:GSE12153", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12153" } ] }, "title" : "Expression data in polysomal and total RNA from perinatal rat lung", "dateAssigned" : "2008-07-17T00:00:00.000-05:00", "summary" : "Keywords: development", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18952566" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12196" }, "primaryId" : "GEO:GSE12196", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12196" } ] }, "title" : "Rat exposure to RDX (3mg/kg or 18mg/kg; 0, 4, 24, 48 hr)", "dateAssigned" : "2008-07-22T00:00:00.000-05:00", "summary" : "Keywords: time course, dose response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19239275" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12206" }, "primaryId" : "GEO:GSE12206", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12206" } ] }, "title" : "Genome-wide analysis of mechano-responsive gene expression by tenocytes in fascicles subjected to cyclic tensile strain", "dateAssigned" : "2008-07-22T00:00:00.000-05:00", "summary" : "Keywords: gene expression array-based, stress response, functional analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20497018" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12217" }, "primaryId" : "GEO:GSE12217", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12217" } ] }, "title" : "Dietary soy effects on early rat mammary gland development", "dateAssigned" : "2008-07-23T00:00:00.000-05:00", "summary" : "The linkage between nutrition and cancer prevention is an intriguing concept that is gaining widespread support based on epidemiological and animal studies. Multiple mechanisms likely underlie dietary protection against cancer, with effects influenced by target tissue response, cell-cell interactions and developmental context. Given the negative correlation between breast cancer incidence and intake of soy foods by Asian women, and the increasing consumption of soy protein-based formula by infants in the Western world, we have studied soy protein isolate (SPI) used in most infant formula as a paradigm to evaluate diet as a risk factor in a rodent model of mammary cancer. We previously demonstrated that lifetime exposure to dietary SPI reduced the incidence of N-methyl-N-nitrosourea-induced mammary tumors in young adult rats relative to those fed the control diet Casein (CAS). This protection was associated with increased tumor suppressor PTEN and decreased Wnt signaling component expression in mammary epithelial cells at postnatal day (PND) 50 prior to carcinogen insult. To identify early events contributing to mammary tumor suppression by diet, we used Affymetrix RAE230A GeneChips containing 14280 probe sets and the GeneSpring Robust Multi-array program to analyze genomic profiles of mammary glands of prepubertal (PND21) rats lifetime exposed to SPI or CAS. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19321580" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12255" }, "primaryId" : "GEO:GSE12255", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12255" } ] }, "title" : "Arterial vs venous expression of genes: differences in inflammatory genes", "dateAssigned" : "2008-07-25T00:00:00.000-05:00", "summary" : "Arteries and veins modulate cardiovascular homeostasis and contribute to the pathogenesis of hypertension. Functional differences between normal arteries and veins are based upon differences in gene expression. To better characterize these expression patterns, and to identify candidate genes that could be manipulated selectively in the venous system, we performed whole genome expression profiling of rat arteries and veins using the CodeLink platform. We used the major artery and vein of the rat, the thoracic aorta and caudal vena cava, respectively. Expression of mRNA for thrombospondins (TSP-1, 2, 4) was greater than 5-fold higher in veins vs arteries. The most prominent gene expression difference between the normal aorta and vena cava was pancreatitis associated protein (PAP1), a protein with anti-inflammatory functions that was 64-fold higher in vena cava vs aorta. Higher mRNA expression of TSP-1, TSP-2, TSP-4 and PAP1 in vena cava vs aorta was confirmed with real time RT-PCR. Importantly, immunohistochemical analysis of blood vessels sections qualitatively confirmed a higher expression of proteins in vena cava vs aorta. These studies report a difference in inflammatory genes in arteries vs veins. A particularly notable finding is the discovery of PAP1 mRNA and protein expression in peripheral blood vessels with a substantially higher expression in the veins. Data from these studies may provide novel insights into the genetic basis for functional differences between arteries and veins in health and disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19571575" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12260" }, "primaryId" : "GEO:GSE12260", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12260" } ] }, "title" : "Expression data from isolated perfused rat hearts exposed to doxorubicin", "dateAssigned" : "2008-07-28T00:00:00.000-05:00", "summary" : "Keywords: treatment vs control", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20053966" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12282" }, "primaryId" : "GEO:GSE12282", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12282" } ] }, "title" : "Normal rat diaphragm vs sternohyoid", "dateAssigned" : "2008-07-29T00:00:00.000-05:00", "summary" : "Normal young adult Sprague Dawley rats (male)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20337195" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12289" }, "primaryId" : "GEO:GSE12289", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12289" } ] }, "title" : "Identifying Significant Temporal Variation in Time Course Microarray Data Without Replicates", "dateAssigned" : "2008-07-30T00:00:00.000-05:00", "summary" : "Keywords: developmental time course (time series) throughout the estrus cycle in rat mammary gland singlet data", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19323838" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12296" }, "primaryId" : "GEO:GSE12296", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12296" } ] }, "title" : "Effects of testosterone on dexamethasone-induced changes in gene expression in gastrocnemius muscles from male rats", "dateAssigned" : "2008-07-30T00:00:00.000-05:00", "summary" : "Keywords: Evaluate drug effects at a single time point", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20032058" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12304" }, "primaryId" : "GEO:GSE12304", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12304" } ] }, "title" : "Albumin, TGF-Beta1 and Blood-Brain Barrier opening induce cortical epileptogenesis.", "dateAssigned" : "2008-07-30T00:00:00.000-05:00", "summary" : "Insults to the cerebral cortex, such as trauma, ischemia or infections, may result in the development of epilepsy, one of the most common neurological disorders. Previous studies have suggested that perturbations in neurovascular integrity and breakdown of the blood-brain barrier (BBB) lead to neuronal hypersynchronization and epileptiform activity, but the underlying mechanisms are unknown. As with BBB opening, treatment with albumin or with TGF-ß1 results in the development of hypersynchronized epileptiform activity. Given the latent period before the appearance of epileptiform activity, we hypothesized the underlying mechanism is a transcriptional response which would be similar for BBB breakdown and exposure to albumin or TGF-ß1. In search of a common pathway and transcriptional activation pattern we performed a genome wide analysis. Genomic expression analyses demonstrated similar expression patterns for BBB opening, albumin and TGF-ß1 exposure. Most importantly, TGF-ß pathway blockers suppressed most albumin-induced transcriptional changes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19710312" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12324" }, "primaryId" : "GEO:GSE12324", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12324" } ] }, "title" : "Alterations in Neuronal Gene Expression Profiles in Response to Experimental Demyelination and Axonal Transection", "dateAssigned" : "2008-08-03T00:00:00.000-05:00", "summary" : "The pathological basis of multiple sclerosis involves damage to both myelin sheaths and axons. Demyelination and axonal transection are considered to cause reversible and irreversible neurological deficits respectively, gradually destroying the neuronal circuitry of the CNS. In order to analyse the individual effects of the pathological hallmarks of multiple sclerosis on neurons, the pontocerebellar pathway was targeted with either lysolecithin-induced chemical demyelination or complete pathway transection. Transcriptional changes in the pontocerebellar neuronal nuclei were investigated with microarrays at days 4, 10 and 37 post-intervention to identify underlying molecular responses. A common as well as unique set of injury response genes was identified in the transection and the demyelination conditions. The increased expression of activating transcription factor 3 (Atf3) and thyrotropin-releasing hormone (Trh) in both injury paradigms was validated by immunohistochemistry. Expression of Atf3 in a patient with Marburg’s variant of multiple sclerosis was also detected in the pons with large cerebellar demyelination, confirming the activation of the Atf3 pathway in a human disease sample as well. This experimental approach may be useful for the identification of pathways that could be targeted for remyelinative and neuroprotective drug development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20086029" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12341" }, "primaryId" : "GEO:GSE12341", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12341" } ] }, "title" : "Expt. A; Daily Rhythm in Expression of >600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling", "dateAssigned" : "2008-08-05T00:00:00.000-05:00", "summary" : "Keywords: Time course (2 points)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21367864" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12342" }, "primaryId" : "GEO:GSE12342", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12342" } ] }, "title" : "Expt. B; Daily Rhythm in Expression of >600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling", "dateAssigned" : "2008-08-05T00:00:00.000-05:00", "summary" : "Keywords: Time course (2 points)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21367864" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12343" }, "primaryId" : "GEO:GSE12343", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12343" } ] }, "title" : "Expt. C; Daily Rhythm in Expression of >600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling", "dateAssigned" : "2008-08-05T00:00:00.000-05:00", "summary" : "Keywords: Time course (2 points) for in vivo pineal glands and various tissues; Treatment groups for cultured pineal glands", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21367864" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12423" }, "primaryId" : "GEO:GSE12423", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12423" } ] }, "title" : "Renal Expression of Dahl SS/Jr (S) and Congenic Rats after 28 days of dietary salt elevation", "dateAssigned" : "2008-08-12T00:00:00.000-05:00", "summary" : "Keywords: strain differences in response to dietary changes", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12424" }, "primaryId" : "GEO:GSE12424", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12424" } ] }, "title" : "Renal Expression of Dahl SS/Jr (S) and Congenic Rats after 24 hours of Dietary Salt Loading", "dateAssigned" : "2008-08-12T00:00:00.000-05:00", "summary" : "Keywords: strain differences in response to dietary changes", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12457" }, "primaryId" : "GEO:GSE12457", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12457" } ] }, "title" : "Comparison of Environmental and Genetic models of ADHD", "dateAssigned" : "2008-08-15T00:00:00.000-05:00", "summary" : "ADHD is the most common neurobehavioral disorder in school-aged children. In addition to genetic factors, environmental influences or gene x environmental interactions also play an important role in ADHD. One example of a well studied environmental risk factor for ADHD is exposure to polychlorinated biphenyls (PCBs). In this study, we investigated whether the well-established genetic model of ADHD based on the Spontaneously Hypertensive Rat (SHR) and a well established PCB-based model of ADHD exhibited similar molecular changes in brain circuits involved in ADHD. The brains from 28 male rats (8 SHR, 8 Sprague-Dawley (SD) controls, 8 Wistar-Kyoto (WKY) controls, and 4 PCB-exposed SD rats) were harvested at postnatal day 55-65 and RNA was isolated from six brain regions of interest. The RNA was analyzed for differences in expression of a set of 308 probe sets interrogating 218 unique genes considered highly relevant to ADHD or epigenetic gene regulation using the Rat RAE 230 2.0 GeneChip (Affymetrix). Selected observations were confirmed by real time quantitative RT-PCR. The results show that the expression levels of genes Gnal, COMT, Adrbk1, Ntrk2, Hk1, Syt11 and Csnk1a1 were altered in both the SHR rats and the PCB-exposed SD rats. Arrb2, Stx12, Aqp6, Syt1, Ddc and Pgk1 expression levels were changed only in the PCB-exposed SD rats. Genes with altered expression only in the SHRs included Oprm1, Calcyon, Calmodulin, Lhx1 and Hes6.The epigenetic genes Crebbp, Mecp2 and Hdac5 are significantly altered in both models. The data provide strong evidence that genes and environment can affect different set of genes in two different models of ADHD and yet result in the similar disease-like symptoms. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18937310" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12481" }, "primaryId" : "GEO:GSE12481", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12481" } ] }, "title" : "TRE-Htt-N853 Huntington's Disease in vitro model", "dateAssigned" : "2008-08-19T00:00:00.000-05:00", "summary" : "Keywords: gene expression study", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18815258" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12483" }, "primaryId" : "GEO:GSE12483", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12483" } ] }, "title" : "Anti-Nogo-A antibody treatment of Rat Hippocampal Slice Cultures", "dateAssigned" : "2008-08-19T00:00:00.000-05:00", "summary" : "In vitro cultures treated with anti-Nogo-A antibody showed an elicited growth response. The results also gave indications that hippocampal circuitry might be altered due to the regulation at the synaptic and neurotransmission level.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18973596" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12596" }, "primaryId" : "GEO:GSE12596", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12596" } ] }, "title" : "Global gene expression changes in rat retinal ganglion cells after experimental glaucoma ", "dateAssigned" : "2008-08-27T00:00:00.000-05:00", "summary" : "However, the retina is a complex tissue composed of neuronal, glial and vascular cell types. The RGCs only comprise 5% or less of retinal cells. The gene expression profiles from whole retina can not represent of RGC gene expression. In the current study, we sought to investigate the whole genome regulation of the RGCs in glaucoma.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20335623" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12639" }, "primaryId" : "GEO:GSE12639", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12639" } ] }, "title" : "diabetes mellitus and the progression of post-infarction genetic regulatory expression", "dateAssigned" : "2008-09-02T00:00:00.000-05:00", "summary" : "CONCLUSION: The genetic findings in this study might be the possible mechanism that diabetes mellitus can accerate the progression of post-infarction genetic regulatory expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19789393" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12670" }, "primaryId" : "GEO:GSE12670", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12670" } ] }, "title" : "Renal gene expression analysis: transcript-level data", "dateAssigned" : "2008-09-04T00:00:00.000-05:00", "summary" : "This is a SubSeries of GSE12672", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19307186" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12671" }, "primaryId" : "GEO:GSE12671", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12671" } ] }, "title" : "Renal gene expression analysis: exon-level data", "dateAssigned" : "2008-09-04T00:00:00.000-05:00", "summary" : "This is a SubSeries of GSE12672", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19307186" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12724" }, "primaryId" : "GEO:GSE12724", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12724" } ] }, "title" : "Positional identification of Adamts16 variants linked to inherited hypertension: knockdown of Adamts16 in NRK-52E cells", "dateAssigned" : "2008-09-10T00:00:00.000-05:00", "summary" : "Keywords: Gene knockdown with siRNA", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19423552" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12725" }, "primaryId" : "GEO:GSE12725", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12725" } ] }, "title" : "Positional identification of Adamts16 variants linked to inherited hypertension: gene expression of congenic vs S rats", "dateAssigned" : "2008-09-10T00:00:00.000-05:00", "summary" : "Keywords: Genetic modification, disease state analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19423552" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12743" }, "primaryId" : "GEO:GSE12743", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12743" } ] }, "title" : "pCMV-FAK vs pCMV in CTL", "dateAssigned" : "2008-09-11T00:00:00.000-05:00", "summary" : "CMV-driven FAK overexpression in soleus muscle was compared vs empty transfection in contralateral muscle", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19470782" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12744" }, "primaryId" : "GEO:GSE12744", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12744" } ] }, "title" : "pCMV-FRNK/pCMV-FAK vs pCMV-FAK in CTL", "dateAssigned" : "2008-09-11T00:00:00.000-05:00", "summary" : "CMV-driven inhibition of FAK in soleus muscle was compared vs contralateral muscle", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19470782" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12745" }, "primaryId" : "GEO:GSE12745", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12745" } ] }, "title" : "pCMV-FAK vs pCMV in HU", "dateAssigned" : "2008-09-11T00:00:00.000-05:00", "summary" : "CMV-driven FAK overexpression in soleus muscle was compared vs empty transfection in contralateral muscle after unloading", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19470782" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12746" }, "primaryId" : "GEO:GSE12746", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12746" } ] }, "title" : "pCMV-FAK vs pCMV in R1", "dateAssigned" : "2008-09-11T00:00:00.000-05:00", "summary" : "CMV-driven FAK overexpression in soleus muscle was compared vs empty transfection in contralateral muscle after 1 day of reloading", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19470782" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12747" }, "primaryId" : "GEO:GSE12747", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12747" } ] }, "title" : "pCMV-FAK vs pCMV in R5", "dateAssigned" : "2008-09-11T00:00:00.000-05:00", "summary" : "CMV-driven FAK overexpression in soleus muscle was compared vs empty transfection in contralateral muscle after 5 day of reloading", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19470782" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12752" }, "primaryId" : "GEO:GSE12752", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12752" } ] }, "title" : "Gene expression data from corticosteroid-treated neonatal rat cardiomyocytes", "dateAssigned" : "2008-09-12T00:00:00.000-05:00", "summary" : "Keywords: comparison of the effect of steroidal ligands", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19293335" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12754" }, "primaryId" : "GEO:GSE12754", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12754" } ] }, "title" : "Expression data from 28 day sham and shunt atrial and ventricular tissues (set 1)", "dateAssigned" : "2008-09-12T00:00:00.000-05:00", "summary" : "To identify genes involved in the transcriptional response of the endocrine heart under normal and stimulated states, we conducted differential gene expression studies of the rat atria and ventricles under normal or chronic volume overload, induced by aorto-caval shunt.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22408026" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12755" }, "primaryId" : "GEO:GSE12755", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12755" } ] }, "title" : "Expression data from 28 day sham and shunt atrial tissues (set 2)", "dateAssigned" : "2008-09-12T00:00:00.000-05:00", "summary" : "To identify genes involved in the transcriptional response of the endocrine heart under normal and stimulated states, we conducted differential gene expression studies of the rat atria under normal or chronic volume overload, induced by aorto-caval shunt.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22408026" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12799" }, "primaryId" : "GEO:GSE12799", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12799" } ] }, "title" : "Changes in Global Gene Expression in Rat Myometrium in the Transition from Late Pregnancy to Parturition", "dateAssigned" : "2008-09-16T00:00:00.000-05:00", "summary" : "The process of parturition involves the complex interplay of factors that changes the excitability and contractile activity of the uterus. We have compared the relative gene expression profile of myometrium from rats before parturition (21 days pregnant) and during delivery using high-density DNA microarray. Of 8740 sequences available in the array a total of 3782 were detected as present. From the sequences that were significantly altered, 59 genes were upregulated and 82 genes were downregulated. We were able to detect changes in genes described to have altered expression level at term including connexin 43 and 26, cyclo-oxygenase 2 and oxytocin receptor as well as novel genes that have been not previously associated with parturition. Quantitative real time PCR on selected genes further confirmed the microarray data. Here we report for the first time that aquaporin5 (AQP5), a member of aquaporin (AQP) water channel family, was dramatically downregulated during parturition (~100 fold by microarray and ~50 fold by Real Time PCR). The emerging profile highlights biochemical cascades occurring in a period of about 36 hours that triggers parturition and the initiation of myometrium reverse remodeling after partum. The microarray analysis uncovered genes that were previously suspected to play a role in parturition. This regulation involves genes from immune/inflammatory response, steroid/lipids metabolism, calcium homeostasis, cell volume regulation, cell signaling, cell division, and tissue remodeling, suggesting the presence of multiple and redundant mechanisms altered in the process of birth. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19001510" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12817" }, "primaryId" : "GEO:GSE12817", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12817" } ] }, "title" : "Cluster analysis of rat pancreatic islet gene mRNA levels after culture in low, intermediate and high [glucose]", "dateAssigned" : "2008-09-17T00:00:00.000-05:00", "summary" : "Keywords: Dose response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19165461" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12966" }, "primaryId" : "GEO:GSE12966", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12966" } ] }, "title" : "Basal gene expression in bone", "dateAssigned" : "2008-09-29T00:00:00.000-05:00", "summary" : "Analysis of basal gene expression of the protective bones of the skull (parietals) and weight-bearing bones of the limb (ulnae)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23182809" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12978" }, "primaryId" : "GEO:GSE12978", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE12978" } ] }, "title" : "Microarray Analysis of the transcriptome of the Subfornical Organ in the rat", "dateAssigned" : "2008-09-30T00:00:00.000-05:00", "summary" : "In these studies we have for the first time described the transcriptome of the rat SFO, and have in addition identified genes the expression of which is significantly modified by either water or food deprivation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18832082" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13003" }, "primaryId" : "GEO:GSE13003", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13003" } ] }, "title" : "Gene expression profiling of rat endometrial cancer", "dateAssigned" : "2008-10-01T00:00:00.000-05:00", "summary" : "Keywords: Endometrial tumors developed in crosses with the BDII inbred rat strain (from backcrosses, NUT, and intercrosses, RUT) and Sprague Dawley curley-3 and Brown Norway", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19426485" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13014" }, "primaryId" : "GEO:GSE13014", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13014" } ] }, "title" : "Gene profiling of young rats susceptible to malaria infection", "dateAssigned" : "2008-10-02T00:00:00.000-05:00", "summary" : "The study was performed in order to determine molecular markers potentially involved in the susceptibility of young rats to the infection with Plasmodium berghei Anka", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21323829" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13065" }, "primaryId" : "GEO:GSE13065", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13065" } ] }, "title" : "Expression data from kidney of 36d old PKD/Mhm rats.", "dateAssigned" : "2008-10-06T00:00:00.000-05:00", "summary" : "Keywords: gender, genotype", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13112" }, "primaryId" : "GEO:GSE13112", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13112" } ] }, "title" : "DNA topoisomerase IIbeta (topo IIbeta) regulates gene expression in developing cerebellar granule cells (CGC)", "dateAssigned" : "2008-10-08T00:00:00.000-05:00", "summary" : "We used microarrays to determine the global programme of gene expression regulated by topo IIbeta.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19116664" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13145" }, "primaryId" : "GEO:GSE13145", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13145" } ] }, "title" : "Mapping of genome-wide action sites of topoisomerase IIbeta by a functional ChIP-chip technique (eTIP-tiling array)", "dateAssigned" : "2008-10-10T00:00:00.000-05:00", "summary" : "DNA topoisomerase II (topo II) catalyzes a strand passage reaction in that one duplex is passed through a transient brake in another. Completion of late stages of neuronal development depends on the presence of active isoform (topo IIbeta). We identified topo IIbeta action sites on 7 selected genomic regions (about 79 Mb in total), each containing at least one gene that is controlled by topo IIbeta in neuronal differentiation. We used a novel method, etoposide-mediated topoisomerase immunoprecipitation (eTIP), followed by identification of precipitated DNA fragments on genomic tiling arrays. These DNA fragments were first fractionated by concentrated salt prior to the array analysis. The 0.5 M NaCl-released fraction was analyzed as P2 and the salt-resistant fraction wad analyzed as P1.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19116664" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13153" }, "primaryId" : "GEO:GSE13153", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13153" } ] }, "title" : "Stimulation of Human and Rat Islet ß-Cell Proliferation with Retention of Function by Nkx6.1", "dateAssigned" : "2008-10-10T00:00:00.000-05:00", "summary" : "Keywords: Insulin secretion, islet biology, transcription factor, cell cycle regulation, diabetes", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18347054" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13166" }, "primaryId" : "GEO:GSE13166", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13166" } ] }, "title" : "Rat medial prefrontal cortex gene expression following heroin self-administration, abstinence, and extinction", "dateAssigned" : "2008-10-13T00:00:00.000-05:00", "summary" : "Keywords: heroin self-administration", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19664213" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13193" }, "primaryId" : "GEO:GSE13193", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13193" } ] }, "title" : "The effects of edema on intestinal smooth muscle", "dateAssigned" : "2008-10-14T00:00:00.000-05:00", "summary" : "Keywords: disease state analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22235829" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13220" }, "primaryId" : "GEO:GSE13220", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13220" } ] }, "title" : "Transcriptomics of Rat Striata 16 h after Gamma Knife Surgery: Distinct Bilateral Effects in the Un-irradiated Striatum", "dateAssigned" : "2008-10-16T00:00:00.000-05:00", "summary" : "Gamma knife surgery (GKS) is used for treatment of various brain disorders. The effects of gamma irradiation to targeted and un-targeted regions were evaluated by monitoring gene expression changes in the unilateral irradiated (60 Gy) and contralateral un-irradiated striata in the rat. Striata of irradiated and control brains were dissected 16 h post-irradiation for analysis by rat whole genome 44K DNA oligo microarray. Results revealed 230 induced and 144 repressed genes in the irradiated striatum and 432 induced and 239 repressed genes in the un-irradiated striatum. The number of altered genes in un-irradiated striatum was more than that in irradiated striatum. Results of RT-PCR and western analyses suggested that gamma-irradiation caused cellular damage, including oxidative stress, in both striata of both hemispheres. Our present results indicate that unilateral irradiation during GKS produce bilateral effects as early as 16 h, the time-period analyzed, and these molecular changes in the un-irradiated striatum are ample proof.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19277511" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13249" }, "primaryId" : "GEO:GSE13249", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13249" } ] }, "title" : "Gene expression profiles in rat lung after inhalation exposure to C60 fullerene or ultrafine NiO particles", "dateAssigned" : "2008-10-17T00:00:00.000-05:00", "summary" : "Gene expression profiling of the rat lung after whole-body inhalation exposure to C60 fullerene and ultrafine nickel oxide (Uf-NiO) particles as a positive control were employed to gain insights into these molecular events.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19167457" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13268" }, "primaryId" : "GEO:GSE13268", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13268" } ] }, "title" : "Diabetes biomarker disease progression study in rat adipose tissue", "dateAssigned" : "2008-10-18T00:00:00.000-05:00", "summary" : "Keywords: Type 2 diabetes, biomarker, adipose tissue, rat, time series", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23236253" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13269" }, "primaryId" : "GEO:GSE13269", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13269" } ] }, "title" : "Diabetes biomarker disease progression study in rat gastrocnemius muscle", "dateAssigned" : "2008-10-18T00:00:00.000-05:00", "summary" : "Keywords: Type 2 diabetes, biomarker, rat, muscle, time series", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23236253" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13270" }, "primaryId" : "GEO:GSE13270", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13270" } ] }, "title" : "Diabetes biomarker disease progression study in rat liver", "dateAssigned" : "2008-10-18T00:00:00.000-05:00", "summary" : "Keywords: Type 2 diabetes, biomarker, rat, liver, time series", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23236253" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13311" }, "primaryId" : "GEO:GSE13311", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13311" } ] }, "title" : "Whole genome analysis of nicotine-exposed cells from the brainstem of spontaneously hypertensive and Wistar Kyoto rats", "dateAssigned" : "2008-10-22T00:00:00.000-05:00", "summary" : "The development of hypertension may be highly influenced by the use of nicotine especially in genetically susceptible subjects. In this study the effects of nicotine on gene expression of cultured cells from the brainstem of spontaneously hypertensive (SHR) and Wistar Kyoto (WKY) rats were evaluated using whole genome microarray platforms. It was described for the first time that nicotine may act differentially on the gene expression profile of SHR and WKY. The influence of strain was present in 348 genes that were differentially expressed in SHR as compared to WKY brainstem cells independently of the nicotine treatment. 176 genes had their expression altered in both strains after nicotine exposure. Interaction between nicotine treatment and the strain was observed for the expression of 269 genes which participate of cellular pathways related to neurotrabnsmitter secretion, intracellular trafficking and cell communication. In conclusion, this study leaves a list of genes whose expression shall be better studied since they are good candidates to the phenotypic differentiation between SHR and WKY, including hypertension as well as demonstrated that alterations in the systems of intracellular trafficking and neurotransmission may be relevant to the development of hypertension.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19752883" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13319" }, "primaryId" : "GEO:GSE13319", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13319" } ] }, "title" : "Comparison of Human and Rat Uterine Leiomyoma: Identification of a Dysregulated mTOR Pathway", "dateAssigned" : "2008-10-23T00:00:00.000-05:00", "summary" : "Keywords: Disease State Analysis: Animal Model Validation", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19622772" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13356" }, "primaryId" : "GEO:GSE13356", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13356" } ] }, "title" : "Microarray analysis of rat mammary carcinogenesis", "dateAssigned" : "2008-10-27T00:00:00.000-05:00", "summary" : "Keywords: Comparative experiments of sesame oil treatment(control)and 7,12-Dimethylbenz[a]anthracene(DMBA)treatment group. Or comparative experiments of tissue type", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19480007" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13359" }, "primaryId" : "GEO:GSE13359", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13359" } ] }, "title" : "Rat iPS F65 cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells", "dateAssigned" : "2008-10-27T00:00:00.000-05:00", "summary" : "Rat iPS F65 cells had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave rat iPS F65 cells unique characteristics which could then be compared with other species' ES cells or iPS cells like human ES cells and mouse ES cells by the homologue genes comparison to show which species' ES cells or iPS cells were more competitive with the other.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19097959" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13360" }, "primaryId" : "GEO:GSE13360", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13360" } ] }, "title" : "Rat iPS M13 cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells", "dateAssigned" : "2008-10-27T00:00:00.000-05:00", "summary" : "Rat iPS M13 cells had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave rat iPS M13 cells unique characteristics which could then be compared with other species' ES cells or iPS cells like human ES cells and mouse ES cells by the homologue genes comparison to show which species' ES cells or iPS cells were more competitive with the other.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19097959" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13368" }, "primaryId" : "GEO:GSE13368", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13368" } ] }, "title" : "Expression data from kidney transplantions in a fisher-lewis rat model", "dateAssigned" : "2008-10-27T00:00:00.000-05:00", "summary" : "Keywords: timecourse analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19681821" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13381" }, "primaryId" : "GEO:GSE13381", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13381" } ] }, "title" : "Detailed transcriptome atlas of the pancreatic beta cell", "dateAssigned" : "2008-10-28T00:00:00.000-05:00", "summary" : "The aim of the present study was to explore the transcriptome of pancreatic islets and, based on this information, to prepare a comprehensive and open access inventory of insulin-producing ß-cell gene expression, the beta-Cell Gene Atlas (BCGA).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19146692" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13413" }, "primaryId" : "GEO:GSE13413", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13413" } ] }, "title" : "Influence of hyperthyroid conditions on gene expression in rat tibialis anterior", "dateAssigned" : "2008-10-30T00:00:00.000-05:00", "summary" : "RNA isolated from tibialis anterior muscles of the same animals was used as a reference fast-twitch muscle.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19276241" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13414" }, "primaryId" : "GEO:GSE13414", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13414" } ] }, "title" : "Influence of hyperthyroid conditions on gene expression in rat extraocular muscles", "dateAssigned" : "2008-10-30T00:00:00.000-05:00", "summary" : "Extraocular muscles (EOMs) are a highly specialized type of tissue with a wide range of unique properties, including characteristic innervation, development, and structural proteins. Even though EOMs are frequently and prominently involved in thyroid-associated diseases, little is known about the immediate effects of thyroid hormone on these muscles. In order to create a comprehensive profile of changes in gene expression levels in EOMs induced by thyroid hormone, hyperthyroid conditions were simulated by treating adult Sprague-Dawley rats with intraperitoneal injections of 25 µg T3 per 100 g body weight over the course of six weeks; subsequently, microarray analysis was used to determine changes in mRNA levels in EOMs from T3-treated animals relative to untreated controls.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19276241" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13428" }, "primaryId" : "GEO:GSE13428", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13428" } ] }, "title" : "Gene Expression Profiling of Rat Hippocampus Following Exposure to the Acetylcholinesterase Inhibitor Soman", "dateAssigned" : "2008-10-31T00:00:00.000-05:00", "summary" : "Keywords: Time-course; toxicant exposure", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19281266" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13442" }, "primaryId" : "GEO:GSE13442", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13442" } ] }, "title" : "Blood gene expression of rats exposed to acetaminophen or methyl parathion", "dateAssigned" : "2008-11-03T00:00:00.000-06:00", "summary" : "Keywords: blood, acetaminophen, methyl parathion, rat, hepatotoxicity, neurotoxicity", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19784758" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13461" }, "primaryId" : "GEO:GSE13461", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13461" } ] }, "title" : "Sexual Dimorphic Regulation of Liver Gene Expression by Glucocorticoids", "dateAssigned" : "2008-11-04T00:00:00.000-06:00", "summary" : "Males and females exhibit differences in the incidence of many major diseases including auto-immune diseases, hepatocellular carcinoma, diabetes, and osteoporosis, which all have important inflammatory components in their etiology. Glucocorticoids are the primary physiological anti-inflammatory hormone in all mammals and synthetic derivatives of these hormones are widely prescribed as anti-inflammatory agents irrespective of gender. Surprisingly we report a marked sexually dimorphic regulation of gene expression by glucocorticoids in the rat liver. Eight distinct patterns of glucocorticoid regulated genes were identified and two revealed genes that respond to glucocorticoid treatment in both sexes in opposite directions (anti-correlated genes. We also identified gender-specific groups of genes regulated by glucocorticoids. Pathways analysis identified sex-specific glucocorticoid regulated gene expression in several canonical pathways that have been implicated in human disease in which disease susceptibility is sex-biased. For example, comparison of number of genes involved in inflammatory disorders between sexes, revealed 84 additional glucocorticoid responsive genes in the male rat. Our data suggests that glucocorticoids thorough sexually-dimorphic regulation of gene expression modulate gender specific homeostatic functions in male and female liver.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20940427" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13465" }, "primaryId" : "GEO:GSE13465", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13465" } ] }, "title" : "Acetaminophen-induced gene expression profiles in sandwich-cultured primary rat hepatoctyes", "dateAssigned" : "2008-11-04T00:00:00.000-06:00", "summary" : "Keywords: Toxicogenomics, dose response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19008212" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13499" }, "primaryId" : "GEO:GSE13499", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13499" } ] }, "title" : "Transcriptome responses of duodenal epithelial cells to endurance swimming in female rats.", "dateAssigned" : "2008-11-06T00:00:00.000-06:00", "summary" : "Keywords: Gene expression; Comparative genomic hybridization", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19176351" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13513" }, "primaryId" : "GEO:GSE13513", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13513" } ] }, "title" : "Patterns of dioxin-altered mRNA expression in livers of dioxin-sensitive versus dioxin-resistant rats", "dateAssigned" : "2008-11-07T00:00:00.000-06:00", "summary" : "The dioxin congener 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) causes a wide range of toxic effects in rodent species, all of which are mediated by a ligand-dependent transcription-factor, the aryl hydrocarbon receptor (AHR). The Han/Wistar (Kuopio) (H/W) strain shows exceptional resistance to many TCDD-induced toxicities; the LD50 of >9600 µg/kg for H/W rats is higher than for any other wild-type mammal known. We have previously shown that this resistance primarily results from H/W rats expressing a variant AHR isoform that has a substantial portion of the AHR transactivation domain deleted. Despite this large deletion, H/W rats are not entirely refractory to the effects of TCDD; the variant AHR in these animals remains fully competent to up-regulate well-known dioxin-inducible genes. TCDD-sensitive (Long-Evans, L-E) and resistant (H/W) rats were treated with either corn-oil (with or without feed-restriction) or 100 µg/kg TCDD for either four or ten days. Hepatic transcriptional profiling was done using microarrays, and was validated by RT-PCR analysis of 41 genes. . A core set of genes was altered in both strains at all time points tested, including CYP1A1, CYP1A2, CYP1B1, Nqo1, Aldh3a1, Tiparp, Exoc3, and Inmt. Outside this core, the strains differed significantly in the breadth of response: three-fold more genes were altered in L-E than H/W rats. At ten days almost all expressed genes were dysregulated in L-E rats, likely reflecting emerging toxic responses. Far fewer genes were affected by feed-restriction, suggesting that only a minority of the TCDD-induced changes are secondary to the wasting syndrome.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21215274" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13524" }, "primaryId" : "GEO:GSE13524", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13524" } ] }, "title" : "Changes in gene expression in the nucleus accumbens of alcohol-preferring rats following chronic ethanol consumption", "dateAssigned" : "2008-11-07T00:00:00.000-06:00", "summary" : "Keywords: comparison of gene expression profiles for treated vs. control", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19666046" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13535" }, "primaryId" : "GEO:GSE13535", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13535" } ] }, "title" : "Rat lung gene expression during acute pulmonary embolism", "dateAssigned" : "2008-11-08T00:00:00.000-06:00", "summary" : "Keywords: time course and dose response", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13537" }, "primaryId" : "GEO:GSE13537", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13537" } ] }, "title" : "MEF2 Regulated Genes", "dateAssigned" : "2008-11-10T00:00:00.000-06:00", "summary" : "Keywords: Gene knockdown and depolarization time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19109909" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13538" }, "primaryId" : "GEO:GSE13538", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13538" } ] }, "title" : "MEF2 Activated Genes", "dateAssigned" : "2008-11-10T00:00:00.000-06:00", "summary" : "Keywords: Gene activation time course", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19109909" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13539" }, "primaryId" : "GEO:GSE13539", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13539" } ] }, "title" : "Novel Environment Expression Profiling", "dateAssigned" : "2008-11-10T00:00:00.000-06:00", "summary" : "Keywords: Gene expression profiling", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19109909" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13550" }, "primaryId" : "GEO:GSE13550", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13550" } ] }, "title" : "Microarray analysis of rat testis following combined fetal and postnatal DBP exposure", "dateAssigned" : "2008-11-10T00:00:00.000-06:00", "summary" : "Provided later", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13551" }, "primaryId" : "GEO:GSE13551", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13551" } ] }, "title" : "MEF2D binding sites in rat hippocampal neurons", "dateAssigned" : "2008-11-10T00:00:00.000-06:00", "summary" : "Keywords: ChIP-chip", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19109909" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13572" }, "primaryId" : "GEO:GSE13572", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13572" } ] }, "title" : "Rat heart cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells", "dateAssigned" : "2008-11-12T00:00:00.000-06:00", "summary" : "Rat somatic heart cell had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave the rat somatic heart cell unique characteristics which could then be compared with the rat iPS cells by genes comparison to show the gene expression difference between rat somatic heart cells and rat iPS cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19097959" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13573" }, "primaryId" : "GEO:GSE13573", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13573" } ] }, "title" : "Rat lung cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells", "dateAssigned" : "2008-11-12T00:00:00.000-06:00", "summary" : "Rat somatic lung cell had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave the rat somatic lung cell unique characteristics which could then be compared with the rat iPS cells by genes comparison to show the gene expression difference between rat somatic lung cells and rat iPS cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19097959" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13594" }, "primaryId" : "GEO:GSE13594", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13594" } ] }, "title" : "Functional relevance of tetraspanin CD9 in vascular smooth muscle cell injury", "dateAssigned" : "2008-11-13T00:00:00.000-06:00", "summary" : "Keywords: vascular smooth muscle cells, vascular injury, tetraspanin, proliferation, neointima, motility, fibronectin (FN), rat aortic smooth muscle (RASM)", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13607" }, "primaryId" : "GEO:GSE13607", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13607" } ] }, "title" : "Basal gene expression of primary osteoblasts", "dateAssigned" : "2008-11-14T00:00:00.000-06:00", "summary" : "Keywords: Cell type comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23182809" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13624" }, "primaryId" : "GEO:GSE13624", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13624" } ] }, "title" : "Epileptogenesis alters gene expression pattern in rats subjected to amygdala-dependent emotional learning", "dateAssigned" : "2008-11-17T00:00:00.000-06:00", "summary" : "Here we tested a hypothesis that epileptogenesis influences expression pattern of genes in the basolateral amygdala that are critical for fear conditioning. Whole genome molecular profiling of basolateral rat amygdala was performed to compare the transcriptome changes underlying fear learning in epileptogenic and control animals. Our analysis revealed that after acquisition of fear conditioning 26 genes were regulated differently in the basolateral amygdala of both groups. Thus, our study provides the first evidence that not only the damage to the neuronal pathways but also altered composition or activity level of molecular machinery responsible for formation of emotional memories within surviving pathways can contribute to impairment in emotional learning in epileptogenic animals. Understanding the function of those genes in emotional learning provides an attractive avenue for identification of novel drug targets for treatment of emotional disorders after epileptogenesis-inducing insult.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19166914" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13668" }, "primaryId" : "GEO:GSE13668", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13668" } ] }, "title" : "Profiling of Transcripts in Rat Proximal Tubule", "dateAssigned" : "2008-11-19T00:00:00.000-06:00", "summary" : "Freshly isolated rat kidney proximal tubules were subjected for transcript profiling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19190182" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13669" }, "primaryId" : "GEO:GSE13669", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13669" } ] }, "title" : "Profiling of Transcripts in Rat Kidney Medullary Thick Ascending Limb", "dateAssigned" : "2008-11-19T00:00:00.000-06:00", "summary" : "Freshly isolated rat kidney medullary thick ascending limbs were subjected for transcript profiling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19190182" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13676" }, "primaryId" : "GEO:GSE13676", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13676" } ] }, "title" : "Gene Expression Analysis in an Animal Model of Cortical Dysplasia-CONTROL GROUP", "dateAssigned" : "2008-11-19T00:00:00.000-06:00", "summary" : "Cortical Dysplasia (CD) is the histopathological substrate in almost half of all drug-resistant epilepsy. Little is known about the gene expression profile of CD. As such information may help target therapeutics more effectively, our aim was to perform a gene expression analysis of an animal model of cortical dysplasia induced by in utero irradiation. THIS SERIES (GSE13676) INCLUDES ALL (AND ONLY) CONTROL SAMPLES (9).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13681" }, "primaryId" : "GEO:GSE13681", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13681" } ] }, "title" : "Genome wide analysis of gene expression of rat ES cells, rat embryonic fibroblast cells and mouse ES cells", "dateAssigned" : "2008-11-20T00:00:00.000-06:00", "summary" : "Keyword: 3I medium; rat embryonic stem cells; mouse ES cells; rat embryonic fibroblast cells", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19109898" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13697" }, "primaryId" : "GEO:GSE13697", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13697" } ] }, "title" : "Gene Expression Analysis in an Animal Model of Cortical Dysplasia-IRRADIATED GROUP", "dateAssigned" : "2008-11-20T00:00:00.000-06:00", "summary" : "Cortical Dysplasia (CD) is the histopathological substrate in almost half of all drug-resistant epilepsy. Little is known about the gene expression profile of CD. As such information may help target therapeutics more effectively, our aim was to perform a gene expression analysis of an animal model of cortical dysplasia induced by in utero irradiation. THIS SERIES (GSE13697) INCLUDES ALL (AND ONLY) EXPERIMENTAL SAMPLES--I.E. IRRADIATED/CORTICAL DYSPLASIA (9).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13708" }, "primaryId" : "GEO:GSE13708", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13708" } ] }, "title" : "Stem Cells Secrete Factors That Induce Proliferation In Differentiated Cardiomyocytes", "dateAssigned" : "2008-11-21T00:00:00.000-06:00", "summary" : "Media conditioned by undifferentiated human embryonic stem cells enhanced karyokinesis, cytokinesis and cell proliferation in cultures of differentiated, beating primary rat cardiomyocytes without altering their final contractile phenotype. Transcriptome analysis of proliferating cardiomyocytes revealed comprehensive activation of the ROCK 1 and 2 G-protein coupled receptor (GPCR) pathway associated with cytokinesis, and the RAS/RAF/MEK/ERK receptor tyrosine kinase pathways (RTK) and JAK/STAT-cytokine pathway involved in cell cycle progression. Correlative multi-analyte profiling (85 proteins) of conditioned media identified 33 proteins at significantly elevated levels compared to unconditioned media including ligands specific to the GPCR signal transduction pathways (serum amyloid A, monocyte chemoattractant protein-1, macrophage inhibitory protein, IL-8, macrophage inflammatory protein 1-alpha, eotaxin), RTK activation (IGFbp-1, IGFbp-2, HGF) and JAK-STAT stimulation pathways (IL-6, IFNa) activated in the treated cardiomyocytes. These data indicated that ES cells secreted a unique admixture of factors associated with induction of mitotic replication, cytokinesis and proliferation in cardiomyocytes. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20045494" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13716" }, "primaryId" : "GEO:GSE13716", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13716" } ] }, "title" : "Persistent Organic Pollutants cause insulin resistance and ruin the health effects of salmon oil", "dateAssigned" : "2008-11-24T00:00:00.000-06:00", "summary" : "Keywords: transcriptomic analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20064776" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13747" }, "primaryId" : "GEO:GSE13747", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13747" } ] }, "title" : "Ghrelin treatment effects on hepatic gene expression in rats submitted to Bile Duct Ligation", "dateAssigned" : "2008-11-26T00:00:00.000-06:00", "summary" : "Hepatic fibrosis, the wound-healing response to repeated liver injury, ultimately leads to cirrhosis. There is an urgent need to develop effective antifibrotic therapies. Ghrelin (encoded by Ghrl) is an orexigenic hormone that has pleiotrophic functions including protection against cell death1. Here we investigate whether ghrelin modulates liver fibrosis and protects from acute liver injury. Recombinant ghrelin reduced the fibrogenic response to prolonged bile duct ligation in rats. This effect was associated with decreased liver injury and myofibroblast accumulation as well as attenuation of the altered gene expression profile. Ghrelin also reduced fibrogenic properties in cultured hepatic stellate cells. Moreover, Ghrl-/- mice developed exacerbated hepatic fibrosis and liver damage after chronic injury. Ghrelin also protected rat livers from acute liver injury and reduced the extent of oxidative stress and the inflammatory response. In patients with chronic liver diseases, ghrelin serum levels decreased in those with advanced fibrosis and hepatic expression of the ghrelin gene correlated with expression of fibrogenic genes. Finally, in patients with chronic hepatitis C, single nucleotide polymorphisms of the ghrelin gene (-994CT and –604GA) influenced the progression of liver fibrosis. We conclude that ghrelin exerts antifibrotic effects on the liver and may represent a novel antifibrotic therapy. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20077562" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13788" }, "primaryId" : "GEO:GSE13788", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13788" } ] }, "title" : "SAGE libraries from cell bodies and axons of NGF-differentiated sympathetic neurons", "dateAssigned" : "2008-12-02T00:00:00.000-06:00", "summary" : "The subcellular localization of specific mRNAs is an evolutionary conserved mechanism that underlies the establishment of cellular polarity and specialized cell functions. In neurons, mRNA trafficking and local protein translation in dendrites provides an important mechanism that mediates synaptic development and plasticity. The significance of mRNA targeting and protein synthesis in axons, however, is still unclear. Only a small number of transcripts have been identified in axons to date, and their contribution to axon growth and neuronal survival remains largely unknown. Here, we report the results of a novel screen that allowed the separate identification of mRNAs localized in cell bodies and in axons of developing neurons. Using compartmentalized cultures of sympathetic neurons and Sequential Analysis of Gene Expression (SAGE), the screen identified more than 200 axonal mRNAs, including ones that encode cytoskeletal proteins and proteins that function in neural development and signal transduction. Importantly, several classes of transcripts were selectively enriched in axons, indicating that an active process drives the targeting of specific mRNAs from the cell bodies to the axons. This study is the first comprehensive and unbiased analysis of mRNA localization in subcellular domains of any neuronal cell type.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20118926" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13793" }, "primaryId" : "GEO:GSE13793", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13793" } ] }, "title" : "Gene expression profiles in the cerebellum and hippocampus following exposure to neurotoxicant Aroclor 1254", "dateAssigned" : "2008-12-02T00:00:00.000-06:00", "summary" : "Keywords: time course, stress response", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13802" }, "primaryId" : "GEO:GSE13802", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13802" } ] }, "title" : "Azoxymethane induced changes in Rat proximal and distal colonic epithelium.", "dateAssigned" : "2008-12-02T00:00:00.000-06:00", "summary" : "Keywords: disease state analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13810" }, "primaryId" : "GEO:GSE13810", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13810" } ] }, "title" : "Microarray analysis of the development of proteinuria in the Dahl salt-sensitive rat", "dateAssigned" : "2008-12-03T00:00:00.000-06:00", "summary" : "Keywords: Time course analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13812" }, "primaryId" : "GEO:GSE13812", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13812" } ] }, "title" : "Consequences of an in utero TCDD exposure on the male reproductive function in 5 postnatal days rat", "dateAssigned" : "2008-12-03T00:00:00.000-06:00", "summary" : "Keywords: transcriptionnal analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13838" }, "primaryId" : "GEO:GSE13838", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13838" } ] }, "title" : "Consequences of an in utero TCDD exposure on the male reproductive function in 28 postnatal days rat", "dateAssigned" : "2008-12-05T00:00:00.000-06:00", "summary" : "Keywords: transcriptionnal analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13883" }, "primaryId" : "GEO:GSE13883", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13883" } ] }, "title" : "Effect of the Methoxychlor Metabolite HPTE on the Rat Ovarian Granulosa Cell Transcriptome in Vitro ", "dateAssigned" : "2008-12-09T00:00:00.000-06:00", "summary" : "Ovarian granulosa cells play a central role in steroidogenesis, which is critical for female reproduction. Follicle-stimulating hormone (FSH) promotes cAMP–mediated signaling to regulate granulosa cell steroidogenesis. We have shown previously that 2, 2-bis-(p-hydroxyphenyl)-1, 1, 1-trichloroethane (HPTE) inhibits FSH- and dibutyryl cAMP-stimulated steroidogenesis, and affects the mRNA levels of steroidogenic pathway enzymes in rat granulosa cells. However, HPTE showed a differential effect in FSH- and cAMP-stimulated cells in that HPTE more completely blocked FSH- when compared to cAMP-driven steroidogenesis. The objective of this study was to analyze the effects of HPTE on global gene expression profiles in untreated granulosa cells and those challenged with FSH or cAMP. Granulosa cells from immature rats were cultured with 0, 1, 5, or 10 µM HPTE in the presence and absence of either 3 ng FSH/ml or 1 mM cAMP for 48 h. Total RNA was isolated for microarray analysis using the GeneChip Rat Genome 230 2.0 and ArrayAssist Microarray Suite. An investigation of changes in gene expression across all HPTE treatments showed that HPTE altered more genes in FSH- (~670 genes) than in cAMP-stimulated cells (~366 genes). Analysis confirmed that HPTE more effectively inhibited FSH- than cAMP-induced steroid pathway gene expression and steroidogenesis. Furthermore, expression patterns of novel genes regulating signal transduction, transport, cell cycle, adhesion, differentiation, motility and growth, apoptosis, development, and metabolism were all altered by HPTE. This study further established that HPTE exerts differential effects within the granulosa cell steroidogenic pathway, and revealed that these effects include broader changes in gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19414516" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13920" }, "primaryId" : "GEO:GSE13920", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13920" } ] }, "title" : "MicroRNA expression profiling in diabetic GK rat model", "dateAssigned" : "2008-12-12T00:00:00.000-06:00", "summary" : "MicroRNAs (miRNAs), which are a newly identified class of small single-stranded non-coding RNAs, regulate their target genes via post-transcriptional pathway. It has been proved that miRNAs play important roles in many biological processes. To better understand miRNA function with type 2 diabetes, we have used an oligonucleotide microarray to monitor miRNA expression profiles of GK and Wistar rats’ muscle. We found 7 miRNAs were down-expressed and 2 were over-expressed in the muscle of GK rats. Among them, miR-24 showed the most prominent change. P38 MAPK, which is a direct target of miR-24 also showed expression difference. All the data give a clue that miR-24 might be associated with diabetes through down regulation of p38 MAPK.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19499150" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13936" }, "primaryId" : "GEO:GSE13936", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE13936" } ] }, "title" : "Hepatic gene expression study", "dateAssigned" : "2008-12-12T00:00:00.000-06:00", "summary" : "Keywords: Hepatic gene expression", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14044" }, "primaryId" : "GEO:GSE14044", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14044" } ] }, "title" : "Effects of exercise training and antioxidant supplementation on endothelial cell gene expression", "dateAssigned" : "2008-12-18T00:00:00.000-06:00", "summary" : "The molecular mechanisms of exercise-induced cardiovascular protection are poorly understood. There is growing evidence that reactive oxygen species (ROS) are necessary for some of these adaptations and antioxidants may be used to investigate this effect. This study aimed to determine the effects of exercise and/or antioxidant supplementation on myocardial and vascular endothelium gene expression. Male Wistar rats were divided into four groups: i) endurance exercise (90min of treadmill running 4d/week, 14 weeks); ii) antioxidant-treated; iii) antioxidant and endurance exercise and iv) control. The supplemented animals received Vitamin E (1000 IU/kg diet) and alpha-lipoic acid (1.6 g/kg diet) mixed with rat chow. cDNA microarray analysis was performed using purified endothelial RNA from myocardial and coronary artery endothelial cells and showed that the expression levels of 35, 40 and 40 genes were altered for groups i, ii, and iii respectively compared to control. Differentially expressed genes were analysed using the KEGG pathway database, hierarchical cluster and DAVID analysis. These analyses revealed that a gene involved in cardiovascular disease progression, Ras homolog gene family member A (RhoA) was down-regulated by exercise, upregulated by antioxidant supplementation and the combination of exercise and antioxidant blunted both effects. These findings were confirmed by real-time PCR. In summary, exercise and antioxidant supplementation affect endothelial cell gene expression and ROS appear necessary for some of these adaptations.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14094" }, "primaryId" : "GEO:GSE14094", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14094" } ] }, "title" : "Diet induced gene expression in rat peripheral blood mononuclear cells", "dateAssigned" : "2008-12-22T00:00:00.000-06:00", "summary" : "Keywords: Dietary treatment, obese-state analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20142826" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14096" }, "primaryId" : "GEO:GSE14096", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14096" } ] }, "title" : "Urinary bladder post-spinal cord injury: time-points", "dateAssigned" : "2008-12-22T00:00:00.000-06:00", "summary" : "Previously, we demonstrated using a rat model of spinal cord injury (SCI) that bladder wall tissue compliance significantly increased within the first 2 weeks following injury. In order to explore the potential molecular-level mechanisms of this event, the present study quantified molecules pertinent to bladder tissue remodeling and changes in mechanical properties. An initial gene array analysis followed by real-time qPCR revealed that the message levels for tropoelastin and lysyl oxidase were as high as 8-fold in SCI rats compared to normal. Furthermore, both the message and protein levels of TGF-beta1 and IGF-1, known stimulators of elastin synthesis, in SCI rat bladders were significantly higher compared to those of normal rats. Taken together, it can be speculated that functional changes of the bladder associated with SCI induce release of select growth factors, which, in turn, stimulate elastogenesis that lead to alteration of biomechanical properties of the wall tissue.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:16038877" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14268" }, "primaryId" : "GEO:GSE14268", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14268" } ] }, "title" : "microRNA expression and opioid signaling", "dateAssigned" : "2009-01-02T00:00:00.000-06:00", "summary" : "Keywords: Expression profiling", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19854889" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14269" }, "primaryId" : "GEO:GSE14269", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14269" } ] }, "title" : "Transgenerational epigenetic programming of the brain transcriptome and anxiety behavior", "dateAssigned" : "2009-01-02T00:00:00.000-06:00", "summary" : "Keywords: expression analysis, transgenerational changes due to vinclozolin", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19015723" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14307" }, "primaryId" : "GEO:GSE14307", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14307" } ] }, "title" : "Gene analysis of the neonatal rat lung exposed to STZ-induced maternal diabetes", "dateAssigned" : "2009-01-06T00:00:00.000-06:00", "summary" : "Keywords: disease state analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14337" }, "primaryId" : "GEO:GSE14337", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14337" } ] }, "title" : "MUC1-induced transcriptional alterations in rat 3Y1 embryonic fibroblasts", "dateAssigned" : "2009-01-08T00:00:00.000-06:00", "summary" : "Keywords: Expression profiling by microarray", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19289846" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14402" }, "primaryId" : "GEO:GSE14402", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14402" } ] }, "title" : "TNF-a-induced MEK/ERK-dependent regulation of Cartilage Matrix Genes", "dateAssigned" : "2009-01-13T00:00:00.000-06:00", "summary" : "Keywords: compound, signalling response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19144181" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14484" }, "primaryId" : "GEO:GSE14484", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14484" } ] }, "title" : "Gene Expression Changes in Response to UV Inactivated Baculoviral Vector Transduction of the Rat Brain In Vivo", "dateAssigned" : "2009-01-21T00:00:00.000-06:00", "summary" : "Keywords: Baculovirus, brain, astrocytes, neurons, transduction, Infection, gene expression analysis, DNA microarray ", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14497" }, "primaryId" : "GEO:GSE14497", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14497" } ] }, "title" : "Diet and feeding condition induced gene expression in rat peripheral blood mononuclear cells", "dateAssigned" : "2009-01-21T00:00:00.000-06:00", "summary" : "Keywords: Dietary treatment, analysis of feeding conditions", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20142826" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14505" }, "primaryId" : "GEO:GSE14505", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14505" } ] }, "title" : "Effect of BDNF on aging-related gene expression changes in young and aged rats", "dateAssigned" : "2009-01-21T00:00:00.000-06:00", "summary" : "Keywords: Treatment effect", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19198615" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14527" }, "primaryId" : "GEO:GSE14527", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14527" } ] }, "title" : "Effects of single oral exposure of adult Sprague-Dawley rats to p-tert-octylphenol on uterine gene expression", "dateAssigned" : "2009-01-23T00:00:00.000-06:00", "summary" : "Keywords: treatment-control", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14528" }, "primaryId" : "GEO:GSE14528", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14528" } ] }, "title" : "Effects of 35 days oral exposure of adult female Sprague-Dawley rats to p-tert-octylphenol on uterine gene expression", "dateAssigned" : "2009-01-23T00:00:00.000-06:00", "summary" : "Keywords: treatment vs control", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14544" }, "primaryId" : "GEO:GSE14544", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14544" } ] }, "title" : "Colon mucosa of F344 rats: control treated with 5% DSS vs Resveratrol + 5% DSS", "dateAssigned" : "2009-01-23T00:00:00.000-06:00", "summary" : "Keywords: Inflammation experiment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19228061" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14554" }, "primaryId" : "GEO:GSE14554", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14554" } ] }, "title" : "Toxicogenomic Comparison of TCDD and PCB 126 Responsiveness in Primary Rat Hepatocytes", "dateAssigned" : "2009-01-23T00:00:00.000-06:00", "summary" : "(Abstract) Toxicogenomics has great potential for enhancing our understanding of environmental chemical toxicity, hopefully leading to better-informed human health risk assessments. This study employed toxicogenomic technology to reveal species differences in response to two prototypical aryl hydrocarbon receptor (AHR) agonists, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and the polychlorinated biphenyl (PCB) congener PCB 126. Dose responses of primary cultures of rat and human hepatocytes were determined using species-specific microarrays sharing over 4,000 gene orthologs. Forty-seven human and 79 rat genes satisfied dose response criteria for both chemicals and were subjected to further analysis including the calculation of EC50 and the relative potency (REP) of PCB 126 for each gene. Only 5 responsive orthologous genes were shared between the two species, yet the geometric mean of the REPs for all rat and human modeled responsive genes were 0.06 (95% Confidence Interval (CI); 0.03-0.1) and 0.002 (95% CI; 0.001-0.005), respectively, suggesting broad species differences in the initial events that follow AHR activation but precede toxicity. This indicates that there are species differences in both the specific genes that responded and the agonist potency and relative potency for those genes. This observed insensitivity of human cells to PCB 126 is consistent with more traditional measurements of AHR activation (i.e., CYP1A1 enzyme activity) and suggests that the species difference in PCB 126 sensitivity is likely due to certain aspects of AHR function. That a species divergence also exists in this expanded AHR-regulated gene repertoire is a novel finding and should help when extrapolating animal data to humans.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19692669" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14556" }, "primaryId" : "GEO:GSE14556", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14556" } ] }, "title" : "Expression data from adult rat subventricular zone cells", "dateAssigned" : "2009-01-23T00:00:00.000-06:00", "summary" : "Keywords: control versus TGFbeta1 treated group", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14562" }, "primaryId" : "GEO:GSE14562", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14562" } ] }, "title" : "Expression data from adult rat subventricular zone cells", "dateAssigned" : "2009-01-25T00:00:00.000-06:00", "summary" : "Keywords: control versus TGFbeta1 treated group", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14658" }, "primaryId" : "GEO:GSE14658", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14658" } ] }, "title" : " Transcription factor HMGA2 controls the K-RAS mediated transformation-specific genetic program", "dateAssigned" : "2009-01-30T00:00:00.000-06:00", "summary" : "(HMGA2). To elucidate the role of HMGA2 in the transcriptional network affected by oncogenic signaling, we used an integrated approach combining RNAi-mediated silencing, microarray-based expression profiling, computational prediction of transcription factor binding sites in target gene promoters and phenotypic analysis. Knocking-down HMGA2 resulted in the reversion of epithelial-mesenchymal transition, loss of anchorage independence and in a substantial restoration of the gene expression pattern characteristic of non-transformed ROSE cells. Computational prediction of transcription factor binding sites in the promoters of HMGA2-regulated genes and expression profiling revealed a preferential role of activator complex-1 (AP-1) components Fra-1 and JunB in target gene regulation. Forced expression of HMGA2 did not transform normal ovarian epithelial cells, suggesting that HMGA2 up-regulation is not sufficient for inducing the transformed phenotype, but mediates cancer-specific phenotypic traits in cells expressing mutated KRAS and, hence, oncogene addiction.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14666" }, "primaryId" : "GEO:GSE14666", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14666" } ] }, "title" : "Expression data from female rat kidney: pathophysiology of proteinuria", "dateAssigned" : "2009-01-30T00:00:00.000-06:00", "summary" : "Keywords: Analysis of genes that are differentially expressed in the kidneys, contrasting between an animal strain that tends to develop proteinuria which is amplified by uninephrectomy and another strain that is relatively resistant to the development of proteinuria", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20876844" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14676" }, "primaryId" : "GEO:GSE14676", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14676" } ] }, "title" : "Expression data from male rat kidney: pathophysiology of proteinuria", "dateAssigned" : "2009-02-02T00:00:00.000-06:00", "summary" : "Keywords: Analysis of genes that are differentially expressed in the kidneys, contrasting between an animal strain that tends to develop proteinuria which is amplified by uninephrectomy and another strain that is relatively resistant to the development of proteinuria", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14712" }, "primaryId" : "GEO:GSE14712", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14712" } ] }, "title" : "Xenobiotic-responsive Nuclear Receptors in Transcriptional Effects Upon Perfluoroalkyl Acid Exposure in Diverse Species", "dateAssigned" : "2009-02-04T00:00:00.000-06:00", "summary" : "Keywords: gene expression/microarray", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19162173" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14720" }, "primaryId" : "GEO:GSE14720", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14720" } ] }, "title" : "Influence of the early stress of maternal separation on the prefrontal cortex transcriptome", "dateAssigned" : "2009-02-05T00:00:00.000-06:00", "summary" : "Exposure to early stress (ES) is known to enhance adult vulnerability for anxiety and depressive behaviors. The molecular and cellular pathways altered in response to ES that contribute to the establishment of a substrate for susceptibility to adult psychopathology are not well understood. Focusing on the prefrontal cortex (PFC), a brain region implicated in the modulation of emotional responses, we examined the consequences of the early stress experience of maternal separation (MS) on the adult PFC transcriptome. Microarray analysis identified alterations in genes associated with signal transduction, neuronal excitability, G-protein signaling and stress responses in the PFC of adult animals previously exposed to ES. Our results also indicated that the pattern of gene expression changes observed in ES animals contains a component in common with that induced by 5-HT2A/C receptor stimulation in control animals, suggesting enhanced 5-HT2A/C receptor-mediated signaling in ES animals. Further, our microarray results reveal that a history of ES alters the DOI-induced transcriptome in the PFC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20826676" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14723" }, "primaryId" : "GEO:GSE14723", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14723" } ] }, "title" : "Gene expression profiling in differential cognitive outcomes in aging: CA1", "dateAssigned" : "2009-02-05T00:00:00.000-06:00", "summary" : "Functional alterations in medial temporal lobe structures, particularly the hippocampus, are central to age-related deficits in episodic memory. Research in aging laboratory animals has characterized physiological and cellular alterations in the hippocampus that occur in association with the presence and severity of such cognitive impairment. The current study compares alterations across hippocampal subregions by gene expression profiling in a rat model that closely mirrors individual differences in neurocognitive features of aging humans across a spectrum of outcomes, including both impaired memory and preserved function. Using mRNA profiling of the CA1, CA3 and dentate gyrus subregions, we have distinguished between gene groups and pathways related to chronological age and those specifically associated with impaired or preserved cognitive ability in aged rats. We confirmed earlier reported changes in gene groups related to inflammation and oxidative stress in multiple subregions and found these to be more associated with chronological age than cognitive function per se. The CA3 profile was best able to segregate aged impaired, aged unimpaired and young subject groups from each other. Characterization of gene changes that distinguished preserved from impaired function among the aged animals found altered expression of synaptic plasticity and neurodegenerative disease-related genes. Together these gene changes suggest recruitment of adaptive mechanisms that mediate synaptic plasticity to maintain function and structural integrity in aged unimpaired rats that does not occur in aged impaired animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19913943" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14724" }, "primaryId" : "GEO:GSE14724", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14724" } ] }, "title" : "Gene expression profiling in differential cognitive outcomes in aging: CA3", "dateAssigned" : "2009-02-05T00:00:00.000-06:00", "summary" : "Functional alterations in medial temporal lobe structures, particularly the hippocampus, are central to age-related deficits in episodic memory. Research in aging laboratory animals has characterized physiological and cellular alterations in the hippocampus that occur in association with the presence and severity of such cognitive impairment. The current study compares alterations across hippocampal subregions by gene expression profiling in a rat model that closely mirrors individual differences in neurocognitive features of aging humans across a spectrum of outcomes, including both impaired memory and preserved function. Using mRNA profiling of the CA1, CA3 and dentate gyrus subregions, we have distinguished between gene groups and pathways related to chronological age and those specifically associated with impaired or preserved cognitive ability in aged rats. We confirmed earlier reported changes in gene groups related to inflammation and oxidative stress in multiple subregions and found these to be more associated with chronological age than cognitive function per se. The CA3 profile was best able to segregate aged impaired, aged unimpaired and young subject groups from each other. Characterization of gene changes that distinguished preserved from impaired function among the aged animals found altered expression of synaptic plasticity and neurodegenerative disease-related genes. Together these gene changes suggest recruitment of adaptive mechanisms that mediate synaptic plasticity to maintain function and structural integrity in aged unimpaired rats that does not occur in aged impaired animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19913943" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14725" }, "primaryId" : "GEO:GSE14725", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14725" } ] }, "title" : "Gene expression profiling in differential cognitive outcomes in aging: Dentate Gyrus", "dateAssigned" : "2009-02-05T00:00:00.000-06:00", "summary" : "Functional alterations in medial temporal lobe structures, particularly the hippocampus, are central to age-related deficits in episodic memory. Research in aging laboratory animals has characterized physiological and cellular alterations in the hippocampus that occur in association with the presence and severity of such cognitive impairment. The current study compares alterations across hippocampal subregions by gene expression profiling in a rat model that closely mirrors individual differences in neurocognitive features of aging humans across a spectrum of outcomes, including both impaired memory and preserved function. Using mRNA profiling of the CA1, CA3 and dentate gyrus subregions, we have distinguished between gene groups and pathways related to chronological age and those specifically associated with impaired or preserved cognitive ability in aged rats. We confirmed earlier reported changes in gene groups related to inflammation and oxidative stress in multiple subregions and found these to be more associated with chronological age than cognitive function per se. The CA3 profile was best able to segregate aged impaired, aged unimpaired and young subject groups from each other. Characterization of gene changes that distinguished preserved from impaired function among the aged animals found altered expression of synaptic plasticity and neurodegenerative disease-related genes. Together these gene changes suggest recruitment of adaptive mechanisms that mediate synaptic plasticity to maintain function and structural integrity in aged unimpaired rats that does not occur in aged impaired animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19913943" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14763" }, "primaryId" : "GEO:GSE14763", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14763" } ] }, "title" : "Whole transcriptome analysis of the hippocampus: toward a molecular portrait of epileptogenesis", "dateAssigned" : "2009-02-09T00:00:00.000-06:00", "summary" : "Keywords: gene expression changes during epileptogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20377889" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14848" }, "primaryId" : "GEO:GSE14848", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14848" } ] }, "title" : "Cadiac GATA-4 overexpression in vivo", "dateAssigned" : "2009-02-16T00:00:00.000-06:00", "summary" : "The objective of the study was to find cardiac GATA-4 target genes by overexpressing GATA-4 transcription factor in the left ventricle by adenoviral gene transfer.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20200331" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14902" }, "primaryId" : "GEO:GSE14902", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14902" } ] }, "title" : "The relationship between brain mRNA levels and behaviour among inbred Lewis rats: Experiment 1", "dateAssigned" : "2009-02-19T00:00:00.000-06:00", "summary" : "Keywords: Phenotype-Association Study", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14903" }, "primaryId" : "GEO:GSE14903", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14903" } ] }, "title" : "The relationship between brain mRNA levels and behaviour among inbred Lewis rats: Experiment 2", "dateAssigned" : "2009-02-19T00:00:00.000-06:00", "summary" : "Keywords: Phenotype-Association Study", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14933" }, "primaryId" : "GEO:GSE14933", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14933" } ] }, "title" : "Influence of Fatty Acid Diets on Gene Expression in Rat Mammary Epithelial Cells", "dateAssigned" : "2009-02-20T00:00:00.000-06:00", "summary" : "Conclusion: Fatty acid-enriched diets significantly up-regulated proliferation above the normal physiological level at day 50. The higher cellular proliferation during puberty caused by enriched fatty acid diets pose a potential increase risk of mammary cancer in later life. The human homologs of 27 of 62 cell cycle cluster of rat genes are included in a human breast cancer cluster of 45 cell cycle related genes further emphasizing the importance of our findings in the rat model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19351911" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14944" }, "primaryId" : "GEO:GSE14944", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14944" } ] }, "title" : "Investigation of colominic acid effects on immortalized Schwann cells", "dateAssigned" : "2009-02-23T00:00:00.000-06:00", "summary" : "For this purpose self-spotted microarrays with 352 neurospecific genes were hybridized with mRNA from immortalized Schwann cells cultivated on different coating conditions: In order to enable a comprehensive comparison to the established coating material laminin as well as to standard coating conditions (cultivation on the cell culture surface) a loop-design has been chosen, which is based on the dye-swap design and facilitates a direct comparison of the different states.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14962" }, "primaryId" : "GEO:GSE14962", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14962" } ] }, "title" : "Temporal Profiling of Rat Transcriptomes in Retinol-Replenished Vitamin A-Deficient Testis", "dateAssigned" : "2009-02-23T00:00:00.000-06:00", "summary" : "We used microarrays to examine the temporal transcriptome changes of vitamin a deficient rats testes replenished with retinol", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14968" }, "primaryId" : "GEO:GSE14968", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE14968" } ] }, "title" : "Organic pollutants in salmon oil and health effect", "dateAssigned" : "2009-02-24T00:00:00.000-06:00", "summary" : "Keywords: transcriptomic analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15041" }, "primaryId" : "GEO:GSE15041", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15041" } ] }, "title" : "Postnatal developmental changes in Sprague-Dawley rats in the model of neuropathic pain 'spare nerve injury'", "dateAssigned" : "2009-02-27T00:00:00.000-06:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying the differences in nerve injury between along the postnatal development and identified distinct classes of regulated genes during the injury", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20003309" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15074" }, "primaryId" : "GEO:GSE15074", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15074" } ] }, "title" : "Expression data from Rat heterotopic cardiac transplants", "dateAssigned" : "2009-03-03T00:00:00.000-06:00", "summary" : "Heterotopic cardiac transplants were constructed in male Wistar Furth (allograft donor) and ACI (host) rats. Rats were divided into three groups consisting of no treatment, treatment with a sub-therapeutic dose of cyclosporin A, and treated with combination of a sub-therapeutic dose of cyclosporin A and allochimeric peptide. The allografts were harvested at defined periods post-transplantation and RNA was harvested to monitor gene expression changes resulting from the various treatments in T-cells and in heart cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19882666" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15184" }, "primaryId" : "GEO:GSE15184", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15184" } ] }, "title" : "Global colorectal cancer gene expression in rats", "dateAssigned" : "2009-03-11T00:00:00.000-05:00", "summary" : "The rat models of colorectal cancer (CRC), such as the azoxymethane (AOM) cancer-inducing model, are important tools for researching cancer initiation pathways. However, there is limited understanding of the expression pathways of underlying normal rat colonic epithelium and how this relates to human colonic epithelium. The aim of this study was to study the acute effects of AOM on the gene and pathway expression of the rat's colonic epithelium, whilst contrasting the background normal global expression patterns along the length of the rat as compared to the normal human colonic epithelium.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23343511" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15223" }, "primaryId" : "GEO:GSE15223", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15223" } ] }, "title" : "Radiation effects on gene expression in rat testes (Rattus norvegicus)", "dateAssigned" : "2009-03-13T00:00:00.000-05:00", "summary" : "Analysis of LBNF1 rat testes from controls, containing both somatic and all germ cell types and from irradiated rats in which all cells germ cells except type A spermatgogonia are eliminated. Results provide insight into distinguishing germ and somatic cell genes and identification of somatic cell genes that are upregulated after irradiation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19684331" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15243" }, "primaryId" : "GEO:GSE15243", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15243" } ] }, "title" : "Hormone effects on gene expression in somatic cells of rat testes (Rattus norvegicus)", "dateAssigned" : "2009-03-16T00:00:00.000-05:00", "summary" : "Analysis of hormone effects on irradiated LBNF1 rat testes, which contain only somatic cells except for a few type A spermatgogonia. Rats were treated for 2 weeks with either sham treatment (group X), hormonal ablation (GnRH antagonist and the androgen receptor antagonist flutamide, group XAF), testosterone supplementation (GnRH antagonist and testosterone, group XAT), and FSH supplementation ((GnRH antagonist, androgen receptor antagonist, and FSH, group XAFF). Results provide insight into identifying genes in the somatic testis cells regulated by testosterone, LH, or FSH.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19684331" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15285" }, "primaryId" : "GEO:GSE15285", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15285" } ] }, "title" : "Gene expression in neurons or astrocytes treated with grape seed extract", "dateAssigned" : "2009-03-18T00:00:00.000-05:00", "summary" : "Microarrays are used to examine the effects of GSE on primary cultures of hippocampal neurons and astrocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19381798" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15332" }, "primaryId" : "GEO:GSE15332", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15332" } ] }, "title" : "Proteomics and transcriptomics analysis of rat retinal ganglion cells exposed to chronic ocular hypertension.", "dateAssigned" : "2009-03-22T00:00:00.000-05:00", "summary" : "In this work, we tested feasibility of high content screening of acutely isolated RGCs to generate systems biology knowledge of intrinsic cellular pathways associated with the onset of glaucomatous RGC loss in the retina. We performed differential profiling of these neurons using two complementary techniques: proteomics and microarray-based transcriptomics. The analysis of these RGC-specific proteomic and transcriptomic data using pathway informatics databases and biological network tools have revealed complex metabolic and regulatory changes in the COH-challenged neurons. We used the iTRAQ reagents that allow for the identification and quantitation of up to four different samples simultaneously, to assess the COH-induced changes in protein content of adult rat RGCs. Similar principle is utilized in the two-color Agilent arrays that we used for our transcriptomic analysis of the same RGC samples.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15407" }, "primaryId" : "GEO:GSE15407", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15407" } ] }, "title" : "The Nucleus Accumbens Shell and Central Nucleus of the Amygdala of Alcohol-Preferring Rats Following Binge-Drinking", "dateAssigned" : "2009-03-26T00:00:00.000-05:00", "summary" : "The objective of this study was to determine changes in gene expression within the extended amygdala following binge-like drinking by alcohol-preferring (P) rats. Adult male P rats were given 1-hr access to 15 and 30% ethanol (EtOH) three times daily for 8 weeks. Rats (n = 10/time point for EtOH and n = 6/time point for water) were killed by decapitation 1, 6 and 24 hr after the last drinking episode. Brains were extracted and rapidly frozen in isopentane in dry ice. RNA was prepared from individual micropunch samples of the nucleus accumbens shell (ACB-sh) and central nucleus of the amygada (CeA); microarray analyses were conducted with Affymetrix Rat 230.2 chips. EtOH intakes were 1.5-2 g/kg/session. Because too few genes changed at the individual time points, an overall effect, comparing the water and EtOH groups, was determined. In the ACB-sh and CeA, there were 276 and 402 probe sets for named genes, respectively, that were different between the two groups. There were 1.5- to 3.5- fold more genes up-regulated than down-regulated in both regions, with most differences between 1.1- to 1.2-fold. Although there were several significant Biological Processes categories in common between the 2 regions (e.g., synaptic transmission, neurite development), there were few genes in common between the two regions that differed between the EtOH and water groups. Overall, the results suggest that chronic binge-like alcohol drinking by P rats produces changes in the expression of genes that could alter neuronal function by different mechanisms in the ACB-sh and CeA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20116196" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15415" }, "primaryId" : "GEO:GSE15415", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15415" } ] }, "title" : "Candidate genes for alcohol preference in alcohol-preferring and non-preferring reciprocal congenic rats", "dateAssigned" : "2009-03-26T00:00:00.000-05:00", "summary" : "Keywords: comparison of gene expression profiles for strain1 (P rat) vs. strain2 (P.NP rat)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20128895" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15421" }, "primaryId" : "GEO:GSE15421", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15421" } ] }, "title" : "Gene expressional change along crypt-villus in rats jejunum", "dateAssigned" : "2009-03-27T00:00:00.000-05:00", "summary" : "Transcriptional profiling of jejunal gene expression during the differentiation from crypt to villus cells in rats, using cryostat sections of the villus-crypt columns.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15449" }, "primaryId" : "GEO:GSE15449", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15449" } ] }, "title" : "Thrombopoietin (TPO) protects against heart damage induced by doxorubicin and infarction in rat models", "dateAssigned" : "2009-03-30T00:00:00.000-05:00", "summary" : "In order to examine the mechanism of TPO on cardiac protection against DOX damage, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to delineate the TPO cardioprotective mechanism against DOX-induced cardiomyopathy", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21330293" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15498" }, "primaryId" : "GEO:GSE15498", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15498" } ] }, "title" : "Genome-wide Profiling of Gene Expression in a New Rat Model of Cholangiocarcinoma Progression Mimicking the Human Cancer", "dateAssigned" : "2009-04-01T00:00:00.000-05:00", "summary" : "Microarray analysis was performed on intrahepatic cholangiocarcinomas formed at 10, 15, and 25 days after bile duct inoculation of neu-transformed rat cholangiocytes (BDEneu cells) into rat liver and on peritoneal metastases at the 25 day time period, compared with non-cancerous right liver lobe from the same animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19896103" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15563" }, "primaryId" : "GEO:GSE15563", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15563" } ] }, "title" : "Modifications of the Rat Airway Explant Transcriptome by Cigarette Smoke", "dateAssigned" : "2009-04-06T00:00:00.000-05:00", "summary" : "Although a number of animal model studies have addressed changes in gene expression in the parenchyma and their relationship to emphysema, much less is known about the pathogenesis of cigarette smoke-induced small airway remodeling. In this study, we exposed rat tracheal explants to whole smoke for 15 minutes, and then cultured the explants in air. The airway transcriptome was evaluated using RAE 230_2 GeneChips. By 2 hours after starting smoke exposure, expression levels of 502 genes were changed up or down by more than 1.5 times (p values <0.01 or less), and by 24 hours, 1870 genes were significantly changed up or down. These included genes involved in anti-oxidant protection, epithelial defense and remodeling, inflammatory mediators and transcription factors, and a number of unexpected genes including the MMP-12 inducer, tachykinin-1 (substance P). Pre-treatment of the explants with 1 x 10-7 M dexamethasone reduced the number of significantly changed genes by approximately 47% at 2 hr and 68% at 24 hours, and in almost all instances, reduced the magnitude of the smoke-induced changes. We conclude that even a very brief exposure to cigarette smoke can lead to rapid changes in the expression of a large number of genes in rat tracheal explants, and that these effects are directly mediated by smoke, without a need for exogenous inflammatory cells. Steroids, contrary to the usual belief, are able to ameliorate many of these changes, at least in this very acute model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19883206" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15652" }, "primaryId" : "GEO:GSE15652", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15652" } ] }, "title" : "GDNF-Regulated Gene Expression in Cultures of Rat Spermatogonial Stem Cells", "dateAssigned" : "2009-04-13T00:00:00.000-05:00", "summary" : "GDNF regulated genes were identified using microarray profiling rat spermatogonial stem cells in the presence and absence of GDNF.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19339709" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15713" }, "primaryId" : "GEO:GSE15713", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15713" } ] }, "title" : "Effects of glucose transporter expression on VSMC", "dateAssigned" : "2009-04-16T00:00:00.000-05:00", "summary" : "Hypothesis: Overexpression of the GLUT1 facilitative glucose transporter, in A7r5 vascular smooth muscle cells, is sufficient and/or necessary to induce alterations in gene expression which influence apoptosis, growth, and proliferation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19587217" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15727" }, "primaryId" : "GEO:GSE15727", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15727" } ] }, "title" : "FSH and FOXO1 Regulate Genes in the Sterol/Steroid and Lipid Biosynthetic Pathways in Granulosa Cells", "dateAssigned" : "2009-04-17T00:00:00.000-05:00", "summary" : "The forkhead box transcription factor FOXO1 is highly expressed in granulosa cells of growing follicles but is down-regulated by FSH in culture or by LH-induced luteinization in vivo. To analyze the function of FOXO1, we infected rat and mouse granulosa cells with adenoviral vectors expressing two FOXO1 mutants: a gain-of-function mutant FOXOA3 that has two serine residues and one threonine residue mutated to alanines rendering this protein constitutively active and nuclear, and a FOXOA3-mutant DNA-binding domain (mDBD) in which the DBD is mutated. The infected cells were then treated with vehicle or FSH for specific time intervals. Infection of the granulosa cells was highly efficient, caused only minimal apoptosis, and maintained FOXO1 protein at levels of the endogenous protein observed in cells before exposure to FSH. RNA was prepared from control and adenoviral infected cells exposed to vehicle or FSH for 12 and 24 h. Affymetrix microarray and database analyses identified, and real time RT-PCR verified, that genes within the lipid, sterol, and steroidogenic biosynthetic pathways (Hmgcs1, Hmgcr, Mvk, Sqle, Lss, Cyp51, Tm7sf2, Dhcr24 and Star, Cyp11a1, and Cyp19), including two key transcriptional regulators Srebf1 and Srebf2 of cholesterol biosynthesis and steroidogenesis (Nr5a1, Nr5a2), were major targets induced by FSH and suppressed by FOXOA3 and FOXOA3-mDBD in the cultured granulosa cells. By contrast, FOXOA3 and FOXOA3- mDBD induced expression of Cyp27a1 mRNA that encodes an enzyme involved in cholesterol catabolism to oxysterols. The genes up-regulated by FSH in cultured granulosa cells were also induced in granulosa cells of preovulatory follicles and corpora lutea collected from immature mice primed with FSH (equine choriogonadotropin) and LH (human choriogonadotropin), respectively. Conversely, Foxo1 and Cyp27a1 mRNAs were reduced by these same treatments. Collectively, these data provide novel evidence that FOXO1 may play a key role in granulosa cells to modulate lipid and sterol biosynthesis, thereby preventing elevated steroidogenesis during early stages of follicle development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19196834" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15737" }, "primaryId" : "GEO:GSE15737", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15737" } ] }, "title" : "Fiber and NMJ / synaptic gene expression comparisons in rat extraocular muscle (EOM) and tibialis anterior (TA) muscle.", "dateAssigned" : "2009-04-19T00:00:00.000-05:00", "summary" : "Conclusion: Transcriptome level differences exist between EOM synaptic regions and TA synaptic regions. Our definition of the synaptic transcriptome provides insight into the mechanism of formation and functioning of the unique synapses of EOM and their differential involvement in diseases noted in the EOM allotype. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20393109" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15764" }, "primaryId" : "GEO:GSE15764", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15764" } ] }, "title" : "Comparison of whole brain expression data between selectively bred P and NP, alcohol naïve rats", "dateAssigned" : "2009-04-21T00:00:00.000-05:00", "summary" : "Gene expression was analyzed in brains of 4 male selectively-bred alcohol-preferring (P) rats (generation 63) and 3 male alcohol non-preferring (NP) rats (generation 62) that were obtained from Dr. Richard L. Bell, Indiana University School of Medicine, Indianapolis, IN. These rats had never been exposed to alcohol.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15785" }, "primaryId" : "GEO:GSE15785", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15785" } ] }, "title" : "Profiling of the response of genes in the rat liver to hepatotoxicants", "dateAssigned" : "2009-04-22T00:00:00.000-05:00", "summary" : "This data set comprises of the standardized experimental design for the microarray gene expression data derived from the rat liver (target tissue) after treatment with eight known hepatotoxicants (at multiple time points and doses with multiple biological replicates and a fluor-flip for each biological sample).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18570634" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15813" }, "primaryId" : "GEO:GSE15813", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15813" } ] }, "title" : "High weight differences between donor and recipient affect early kidney graft function -a role for IL-6 signaling", "dateAssigned" : "2009-04-24T00:00:00.000-05:00", "summary" : "The frequency of delayed function of kidney transplants varies greatly and is associated with the quality of graft, donor age, and the duration of cold ischemia time. Body weight differences between donor and recipient can affect primary graft function. The underlying mechanism is poorly understood. Here, we have transplanted kidney grafts from commensurate body weight (L-WD) or reduced body weight (H-WD) donor rats into syngeneic or allogeneic recipients. 24 hours post-transplantation, serum creatinine level in H-WD recipients was significantly higher compared to that of L-WD recipients indicating impaired primary graft function. We detected a 10 fold higher transcription of IL-6 and dramatically increased tubular destruction in grafts from H-WD recipients. This was accompanied by decreased expression of genes associated with kidney function and an up-regulation of other genes such as cytochrome P450 isoforms, FosL and Trib3 as revealed by DNA microarray analysis. A single application of IL-6 into L-WD recipients is sufficient to impair primary graft function and to cause tubular damage. Whereas, immediate neutralization of IL-6 receptor signaling rescued primary graft function resulting in low serum creatinine levels, well-preserved kidney graft architecture and a normalized gene expression profile. These findings have strong clinical implication as anti-IL6R treatment of patients receiving grafts from lower-weight donors could be used to improve primary graft function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19563340" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15841" }, "primaryId" : "GEO:GSE15841", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15841" } ] }, "title" : "Genome-wide analysis of short-term transcriptional responses in thrombin-stimulated vascular smooth muscle cells", "dateAssigned" : "2009-04-27T00:00:00.000-05:00", "summary" : "To understand the mechnaisms underlying this signaling cascade, microarray analysis was performed in vascular smooth muscle cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15856" }, "primaryId" : "GEO:GSE15856", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15856" } ] }, "title" : "Electric stimulation of neonatal rat ventricular cardiomyocytes", "dateAssigned" : "2009-04-27T00:00:00.000-05:00", "summary" : "Through comparing non-stimulated, stimulated and blebbistatin supplemented and stimulated cultures we set out to identify the genes that are specifically activated by electric pulsing separate from cardiomyocyte contractions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20858713" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15878" }, "primaryId" : "GEO:GSE15878", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15878" } ] }, "title" : "Effects of Methylprednisolone (MP) to Spinal Cord Injury", "dateAssigned" : "2009-04-28T00:00:00.000-05:00", "summary" : "Spinal cord injury (SCI) causes serious and complex secondary injury mechanism that leads to function deficit in daily life. How to treat devastating SCI is a critical issue in clinical medicine. This study explores effect of Methylprednisolone (MP) in temporal change of gene expression to look for candidate genes that have potential to develop effective treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34884829" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15887" }, "primaryId" : "GEO:GSE15887", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15887" } ] }, "title" : "Genetic networks regulated by short chain fatty acids in vivo (rat adrenal medulla) and in vitro (in rat PC12 cells)", "dateAssigned" : "2009-04-29T00:00:00.000-05:00", "summary" : "Genome-wide expression profiling showed significant overlap of the genetic networks regulated by butyrate in vivo (rat adrenal medulla) and in vitro (PC12 cells) including TH and other neurotransmitter-related genes (DBH, AADC, GTPCH, ppEnk, NPY).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15900" }, "primaryId" : "GEO:GSE15900", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15900" } ] }, "title" : "Diabetic lung", "dateAssigned" : "2009-04-29T00:00:00.000-05:00", "summary" : "Effect of type 1 diabetes (induced by streptozotocin 60 mg/kg) on lung gene expression. Wistar rats, male. At age 8 weeks control rats got IP buffer, diabetic rats got streptozotocin. At age 12 weeks animals were anesthetized and lungs removed. RNA was extracted with Trizol, and gene expression array analysis was performed using Affymetrix RAE 230A microarrays according to the directions from the manufacturer. Arrays were scanned using a Hewlett Packard Gene Array scanner, and analyzed with Affymetrix MAS 5.0 software. Expression levels reported are the output from the MAS software.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24423257" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15920" }, "primaryId" : "GEO:GSE15920", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15920" } ] }, "title" : "Comparison of gene expression profile in embryonic mesencephalon and neuronal primary cultures", "dateAssigned" : "2009-05-01T00:00:00.000-05:00", "summary" : "In the mammalian central nervous system (CNS) an important contingent of dopaminergic neurons are localized in the substantia nigra and in the ventral tegmental area of the ventral midbrain. They constitute an anatomically and functionally heterogeneous group of cells involved in a variety of regulatory mechanisms, from locomotion to emotional/motivational behavior. Midbrain dopaminergic neuron (mDA) primary cultures represent a useful tool to study molecular mechanisms involved in their development and maintenance. Considerable information has been gathered on the mDA neurons development and maturation in vivo, as well as on the molecular features of mDA primary cultures. Here we investigated in detail the gene expression differences between the tissue of origin and ventral midbrain primary cultures enriched in mDA neurons, using microarray technique. We integrated the results based on different re-annotations of the microarray probes. By using knowledge-based gene network techniques and promoter sequence analysis, we also uncovered mechanisms that might regulate the expression of CNS genes involved in the definition of the identity of specific cell types in the ventral midbrain. We integrate bioinformatics and functional genomics, together with developmental neurobiology. Moreover, we propose guidelines for the computational analysis of microarray gene expression data. Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19305503" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15942" }, "primaryId" : "GEO:GSE15942", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15942" } ] }, "title" : "Genomic Studies upon NeuroD6 overexpression in PC12 cells, in the presence or absence of an apoptotic stimulus", "dateAssigned" : "2009-05-04T00:00:00.000-05:00", "summary" : "During neurogenesis, expression of the basic Helix-Loop-Helix NeuroD6/Nex1/MATH-2 transcription factor parallels neuronal differentiation, while maintaining the differentiated state in the mature nervous system. To further dissect NeuroD6 differentiation properties, we previously generated a NeuroD6-overexpressing stable PC12 cell line, PC12-ND6, which displays a neuronal phenotype characterized by spontaneous neuritogenesis, accelerated NGF-induced differentiation, and increased regenerative capacity. Furthermore, we reported that NeuroD6 promotes long-term neuronal survival upon oxidative stress triggered by serum deprivation. In this study, we identified the NeuroD6-mediated transcriptional regulatory pathways linking neuronal differentiation to survival, by conducting a genome-wide microarray analysis using PC12-ND6 cells and serum deprivation as a stress paradigm. Through a series of filtering steps and a gene-ontology analysis, we found that NeuroD6 promotes distinct but overlapping gene networks, consistent with the differentiation, regeneration, and survival properties of PC12-ND6 cells. Using a gene set enrichment analysis, we provide the first evidence of a compelling link between NeuroD6 and a set of heat shock proteins in the absence of stress, which may be instrumental to confer stress tolerance to PC12-ND6 cells. Immunocytochemistry results showed that HSP27 and HSP70 interact with cytoskeletal elements, consistent with their roles in neuritogenesis and preserving cellular integrity. HSP70 also colocalizes with mitochondria located in the soma, growing neurites and growth cones of PC12-ND6 cells prior to and upon stress stimulus, consistent with its neuroprotective functions. Collectively, our findings support the notion that NeuroD6 links neuronal differentiation to survival via the network of molecular chaperones and endows the cells with increased stress tolerance.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19610105" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15944" }, "primaryId" : "GEO:GSE15944", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15944" } ] }, "title" : "Differentially expressed genes after treatment with hydroxytyrosol in DMBA-induced rat breast tumors", "dateAssigned" : "2009-05-04T00:00:00.000-05:00", "summary" : "The aim of this study was to compare the gene expression profile changes of DMBA-induced rat breast tumors after treatment with hydroxytyrosol (a natural compound from virgin olive oil). To this end, a cDNA microarray experiment was performed (Affymetrix’s Rat Genome 230 2.0 array). This gene expression study was carried out on the tumor biopsy samples prior to hydroxytyrosol treatment, and compared with matched tumor biopsy samples after completion of the hydroxytyrosol treatment schedule. The result of this study was the identification of several genes related to apoptosis, cell cycle arrest, proliferation, differentiation, survival and transformation-related genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21120994" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15952" }, "primaryId" : "GEO:GSE15952", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15952" } ] }, "title" : "RNA profiles of rat olfactory epithelia : individual and age related variations (gender/supplier experiment)", "dateAssigned" : "2009-05-05T00:00:00.000-05:00", "summary" : "Conclusions: Not all OR genes are expressed at a detectable level. Pups expressed fewer OR genes than adult rats, and generally at a lower level; however, a small subset of OR genes were more strongly expressed in these newborn rats. The reasons for these differences are not understood. However, the specific expression of some OR genes in newborn olfactory epithelia may be related to the blindness and deafness of pups at birth, when these pups are heavily reliant on olfaction and their mother.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19954510" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15953" }, "primaryId" : "GEO:GSE15953", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE15953" } ] }, "title" : "RNA profiles of rat olfactory epithelia : individual and age related variations (age experiment)", "dateAssigned" : "2009-05-05T00:00:00.000-05:00", "summary" : "Conclusions: Not all OR genes are expressed at a detectable level. Pups expressed fewer OR genes than adult rats, and generally at a lower level; however, a small subset of OR genes were more strongly expressed in these newborn rats. The reasons for these differences are not understood. However, the specific expression of some OR genes in newborn olfactory epithelia may be related to the blindness and deafness of pups at birth, when these pups are heavily reliant on olfaction and their mother.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19954510" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16003" }, "primaryId" : "GEO:GSE16003", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16003" } ] }, "title" : "Alcohol Consumption Effects During the Inflammatory Stage of Fracture Healing in Rat Bones", "dateAssigned" : "2009-05-06T00:00:00.000-05:00", "summary" : "Sprague-Dawley rats were placed on an ethanol-containing or pair-fed Lieber and DeCarli diets for 4 wks prior to surgical fracture. Following insertion of a medullary pin, a closed mid-diaphyseal fracture was induced using a Bonnarens and Einhorn fracture device. At 3 days post-fracture, the region of the fracture calluses were harvested from the right hind-limb. RNA was extracted and microarray analysis was conducted against the entire rat genome to study the effects of alcohol-consumption on the fracture healing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22087020" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16006" }, "primaryId" : "GEO:GSE16006", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16006" } ] }, "title" : "MicroRNAs regulated by DAC", "dateAssigned" : "2009-05-07T00:00:00.000-05:00", "summary" : "Aberrant expression of microRNA (miRNA) has been reported in various cancers. To clarify the role of miRNA in gastric carcinogenesis, we performed miRNA microarray analysis and investigated expressional changes of miRNAs in a 5-aza-2'-deoxycytidine (DAC)-treated gastric cancer cell line, KATO-¿¿¿.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20080834" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16063" }, "primaryId" : "GEO:GSE16063", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16063" } ] }, "title" : "Prostates of rats with induced partial bladder outlet obstruction and the effect of Eviprostat on those changes", "dateAssigned" : "2009-05-12T00:00:00.000-05:00", "summary" : "Prostatic inflammation plays a role in the progression of benign prostatic hyperplasia (BPH). Eviprostat is an antiinflammatory and antioxidant phytotherapeutic agent widely used to treat lower urinary tract symptoms in BPH. However, because Eviprostat is a mixture of compounds from multiple natural sources, its mechanism of action has been difficult to investigate. In this study, we used oligonucleotide microarrays to identify changes in gene expression that occur in the prostate of rats with surgically induced partial bladder outlet obstruction and the effect of Eviprostat on those changes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19616448" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16128" }, "primaryId" : "GEO:GSE16128", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16128" } ] }, "title" : "Radiation-specific DNA copy number aberration in rat mammary carcinoma.", "dateAssigned" : "2009-05-15T00:00:00.000-05:00", "summary" : "Breast cancer ranks top in the incidence among the main sites of female cancer in Japan. The epidemiological study on atomic bomb survivors has suggested that the excess relative risk for breast cancer is higher than any other sites. Little is known, however, about the molecular mechanisms of breast cancer induction by radiation. Therefore, we analyzed here the genome-wide copy number aberration of radiation-induced rat mammary carcinomas using microarray-based comparative genomic hybridization (array-CGH). Mammary carcinomas were induced by 2 Gy gamma irradiation of Sprague-Dawley (SD) rats at 3 or 7 weeks of age. We examined 14 mammary carcinomas induced by gamma-irradiation (2 Gy) and found 26 aberrations including trisomies of chromosomes 4 and 10 in 3 and 1 carcinomas, respectively, and deletion of chromosomes 3q35q36 and 5q32 (Cdkn2a and Cdkn2b region) in 2 and 2 carcinomas, respectively. On the other hand, only one aberration (amplification of chromosome 10q31) was observed in four spontaneous mammary carcinomas. These results suggest that the trisomy of chromosome 4 and deletion of chromosomes 3q35q36 and 5q32 were associated with radiation exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20681787" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16137" }, "primaryId" : "GEO:GSE16137", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16137" } ] }, "title" : "Differential gene profile of resorbed embryos following paternal tamoxifen treatment", "dateAssigned" : "2009-05-16T00:00:00.000-05:00", "summary" : "Studies from our laboratory have demonstrated that treatment of adult male rats with tamoxifen, a selective estrogen receptor modulator, at a dose of 0.4 mg/kg/day for 60 days resulted in an increase in post-implantation loss at around mid gestation. The present study was done to assess global gene expression profile using Agilent Rat Whole Genome Microarray slides. Differential gene expression profile of resorbed to normal embryos at embryonic day (E) 11 and 13 was studied to identify the causes of resorption. Gene Ontology classification based on biological function revealed significant down regulation of genes associated with development, differentiation, metabolism, transcription, chromatin binding and cell cycle in the resorbed embryos from both the groups at E13. Genes associated with immune response, inflammatory response and angiogenesis were found to be up regulated in the resorbed embryos. Temporal analysis at E11 in the treated resorbed embryos revealed no increase in immune response and inflammation associated genes as seen on E13, indicative of this being a secondary effect. Down regulation of genes associated with development, differentiation, metabolism, transcription, chromatin binding, cell cycle was also evident on E11 in the resorbed embryos. Differential gene expression profile also revealed stochastic expression of imprinted genes, known to modulate embryo-placental growth namely Dlk1, p57, Mash2, Peg3, Lot1 etc. in the resorbed embryos as compared to the normal ones.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21315736" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16138" }, "primaryId" : "GEO:GSE16138", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16138" } ] }, "title" : "Transcriptome analysis of mesothelioma induced by intraperitoneal injections of ferric saccharate in rats", "dateAssigned" : "2009-05-17T00:00:00.000-05:00", "summary" : "Iron plays an important role in oxidative tissue damage and subsequent carcinogenesis. Iron deposition in the peritoneum causes neoplastic changes. Here we used gene expression microarrays to find common genetic alterations in a rat model by repeated intraperitoneal injections of ferric saccharate. Gene expression microarray revealed the expression of uromodulin (Umod) is increased in mesothelioma approximately 250-fold.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20065947" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16199" }, "primaryId" : "GEO:GSE16199", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16199" } ] }, "title" : "Cardiac 12/15-lipoxygenase-induced inflammation is involved in heart failure", "dateAssigned" : "2009-05-22T00:00:00.000-05:00", "summary" : "To identify a novel target for the treatment of heart failure, we examined gene expression in the failing heart. Among the genes analyzed, 12/15 lipoxygenase (12/15-LOX) was markedly up-regulated in heart failure. To determine whether increased expression of 12/15-LOX causes heart failure, we established transgenic mice that overexpressed 12/15-LOX in cardiomyocytes. Echocardiography showed that 12/15-LOX transgenic mice developed systolic dysfunction. Cardiac fibrosis increased in 12/15-LOX transgenic mice with advancing age, and was associated with the infiltration of macrophages. Consistent with these observations, cardiac expression of monocyte chemoattractant protein-1 (Mcp-1) was up-regulated in 12/15-LOX transgenic mice compared with wild-type mice. Treatment with 12-hydroxy-eicosatetraenotic acid, a major metabolite of 12/15-LOX, increased MCP-1 expression in cardiac fibroblasts and endothelial cells, but not in cardiomyocytes. Inhibition of Mcp-1 reduced the infiltration of macrophages into the myocardium and prevented both systolic dysfunction and cardiac fibrosis in 12/15-LOX transgenic mice. Likewise, disruption of 12/15-LOX significantly reduced cardiac Mcp-1 expression and macrophage infiltration, thereby improving systolic dysfunction induced by chronic pressure overload. Our results suggest that cardiac 12/15-LOX is involved in the development of heart failure and that inhibition of 12/15-LOX could be a novel treatment for this condition.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19546247" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16231" }, "primaryId" : "GEO:GSE16231", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16231" } ] }, "title" : "Differentially expressed genes after treatment with adriamycin in DMBA-induced rat breast tumors", "dateAssigned" : "2009-05-26T00:00:00.000-05:00", "summary" : "The aim of this study was to compare the gene expression profile changes of DMBA-induced rat breast tumors after treatment with adriamycin. To this end, a cDNA microarray was performed (Affymetrix’s Rat Genome 230 2.0 array). This gene expression study was carried out on the tumor biopsy samples prior to adriamycin treatment, and compared with matched tumor biopsy samples after completion of the adriamycin treatment schedule.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21120994" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16232" }, "primaryId" : "GEO:GSE16232", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16232" } ] }, "title" : "Gene expression profile in a DMBA-induced rat breast tumor: biopsy vs total tumor", "dateAssigned" : "2009-05-26T00:00:00.000-05:00", "summary" : "The aim of this study was to compare the gene expression profile changes of DMBA-induced rat breast tumors from an initial stage to the moment of sacrifice. To this end, a cDNA microarray was performed (Affymetrix’s Rat Genome 230 2.0 array). This gene expression study was carried out on the umor biopsy samples and compared with matched tumor biopsy samples once the study ended (7 weeks after initial biopsy).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21120994" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16233" }, "primaryId" : "GEO:GSE16233", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16233" } ] }, "title" : "Expression profiles from kidneys of rats treated with nephrotoxicants and with controls", "dateAssigned" : "2009-05-26T00:00:00.000-05:00", "summary" : "The substances were administrated daily for 1, 5 or 28 days at doses that are expected to induce kidney-specific histopathological and clinical chemistry changes not before 28 days of repetitive dosing. At the end of treatment, kidneys from the treated animals were removed; the RNA from these kidneys, and from kidneys of several naive animals was extracted and subjected to microarray expression analysis. Twenty candidate genes which showed significant changes from control were identified using microarray experiments.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16240" }, "primaryId" : "GEO:GSE16240", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16240" } ] }, "title" : "Gene expression-based comparison of PQQ and known transcriptional regulators", "dateAssigned" : "2009-05-27T00:00:00.000-05:00", "summary" : "Pyrroloquinoline quinone (PQQ) is a naturally occurring compound and known to improve growth and reproductive performance when added to diets of PQQ-deprived rodents. To understand its mechanism action, changes in hepatic gene expression were measured in rats fed diets with or without added PQQ. Gene expression changes for PQQ supplemented (EC50 ~ 3 nmol PQQ/Kg diet) or deficient rats were assayed by expression microarray analysis and compared to those for known transcriptional regulators (epicatechin; Epi; dexamethasone, Dex; clofibrate, Clo; phenobarbital, Pb). Two principal expression clusters were observed; one for Dex and another for Pb, Epi, Clo, and PQQ. Within the latter, a PQQ subcluster containing a unique group of genes for cell signaling and transport functions. Next, short and long term PQQ depletion and repletion protocols (48 or 36 h, respectively) were performed, leading to changes in hepatic gene expression for both time periods. Of the ~10,000 genes and ESTs analyzed, 4.7% of the transcripts were sensitive to changes in PQQ dietary status. PQQ deprivation generally caused down regulation of genes associated with mitochondriogenesis, cell differentiation, and immune function. These gene expression changes provide the basis for most of the previously published functional observations associated with PQQ deficiency and PQQ administered in pharmacological amounts. To assess PQQ’s potential functions, we used gene expression profiling through microarray technology as part of a comprehensive approach to identify potential pathways and mechanisms. Given that the systemic effects of PQQ deprivation are influenced at levels of dietary intake in the micromolar range, highly purified diets were used to reduce expression from other bioactive factors and xenobiotics, such as those found in typical rodent chow diets. To establish if the changes in gene expression in response to PQQ exposure will follow a similar pattern as other xenobiotics, the responses to PQQ exposure were contrasted with those from exposure to epicatechin (Epi), dexamethasone (Dex), clofibrate (Clo), or phenobarbital (Pb). Dietary conditions were also chosen to clarify the response to short- and longer-term PQQ deprivation. A goal was to determine if specific changes in dietary protocol or patterns could be used to identify genes important to the function of PQQ. Because it has been observed that mitochondrial-related functions are influenced by PQQ, we hypothesized that changes in genes important to fatty acid and amino acid metabolism and mitochondrial function would be likewise affected by dietary levels of PQQ. The overall study was carried out using two experiments. In this specific experiment, the gene expression profiles of Sprague Dawley (SD) rats treated with different xenobiotics were compared to the gene expression profile of PQQ treated SD rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16340" }, "primaryId" : "GEO:GSE16340", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16340" } ] }, "title" : "Rat liver. Control vs. Chemical treated, 3 days", "dateAssigned" : "2009-05-29T00:00:00.000-05:00", "summary" : "Supplementary file \"15 Compounds for test\" lists the other compounds which are for test.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20011461" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16359" }, "primaryId" : "GEO:GSE16359", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16359" } ] }, "title" : "Rat hindlimb arteries: Shunt versus Control", "dateAssigned" : "2009-06-01T00:00:00.000-05:00", "summary" : "Arteriogenesis is defined as the development of a collateral circulation, bypassing an arterial occlusion. We have previously demonstrated that chronically elevated fluid shear stress completely normalized blood flow in femoral artery ligated rabbits. This was realized by a surgical intervention: the creation of an arterio- venous anastomosis (shunt) between the femoral artery and the accompanying vein. The aim of this study was a gene profiling approach in order to identify differentially expressed genes during collateral growth in the shunt model when compared to pre-existent collaterals (sham).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16369" }, "primaryId" : "GEO:GSE16369", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16369" } ] }, "title" : "Limitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (454)", "dateAssigned" : "2009-06-01T00:00:00.000-05:00", "summary" : "Keywords: Transcriptome analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19564845" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16370" }, "primaryId" : "GEO:GSE16370", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16370" } ] }, "title" : "Limitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (SOLiD)", "dateAssigned" : "2009-06-01T00:00:00.000-05:00", "summary" : "Keywords: Transcriptome analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19564845" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16371" }, "primaryId" : "GEO:GSE16371", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16371" } ] }, "title" : "Limitations and possibilities of small RNA digital gene expression profiling: spleen and liver comparison (SOLiD)", "dateAssigned" : "2009-06-01T00:00:00.000-05:00", "summary" : "Keywords: Transcriptome analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19564845" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16394" }, "primaryId" : "GEO:GSE16394", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16394" } ] }, "title" : "Rat liver. Control vs. Chemical treated, 28 days", "dateAssigned" : "2009-06-02T00:00:00.000-05:00", "summary" : "Supplementary file \"15 Compounds for test\" lists the other compounds which are for test.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20011461" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16437" }, "primaryId" : "GEO:GSE16437", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16437" } ] }, "title" : "Composition of Staufen2 ribonucleoprotein particles in neurons", "dateAssigned" : "2009-06-04T00:00:00.000-05:00", "summary" : "In neurons, many mRNAs are transported along neuronal dendrites to their site of translation by ribonucleoprotein complexes (mRNPs). Numerous mRNA-binding, motor and regulatory proteins within mRNPs finely regulate the fate of each of these mRNAs and their specific combination is likely to define different types of mRNA complexes and their neuronal functions. Staufen2 is a well known mRNA-binding protein present in distinct population of mRNPs in neurons and is implicated in the transport of mRNAs along the dendritic microtubules. However, little is known about the associated mRNAs in Staufen2 neuronal mRNPs complexes. As a means to understand its role in neuronal processes, a genome wide approach has been used to identify mRNAs that are co-immunoprecipitated with Staufen2 complexes from embryonic rat brains. The genome wide approach identified 1780 mRNAs associated with Staufen2 mRNPs that code for proteins involved in cellular processes such as post-translational protein modifications, RNA metabolism, intracellular transport and translation. All these mRNAs are consistent with the role of Staufen2 in synaptogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20510018" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16458" }, "primaryId" : "GEO:GSE16458", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16458" } ] }, "title" : "A simple method to integrate different versions of Affymetrix microarrays using duplicate samples", "dateAssigned" : "2009-06-05T00:00:00.000-05:00", "summary" : "The size and scope of microarray experiments continue to increase. However, datasets generated on different platforms or at different centres contain biases. Improved techniques are needed to remove platform- and batch-specific biases. One experimental control is the replicate hybridization of a subset of samples at each site or on each platform to learn the relationship between the two platforms. To date, no algorithm exists to specifically use this type of control. LTR is a linear-modelling-based algorithm that learns the relationship between different microarray batches from replicate hybridizations. LTR was tested on a new benchmark dataset of 20 samples hybridized to different Affymetrix microarray platforms. Before LTR, the two platforms were significantly different; application of LTR removed this bias. LTR was tested with six separate data pre-processing algorithms, and its effectiveness was independent of the pre-processing algorithm. Sample-size experiments indicate that just three replicate hybridizations can significantly reduce bias. An R library implementing LTR is available.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20838609" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16483" }, "primaryId" : "GEO:GSE16483", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16483" } ] }, "title" : "Modulation of brain dead induced inflammation by vagus nerve stimulation", "dateAssigned" : "2009-06-08T00:00:00.000-05:00", "summary" : "Our study demonstrates impairment of the parasympathetic nervous system during BD and inhibition of serum TNFa through vagal stimulation. Vagus nerve stimulation variably affected gene expression in donor organs and improved renal function in recipients. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20055812" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16624" }, "primaryId" : "GEO:GSE16624", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16624" } ] }, "title" : "Expression data from lungs of rats with pulmonary hypertension", "dateAssigned" : "2009-06-15T00:00:00.000-05:00", "summary" : "Pulmonary hypertension is a frequent consequence of left heart disease and congestive heart failure (CHF) and causes extensive lung vascular remodelling which leads to right ventricular failure. Functional genomics underlying this structural remodelling are unknown but present potential targets for novel therapeutic strategies. We used microarrays to detail the gene expression underlying vascular remodeling in the pathogenesis of pulmonary hypertension and identified distinct classes of up-regulated genes during this process.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21148228" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16695" }, "primaryId" : "GEO:GSE16695", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16695" } ] }, "title" : "Gene expression data from endothelial cells and leukocytes enriched from transplanted rat hearts", "dateAssigned" : "2009-06-18T00:00:00.000-05:00", "summary" : "Transcriptome analyses of organ transplants have until now usually focused on whole tissue samples containing activation profiles from different cell populations. Here, we enriched endothelial cells from rat cardiac allografts and isografts, establishing their activation profile at baseline and on day 2, 3 and 4 after transplantation. Modulated transcripts were assigned to three categories based on their regulation profile in allografts and isografts. Categories A and B contained the majority of transcripts and showed similar regulation in both graft types, appearing to represent responses to surgical trauma. By contrast, category C contained transcripts that were partly allograft-specific and to a large extent associated with interferon-gamma-responsiveness. Several transcripts were verified by immunohistochemical analysis of graft lesions, among them the matricellular protein periostin which was one of the most highly upregulated transcripts but has not been associated with transplantation previously. In conclusion, the majority of the differentially expressed genes in graft endothelial cells are affected by the transplantation procedure whereas relatively few are associated with allograft rejection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20642680" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16710" }, "primaryId" : "GEO:GSE16710", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16710" } ] }, "title" : "Expression data from adult rat tail MNs after spinal cord transection", "dateAssigned" : "2009-06-18T00:00:00.000-05:00", "summary" : "Gene expression changes were studied in motor neurons 21 and 60 days after complete spinal transection where the tail exhibits clear signs of spasticity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19939961" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16725" }, "primaryId" : "GEO:GSE16725", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16725" } ] }, "title" : "Regional brain expression maps for microRNAs in rats", "dateAssigned" : "2009-06-19T00:00:00.000-05:00", "summary" : "MicroRNA transcriptional profiling of male Sprague-Dawley rats rat brains comparing microRNA abundance in five different brain regions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19806225" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16735" }, "primaryId" : "GEO:GSE16735", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16735" } ] }, "title" : "Evidence for a rheostat that determines neuronal survival after traumatic brain injury", "dateAssigned" : "2009-06-20T00:00:00.000-05:00", "summary" : "To investigate the determinants of neuronal survival after traumatic brain injury, we compared the transcriptional profiles of dying (Fluoro-Jade-positive) and immediately adjacent surviving (Fluoro-Jade-negative) neurons from the CA3 subfield of the rat hippocampus 24 hours after experimental TBI. We found that hippocampal neurons that survive TBI invariably express high levels of genes that have cellular functions involved in survival, regeneration, development, proliferation, neuronal plasticity such as cAMP response element binding protein (CREB), brain-derived-neurotrophic factor (BDNF) and mitogen-activated protein kinase 1 (MAPK1). Dying neurons express high levels of genes involved in aberrant cell cycle progression, immune response, inflammation, oxidative stress and apoptosis such as Interleukin-1ß (IL-1ß), caspase 3 and B-cell linker (BLNK). We conclude that shifting the balance between the global levels of these proteins with pharmacotherapeutic drugs that induce expression of cell survival associated genes, is expected to alter the cellular rheostat that determines cell survival or cell death.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21853077" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16743" }, "primaryId" : "GEO:GSE16743", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16743" } ] }, "title" : "Rat liver: Control vs. Chemical treated, 14 days", "dateAssigned" : "2009-06-22T00:00:00.000-05:00", "summary" : "Supplementary file \"15 Compounds for test\" lists the other compounds which are for test.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20011461" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16750" }, "primaryId" : "GEO:GSE16750", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16750" } ] }, "title" : "Aortic gene expression profile of rats exposed in utero to maternal diabetes", "dateAssigned" : "2009-06-23T00:00:00.000-05:00", "summary" : "Epidemiologic studies have clearly identified modifications of fetal environment as a risk factor for the development of cardiovascular diseases and of metabolic syndrome in adulthood. In our experimental model, rats exposed to maternal diabetes develop a volume-dependent hypertension as early as 6 month of age. In order to determine if the development of hypertension results from an abnormal vascular fetal programming, gene expression profile of thoracic aorta were studied in adult rats exposed in utero to maternal hyperglycemia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20622163" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16764" }, "primaryId" : "GEO:GSE16764", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16764" } ] }, "title" : "Comparative microarray analyses between the rat superior olivary complex and the brain", "dateAssigned" : "2009-06-23T00:00:00.000-05:00", "summary" : "Altogether, our study identified a tight genetic link between the SOC-related genetic program and deafness genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23893414" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16792" }, "primaryId" : "GEO:GSE16792", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16792" } ] }, "title" : "Temporal changes of gene expression in rat kidney and lung, and the effect of prior growth inhibition on these changes", "dateAssigned" : "2009-06-24T00:00:00.000-05:00", "summary" : "Using microarrays, we investigated the changes of gene expression that occur with age in kidney and lung as growth slows down, and also investigated whether these changes were growth-driven, by asking whether prior delay of postnatal growth caused by malnutrition (tryptophan deficiency) would also delay these genetic changes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20371622" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16839" }, "primaryId" : "GEO:GSE16839", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16839" } ] }, "title" : "Genome-wide DNA methylation in normal and IUGR pancreatic islets", "dateAssigned" : "2009-06-25T00:00:00.000-05:00", "summary" : "Intrauterine growth restriction (IUGR) increases susceptibility to age-related diseases including type 2 diabetes (T2DM), and is associated with permanent and progressive changes in gene expression and epigenetic regulation. We studied cytosine methylation throughout the genome in pancreatic islets from a rat model of uteroplacental insufficiency, providing a novel and detailed assessment of the genomic distribution and locus-specific patterns of DNA methylation in normal islets as well as the changes that occur as a consequence of IUGR. Utilizing a high throughput approach to study DNA methylation at almost 1 million unique sites throughout the genome, we found ~1,400 changes in methylation (IUGR compared to control) with an estimated false discovery rate of 4.2%. These epigenetic differences were observed in IUGR male rats at 7 weeks of age, preceding the development of diabetes in this model. Therefore, these epigenetic differences represent candidates for mediating the pathogenesis of metabolic disease that occurs later in life in these animals. Moreover, many of the changes we identify are located near genes that regulate processes known to be abnormal in IUGR islets, such as vascularization, ß-cell proliferation, insulin secretion, and cell death. Consistent changes in mRNA expression were identified at some of the epigenetically-dysregulated genes including Fgfr1, Gch1, Pcsk5, and Vgf. Globally, epigenetic dysregulation occurred preferentially at conserved intergenic sequences, which are candidate cis-regulatory elements driving differential expression of nearby genes. These results provide insights into the complex developmental consequences of IUGR, and suggest that changes in DNA methylation could mediate a constellation of changes in both gene expression and pancreatic islet development and function, with relevance to T2DM.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20194508" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16849" }, "primaryId" : "GEO:GSE16849", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16849" } ] }, "title" : "preparative changes in rat intestine and lung for birth", "dateAssigned" : "2009-06-26T00:00:00.000-05:00", "summary" : "Transcript profiling using microarray analysis was performed using lung and intestine RNA from a single animal from each of 10 litters at a given gestational age. Array experiments were performed by the Genomics CoreLab, Cambridge Comprehensive Biomedical Research Centre. Briefly, the Affymetrix Rat Genome 230.2 GeneChip was employed. Total RNA was processed using the standard Affymetrix one-cycle target labeling and hybridization protocols. Data were pre-normalized using robust multiarray averaging and normalization was achieved using the LIMMA software package. Normalized transcript abundance data were compared between E16 and E20 using two independent methods: the Cyber-T algorithm and Rank Product Analysis. Transcripts that were significantly regulated in both Cyber-T (Bayes p value < 0.001, posterior probability of differential expression, ppde > 0.99) and Rank Product Analysis (p<0.0001) and showed an absolute fold change of over 5 were defined as differentially expressed. Microarray data were annotated using the NetAffx Analysis Center (Affymetrix). To generate the list of up-or down-regulated genes only Entrez genes or Unigene clusters were considered if at least one probe set gave an unambiguous match.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20463093" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16899" }, "primaryId" : "GEO:GSE16899", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16899" } ] }, "title" : "Hepatic gene expression profile of rats fed an iron-deficient diet", "dateAssigned" : "2009-06-30T00:00:00.000-05:00", "summary" : "Iron is an essential nutritional element; its deficiency in the body causes nutritional problems and a decrease in iron storage that can lead to anemia. The liver not only stores iron but is an important metabolic target as well. Dietary iron deficiency is associated with changes in the metabolism of nutrients such as lipids. However, to the best of our knowledge, a global analysis detailing the consequences of iron deficiency in the body has not yet been reported. We performed a comprehensive transcriptome analysis using DNA microarray technology to reveal the effects of iron deficiency on hepatic gene expression. Four-week-old rats were fed an iron-deficient diet or a control diet for 16 days. On day 17, the rats were sacrificed under anesthesia, and their livers were dissected for DNA microarray analysis. We identified 600 up-regulated and 500 down-regulated probe sets to characterize the iron-deficient diet group. The up-regulated probe sets contained genes for enzymes that are involved in cholesterol, amino acid, and glucose metabolisms, as well as in apoptosis. The down-regulated probe sets included genes for enzymes associated with lipid metabolism. Additionally, the 16-day iron-deficient diet induced anemia. Our gene expression analysis revealed that, as a result, cholesterol biosynthesis, gluconeogenesis, and apoptosis due to endoplasmic reticulum stress were accelerated, while fatty acid biosynthesis was suppressed by dietary iron deficiency. Our analysis also showed that cholesterol metabolism, including bile acid biosynthesis, was accelerated in the initial stages of cholesterol accumulation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20388835" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16981" }, "primaryId" : "GEO:GSE16981", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16981" } ] }, "title" : "Spatial and Temporal Regulation of Gene Expression in the Mammalian Growth Plate", "dateAssigned" : "2009-07-07T00:00:00.000-05:00", "summary" : "To explore the mechanisms responsible for spatial and temporal regulation of the growth plate, we microdissected postnatal rat growth plates into their constituent zones and then used microarray analysis to characterize the changes in gene expression that occur as chondrocytes undergo spatially-associated differentiation and temporally-associated senescence.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20974641" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16985" }, "primaryId" : "GEO:GSE16985", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE16985" } ] }, "title" : "Neonatal Hydrocephalus: Saline Control vs. Kaolin-Induced", "dateAssigned" : "2009-07-07T00:00:00.000-05:00", "summary" : "Transcriptional profiling of the parietal cortex was performed in postnatal day 22 rats with obstructive hydrocephalus. An intracisternal injection of kaolin was done on postnatal day one, and severe hydrocephalus developed over 3 weeks. Hydrocephalic animals were compared to age-matched saline controls. The goal was to determine the effects of kaolin-induced neonatal hydrocephalus on gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20713048" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17015" }, "primaryId" : "GEO:GSE17015", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17015" } ] }, "title" : "Characterization of the transcriptional heterogeneity present within the rat lymphatic and blood vasculatures", "dateAssigned" : "2009-07-08T00:00:00.000-05:00", "summary" : "The goal and objective of this study was to identify the transcriptional profiles differentiating the artery, vein, and lymphatic lineages in the adult rat vasculature with particular emphasis on the unique elements of the collecting lymphatic vessel transcriptome. A 2 x 3 experimental design was utilized in which parallel arteries, veins, and lymphatics from two different tissue beds were examined. The rat thoracic duct was selected as a large, post-nodal collecting lymphatic vessel that exhibits excellent conduit-type behavior while the rat mesenteric lymphatic was selected as a smaller, pre-nodal collecting lymphatic vessel that exhibits excellent pump behavior (see Gashev AA, et al. Microcirculation. 2004 Sep;11(6):477-92. [PMID: 15371129]). The axillary artery and vein were selected for comparison to the thoracic duct due to their similar anatomical position distal to the common junction of the lymphatic and venous vascular trees and represent a large artery and large vein, respectively. The mesentery artery and vein were selected for comparison to the mesenteric lymphatic vessels due to their parallel position within the mesenteric vasculature and represent a small atery and small vein, respectively.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24044756" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17045" }, "primaryId" : "GEO:GSE17045", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17045" } ] }, "title" : "Expression data from kidney transplantations in a Fisher-Lewis rat model: placebo and 13cisRA treatment", "dateAssigned" : "2009-07-10T00:00:00.000-05:00", "summary" : "Microarray data was used to obtain transcriptomic changes reflecting signaltransduction pathway dysregulation", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17050" }, "primaryId" : "GEO:GSE17050", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17050" } ] }, "title" : "Gene expression profiling in Wistar male rat left ventricle with chronic and severe aortic valve regurgitation", "dateAssigned" : "2009-07-10T00:00:00.000-05:00", "summary" : "Aortic valve regurgitation (AR) imposes a severe volume overload to the left ventricle (LV) which results in dilation, eccentric hypertrophy and eventually loss of function. Little is known about the impact of AR on LV gene expression. We therefore conducted a gene expression profiling study in the LV of male Wistar rats with chronic (9 months) and severe AR.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17058" }, "primaryId" : "GEO:GSE17058", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17058" } ] }, "title" : "MiRNA expression in adipose tissue and liver from a spontaneous rat model of Type 2 diabetes", "dateAssigned" : "2009-07-13T00:00:00.000-05:00", "summary" : "MicroRNAs (miRNAs) are non-coding RNA molecules involved in post-transcriptional control of gene expression of a wide number of genes, including those involved in glucose homeostasis. Type 2 diabetes (T2D) is characterized by hyperglycaemia and defects in insulin secretion and action at target tissues. Using a miRNA microarray platform, we sought to establish differences in miRNA expression in two insulin-target tissues (liver and adipose tissue) from seven-month-old spontaneously diabetic (Goto-Kakizaki [GK]) and non-diabetic (Brown-Norway [BN]) rats. MiRNA data were integrated with gene expression data from the same rats to investigate how differentially expressed miRNAs affected the expression of their predicted target genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19689793" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17059" }, "primaryId" : "GEO:GSE17059", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17059" } ] }, "title" : "Gene expression in adipose tissue and liver from a spontaneous rat model of Type 2 diabetes", "dateAssigned" : "2009-07-13T00:00:00.000-05:00", "summary" : "Type 2 diabetes (T2D) is characterized by hyperglycaemia and defects in insulin secretion and action at target tissues. Using the Illumina RatRef-12 v1.0 array, gene expression was assessed in two insulin-target tissues (liver and adipose tissue) from seven-month-old spontaneously diabetic (Goto-Kakizaki [GK]) and non-diabetic (Brown-Norway [BN]) rats. This study was performed in parallel with miRNA expression profiling of the same rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19689793" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17148" }, "primaryId" : "GEO:GSE17148", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17148" } ] }, "title" : "INS1 cells expressing either WT IRE1a, I642G IRE1a, N906A IRE1a, or spliced XBP1 treated with dox and 1NMPP1", "dateAssigned" : "2009-07-16T00:00:00.000-05:00", "summary" : "Transcriptional profiling of INS1 cells expressing either WT IRE1a, I642G IRE1a, N906A IRE1a, or spliced XBP1 comparing 1µg/mL dox and 5µM 1NMPP1 treated vs control.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17150" }, "primaryId" : "GEO:GSE17150", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17150" } ] }, "title" : "INS1 CAT cells treated with 1µM thapsigargin vs control.", "dateAssigned" : "2009-07-16T00:00:00.000-05:00", "summary" : "Transcriptional profiling of INS1 CAT cells treated with 1µM thapsigargin vs control.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17190" }, "primaryId" : "GEO:GSE17190", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17190" } ] }, "title" : "Skeletal muscle characteristics of inherited low and high aerobic exercise capacity", "dateAssigned" : "2009-07-20T00:00:00.000-05:00", "summary" : "Epidemiological studies reveal a strong link between low aerobic capacity and metabolic and cardiovascular diseases. Two-way artificial selection of rats based on low and high intrinsic exercise capacity has produced two strains that also differ in risk for metabolic syndrome (Koch LG, Britton SL. Artificial selection for intrinsic aerobic endurance running capacity in rats. Physiol Genomics 5:45-52, 2001). Here we investigated skeletal muscle characteristics and genotype-phenotype relationships behind high and low inherited aerobic exercise capacity and the link between oxygen metabolism and metabolic disease risk factors in rats derived from generation 18. This population (n=24) of high capacity runners (HCR) and low capacity runners (LCR) differed by 615% in maximal treadmill running capacity. LCR were significantly significantly heavier and had increased blood glucose, serum insulin and triglyceride concentration. HCR had higher resting metabolic rate than LCR. Capillaries/mm2 and capillary-to-fiber ratio were significantly greater in HCR rats in soleus and gastrocnemius and capillary-to-fiber ratio in extensor digitorum longus (EDL) muscle. Subsarcolemmal mitochondrial area was 96% (p<0.01) and intermyofibrillar area was 32% (p<0.05) larger in HCR soleus. Microarray results showed that 126 genes were significantly up-regulated and 113 genes were down-regulated in HCR (p<0.05). Functional clustering and unbiased correlation analysis of muscle microarray data revealed that genes up-regulated in HCR were related to mitochondria, carboxylic acid and lipid metabolism, and oxidoreductase activity. In conclusion, our data show that aerobic capacity is strongly linked to the architecture of energy transfer and corroborate the importance of oxygen metabolism as the determinant of metabolic health and complex metabolic diseases such as metabolic syndrome and type 2 diabetes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20643908" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17332" }, "primaryId" : "GEO:GSE17332", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17332" } ] }, "title" : "Tissue-specific dysregulation of DNA methylation in aging", "dateAssigned" : "2009-07-26T00:00:00.000-05:00", "summary" : "The normal aging process is a complex phenomenon associated with physiological alterations in the function of cells and organs over time. Although an attractive candidate for mediating transcriptional dysregulation, the contribution of epigenetic dysregulation to these progressive changes in cellular function remains unclear. In this study, we employed the genome-wide HELP assay to define patterns of cytosine methylation throughout the rat genome, and the LUMA assay to measure global levels of DNA methylation in the same samples. We studied both liver and visceral adipose tissue, and demonstrated significant differences in DNA methylation with age at >5% of sites analyzed. Furthermore, we showed that epigenetic dysregulation with age is a highly tissue-dependent phenomenon. The most distinctive loci were located at intergenic sequences and conserved non-coding elements, and not at promoters nor at CG-dinucleotide dense loci. Finally, we demonstrated that changes in methylation occur consistently near genes that are involved in metabolism and metabolic regulation, implicating their potential role in the pathogenesis of age-related diseases. We conclude that different patterns of epigenetic dysregulation occur in each tissue over time and may cause some of the physiological changes associated with normal aging.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20497131" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17384" }, "primaryId" : "GEO:GSE17384", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17384" } ] }, "title" : "Gene expression data from the LEC rat model with naturally occuring and oxidative stress induced liver tumorigenesis", "dateAssigned" : "2009-07-28T00:00:00.000-05:00", "summary" : "We reduced several clinicopathological variables by using the Long-Evans Cinnamon rat, a model with naturally occurring and oxidative stress-induced hepatotumorigenesis. Gene expression patterns were analyzed serially by profiling liver tissue from naïve status (4 weeks old) rats through to those with chronic hepatitis (26 and 39 weeks old) to tumor development (67 weeks old).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20015863" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17388" }, "primaryId" : "GEO:GSE17388", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17388" } ] }, "title" : "Gene expression analysis of rat livers treated with pharmaceutical development compounds", "dateAssigned" : "2009-07-28T00:00:00.000-05:00", "summary" : "R1 corresponds to 36, R2 corresponds to 38", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21671310" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17430" }, "primaryId" : "GEO:GSE17430", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17430" } ] }, "title" : "Transcript Profiling of Different CNS Regions in Response to Experimental Restraint Stress on Rats", "dateAssigned" : "2009-07-30T00:00:00.000-05:00", "summary" : "Keywords: Transcriptome analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20218974" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17598" }, "primaryId" : "GEO:GSE17598", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17598" } ] }, "title" : "5-aza-2-deoxycytidine treatment of Swarm rat chondrosarcoma cells", "dateAssigned" : "2009-08-11T00:00:00.000-05:00", "summary" : "The puropose of this experiment was to identify gene expression changes that result from 5-aza-2-deoxycytidine induced DNA demethylation of Swarm rat chondrosarcoma cells. The gene expression profiles of untreated Swarm rat chondrosarcoma cells were compared to the gene expression profiles of Swarm rat chondrosarcoma cells that were treated for 5 passages with a low dose of 5-aza-2-deoxycytidine (0.1uM).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20019818" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17651" }, "primaryId" : "GEO:GSE17651", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17651" } ] }, "title" : "Transitions in infant learning are modulated by dopamine within the amygdala", "dateAssigned" : "2009-08-14T00:00:00.000-05:00", "summary" : "Microarray results showed downregulated dopaminergic presynaptic function in the amygdala with preference learning. Corticosterone injected 8-day-old pups and untreated 12-day-old pups learn aversions and had dopaminergic upregulation in the amygdala.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19783994" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17661" }, "primaryId" : "GEO:GSE17661", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17661" } ] }, "title" : "Modulation of gene expression by rapamycin in hepatic cell lines, WB-F344 and WB311", "dateAssigned" : "2009-08-14T00:00:00.000-05:00", "summary" : "Two rat hepatic cell lines, WB-F344 and WB311, were characterized for the effect of rapamycin on gene expression. The WB311 cell line, which is tumorigenic and resistant to the growth inhibitory effects of rapamycin, was originally derived from the WB-F344 parental hepatic epithelial cell line. The goal of this experiment was to identify genes that responded to rapamycin in the sensitive cells but not the resistant cells, thereby providing insight into the mechanism of rapamycin resistance.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19816606" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17662" }, "primaryId" : "GEO:GSE17662", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17662" } ] }, "title" : "Modulation of gene expression by rapamycin in hepatic cell lines, H5D and GN5", "dateAssigned" : "2009-08-14T00:00:00.000-05:00", "summary" : "Two rat hepatic cell lines, GN5 and H5D, were characterized for the effect of rapamycin on gene expression. These cells lines are tumorigenic and display intermediate sensitivity to the growth inhibitory effects of rapamycin. The goal of this experiment was to assess the effect of rapamycin on gene expression independent of effects on cell proliferation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19816606" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17665" }, "primaryId" : "GEO:GSE17665", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17665" } ] }, "title" : "Methamphetamine preconditioning responses to methamphetamine-induced injury in the rat ventral midbrain", "dateAssigned" : "2009-08-14T00:00:00.000-05:00", "summary" : "Methamphetamine (METH) is an illicit drug which is neurotoxic to the mammalian brain. Numerous studies have revealed significant decreases in dopamine and serotonin levels in the brains of animals exposed to moderate-to-large METH doses given within short intervals of time. In contrast, repeated injections of small nontoxic doses of the drug followed by a challenge with toxic METH doses afford significant protection against monoamine depletion. The present study was undertaken to test the possibility that repeated injections of the drug might be accompanied by transcriptional changes involved in rendering the nigrostriatal dopaminergic system refractory to METH toxicity. Our results confirm that METH preconditioning can provide significant protection against METH-induced striatal dopamine depletion. In addition, the presence and absence of METH preconditioning were associated with substantial differences in the identity of the genes whose expression was affected by a toxic METH challenge.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19915665" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17698" }, "primaryId" : "GEO:GSE17698", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17698" } ] }, "title" : "The genetics of wound healing in tympanic membranes in rats", "dateAssigned" : "2009-08-18T00:00:00.000-05:00", "summary" : "The aim of this study was to identify the genes differentially expressed between timepoints in the week following tympanic membrane perforation in rats. Tissue from 240 individual rats was used in this study following random allocation into timepoint groups to be sacrificed over 7 days. An Agilent one color microarray technique was performed and the results were analyzed using Genespring GX9 software. A total of 3262 genes were identified as significant (p<0.05) and differentially expressed above a two-fold threshold between the timepoints. This study provides a complete genetic review of rat tympanic membrane wound healing over 7 days. The results can be used as a model for other wound healing in other mammals and in different parts of the body. The information on differential gene expression can be used in research towards developing chronic tympanic membrane perforations and also in research to treat acute and chronic tympanic membrane perforations. The microarray was performed on animals in a disease free environment and the genetic information can be compared to future research in disease states of the TM including Otitis media, cholesteatoma, chronic perforation and tympanosclerosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21919009" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17747" }, "primaryId" : "GEO:GSE17747", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17747" } ] }, "title" : "Gene expression profiles in rat lung following intratracheal instillation with C60 fullerene particles", "dateAssigned" : "2009-08-20T00:00:00.000-05:00", "summary" : "Gene expression profiling of the rat lung following intratracheal instillation with C60 fullerene particles was employed to gain insights into these molecular events.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20471445" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17776" }, "primaryId" : "GEO:GSE17776", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17776" } ] }, "title" : "MicroRNA expression in rat soleus muscle during atrophy induced by hindlimb suspension", "dateAssigned" : "2009-08-24T00:00:00.000-05:00", "summary" : "The objective of the study was to identify microRNAs expressed in the rat soleus muscle and determine if their expression was changed in response to hindlimb suspension.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19690046" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17811" }, "primaryId" : "GEO:GSE17811", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17811" } ] }, "title" : "Gene expression-based assessment of the effect of PQQ", "dateAssigned" : "2009-08-25T00:00:00.000-05:00", "summary" : "Pyrroloquinoline quinone (PQQ) is a naturally occurring compound and known to improve growth and reproductive performance when added to diets of PQQ-deprived rodents. To understand its mechanism of action, changes in hepatic gene expression were measured in rats fed diets with or without added PQQ. Of the ~10,000 genes and ESTs analyzed, 4.7% of the transcripts were sensitive to changes in PQQ dietary status. PQQ deprivation generally caused downregulation of genes associated with mitochondriogenesis, cell differentiation, and immune function. These gene expression changes provide the basis for most of the previously published functional observations associated with PQQ deficiency and PQQ administered in pharmacological amounts. To assess PQQ’s potential functions, we used gene expression profiling through microarray technology as part of a comprehensive approach to identify potential pathways and mechanisms. Given that the systemic effects of PQQ deprivation are influenced at levels of dietary intake in the micromolar range, highly purified diets were used to reduce expression from other bioactive factors and xenobiotics, such as those found in typical rodent chow diets. Dietary conditions were also chosen to clarify the response to PQQ deprivation. A goal was to determine if specific changes in dietary protocol or patterns could be used to identify genes important to the function of PQQ. Because it has been observed that mitochondrial-related functions are influenced by PQQ, we hypothesized that changes in genes important to fatty acid and amino acid metabolism and mitochondrial function would be likewise affected by dietary levels of PQQ. The overall study was carried out using two experiments. In this specific experiment, PQQ depletion and repletion was studied to understand the effect of PQQ on gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20491655" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17819" }, "primaryId" : "GEO:GSE17819", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17819" } ] }, "title" : "Estrogen-driven Prolactin-mediated Gene Expression Networks Hormone Induced Prostatic Dysplasia", "dateAssigned" : "2009-08-26T00:00:00.000-05:00", "summary" : "Emerging evidence suggests that estrogen and prolactin (PRL) play a key role in prostate cancer development, yet their relationship and molecular actions in prostate is not well understood. To address this issue, we made the first direct comparison of estrogen and PRL actions in the Noble rat (NBL) prostate dysplasia model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20861223" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17859" }, "primaryId" : "GEO:GSE17859", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17859" } ] }, "title" : "Microarray analysis of rat hepatic gene expression identifies new genes associated with postprandial triglyceridemia", "dateAssigned" : "2009-08-28T00:00:00.000-05:00", "summary" : "The acute response four hours after a fat load of extra virgin olive oil was investigated using DNA microarrays. Hepatic gene expression was analysed in Wistar Rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21196280" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17928" }, "primaryId" : "GEO:GSE17928", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17928" } ] }, "title" : "Expression profiling of rat MHC and NKC genes in skin explant assays reveals genes that are regulated in GVHD", "dateAssigned" : "2009-09-01T00:00:00.000-05:00", "summary" : "The major histocompatibility complex (MHC) is the most important genomic region that contributes to the genetic risk of graft rejection and graft versus host disease (GVHD) after haematopoietic stem cell transplantation. Therefore, MHC matching is most essential for the success of clinical transplantations. However, the MHC contains in addition to MHC class I and class II genes that are genotyped for selection of donors further so far unidentified genes that also contribute significantly to the risk to develop acute GVHD. It is difficult to identify these MHC genes by genetic association studies alone due to linkage disequilibrium in this region. Therefore, we aimed to identify MHC genes that might be involved in the pathohysiology of GVHD by expression profiling. To reduce the complexity of our model, we used genetically well-defined inbred rat strains (PVG and BN) and skin explant assays, an in-vitro-model of graft versus host reaction (GVHR), to analyse the expression of MHC and natural killer complex (NKC) genes in a cutaneous GVHR by a custom microarray. A higher percentage of genes in these immunologically highly important genomic regions were regulated than in the rest of the genome. We observed a statistically significant regulation of 25 MHC and 6 NKC genes and 168 other genes (i.e., 4.9%, 14.0%, and 6.6%, respectively) in rat skin explants cultured in the presence of pre-stimulated allogeneic lymphocytes compared to control samples cultured in the presence of syngeneic lymphocytes. Seven MHC and 3 NKC genes were selected for analysis by quantitative real-time polymerase chain reaction PCR. Most of the results of the microarray were confirmed in the same experimental set that was used for the microarray analysis and in a second independent experimental set of skin explant samples. In addition, GVHD-affected skin lesions of transplanted rats were analysed and similar regulations of most of the selected MHC and NKC genes were observed. Thus, our skin explant model of GVHR is informative for the gene regulation during GVHD. Interestingly, the human homologues of several of the regulated genes are polymorphic and could therefore contribute to the genetic risk of GVHD. These genes include RT1-Dmb, C2, Aif1, Spr1, Ubd, and Olr1. The human homologues of these genes might be useful for risk assessment and diagnosis of GVHD in patients.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21305040" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17929" }, "primaryId" : "GEO:GSE17929", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17929" } ] }, "title" : "Expression data from rat (Sprague Dawley) brain subjected to MCAo.", "dateAssigned" : "2009-09-01T00:00:00.000-05:00", "summary" : "We studied the global gene expression of the reduction in infarct volume using Affymetrix Gene Chips. We analysed all the genes that were up or down regulated in the study.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19775433" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17959" }, "primaryId" : "GEO:GSE17959", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE17959" } ] }, "title" : "Gene expression profiles from nandrolone-treated rats with denervation", "dateAssigned" : "2009-09-03T00:00:00.000-05:00", "summary" : "We showed that nandrolone attenuated subacute, but not acute, denervation atrophy and upregulation of MAFbx. The present study explored the molecular determinants for this time-dependent effect using microarray analysis to identify genes that were differentially regulated by administration of nandrolone for 7 days beginning either concomitantly with denervation (7 days) or 29 days later (35 days)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20969782" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18016" }, "primaryId" : "GEO:GSE18016", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18016" } ] }, "title" : "Identification of genes which are responsible for induction of the initial differentiation process of PC12 cells", "dateAssigned" : "2009-09-08T00:00:00.000-05:00", "summary" : "Continuous NGF stimulation induces PC12 cell differentiation; however, it is unclear whether NGF is continuously required for differentiation. We found that discontinuous NGF stimulation, consisting of the first transient stimulation followed by an interval and the second sustained stimulation, similarly induces differentiation. The first stimulation did not induce neurite extension, whereas the second stimulation induced fast neurite extension; therefore, the first stimulation is required as prerequisite conditions. This indicates that the action of NGF can be divided into two processes: the first stimulation-driven latent process and the second stimulation-driven extension process. The latent process appears to require ERK and transcription, but not PI3K, activities, whereas the extension-process requires ERK and PI3K, but not transcription, activities. We also found that NGF in the first stimulation can be replaced by PACAP, but not by insulin, EGF, bFGF or forskolin, whereas NGF in the second stimulation cannot be replaced by any of these stimulants. These findings allowed us to identify potential genes specifically involved in the latent process, rather than in other processes. These results demonstrate that NGF induces differentiation of PC12 cells via mechanically distinct processes: the ERK-driven and transcription-dependent latent process; and the ERK- and PI3K-driven, and transcription-independent extension process.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20126402" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18055" }, "primaryId" : "GEO:GSE18055", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18055" } ] }, "title" : "Expression profiling in dopaminergic brain structures of rats self-administering cocaine", "dateAssigned" : "2009-09-10T00:00:00.000-05:00", "summary" : "We used Affymetrix microarrays to identify genes the expression of which was up-regulated or downregulated during this process.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20132486" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18129" }, "primaryId" : "GEO:GSE18129", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18129" } ] }, "title" : "MicroRNA Expression in Rat Myocardial Infarction intervened by propranolol", "dateAssigned" : "2009-09-16T00:00:00.000-05:00", "summary" : "We established a rat model of myocardial Infarction by performing a surgical operation of left anterior descending coronary artery occlusion under sterie conditions. Wistar rats were previously randomly divided into 4 groups: control, ischemia, ischemia-propranolol, and non-ischemia-propranolol. Our data suggested that propranolol could reverse many microRNAs with too high or too low expression in the ischemia group versus control group.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21386882" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18133" }, "primaryId" : "GEO:GSE18133", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18133" } ] }, "title" : "Genome-wide analysis of gene expression in colon and brain during the suckling period.", "dateAssigned" : "2009-09-16T00:00:00.000-05:00", "summary" : "Gene expression was analysed in the colon and brain of normal rat pups from late prenatal through early postnatal development. Tissue was isolated from pups one day prior to the anticipated date of birth and throughout the suckling period until the end of weaning.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20011510" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18157" }, "primaryId" : "GEO:GSE18157", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18157" } ] }, "title" : "Gene expression underlying the effects of biotin deficiency in rat liver, worms and yeast", "dateAssigned" : "2009-09-17T00:00:00.000-05:00", "summary" : "We used affymetrix microarrays to detail the global gene expression underlying the effects of biotin deficiency in Rattus norvegicus liver, Caenorhabditis elegans and Saccharomyces cerevisiae and identified distinct classes of up-regulated genes during this event.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20798549" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18162" }, "primaryId" : "GEO:GSE18162", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18162" } ] }, "title" : "Effects of moderate ethanol consumption during pregnancy on placental gene expression", "dateAssigned" : "2009-09-18T00:00:00.000-05:00", "summary" : "We conducted a preliminary investigation to determine whether ethanol-induced alterations in placental gene expression may have some utility as a diagnostic indicator of maternal drinking during pregnancy as well as a prognostic indicator of risk for adverse neurobehavioral outcomes in affected offspring.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20053520" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18175" }, "primaryId" : "GEO:GSE18175", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18175" } ] }, "title" : "Transcriptomic alterations in a myoblast cell line infected with four distinct strains of Trypanosoma cruzi ", "dateAssigned" : "2009-09-19T00:00:00.000-05:00", "summary" : "We examined the extent to which different Trypanosoma cruzi strains induce transcriptomic changes in cultured L6E9 myoblasts 72 hours or 48 hours after infection with four strains of the parasite [Brazil (TCI); Y, CL and Tulahuen (TC II) strains]. Expression of 6,289 distinct fully annotated unigenes was quantified with 27k rat oligonucleotide arrays in each of the four replicas of all control and infected RNA samples. Considering changes >1.5-fold and p-val<0.05, the Tulahuen strain was the most disruptive to host transcriptome, with (17% significantly altered genes), while in Y strain altered only 6% of the genes were altered. The significantly altered genes in the infected cells were largely different among the four strains, with only 21 genes changed in the same direction being similarly changed by all four strains. However, when expression ratios of all genes were compared, myoblasts infected with different strains showed proportional overall genbe expression alterations. These results indicate that infection with different parasite strains modulates similar but not identical pathways in the host cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20439965" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18257" }, "primaryId" : "GEO:GSE18257", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18257" } ] }, "title" : "Transcriptional profiling of the rat hypothalamus response to TCDD", "dateAssigned" : "2009-09-24T00:00:00.000-05:00", "summary" : "Rodents exposed to the environmental contaminant, TCDD, suffer from a number of acute and chronic toxicities, including lethality and a wasting syndrome. Hypothesizing that the wasting syndrome may be caused by changes in neural control of energy flux and metabolism, we profiled the transcriptional response of rat hypothalamus to TCDD. We employed two separate rat strains: the Long-Evans strain is sensitive to TCDD toxicities while the Han/Wistar strain is over four orders of magnitude more resistant. Surprisingly, few transcriptional changes were induced by TCDD in either strain. Only four genes were altered in Long-Evans rats, including three classic TCDD-responsive genes: Cyp1a1, Cyp1b1, and Nqo1. These three genes were also altered in Han/Wistar rats, along with 133 additional genes. However, the magnitudes of alteration of these additional genes was very modest, with most changes well below two-fold in magnitude. We therefore concluded that rat hypothalamus is mostly refractory to TCDD exposure, at least at the doses and time-points surveyed here.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18260" }, "primaryId" : "GEO:GSE18260", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18260" } ] }, "title" : "Expression data for kidney progenitor tissue from rat embryo at E13", "dateAssigned" : "2009-09-24T00:00:00.000-05:00", "summary" : "We used microarrays to find novel genes regulating early kidney formation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19934016" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18266" }, "primaryId" : "GEO:GSE18266", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18266" } ] }, "title" : "Leukocyte accumulation in graft blood vessels during self-limiting acute rejection of rat kidneys Immunobiology", "dateAssigned" : "2009-09-24T00:00:00.000-05:00", "summary" : "Acute rejection episodes trigger chronic renal allograft vasculopathy. Numerous leukocytes, predominantly monocytes, accumulate in graft blood vessels during reversible acute rejection preceding chronic rejection of rat kidneys. We speculate that they contribute to transplant vasculopathy and set out to characterize them. Allogeneic renal transplantation was performed in the Fischer 344 to Lewis rat strain combination, Lewis isografts served as controls. Leukocytes were harvested by intensive perfusion of graft blood vessels and subjected to flow cytometry, quantitative RT-PCR and genome-wide transcriptional profiling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21035231" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18297" }, "primaryId" : "GEO:GSE18297", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18297" } ] }, "title" : "Mild food restriction and gene expression profile", "dateAssigned" : "2009-09-27T00:00:00.000-05:00", "summary" : "The aim of this study is to obtain the gene expression profiles of the liver of young growing rats after mild restriction of food intake for one week or one month.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21256116" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18298" }, "primaryId" : "GEO:GSE18298", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18298" } ] }, "title" : "Gene expression profiling of aortic media after long-term treatment with an angiotensin II-receptor blocker, Losartan", "dateAssigned" : "2009-09-27T00:00:00.000-05:00", "summary" : "Rats (Wag/Rij, females) were chronically treated with Losartan (20mg/d), an angiotensin II-receptor blocker during 9 months. Gene expression profiling was performed on aortic media to understand the long-term effect of this molecule on the cardiovascular system.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18301" }, "primaryId" : "GEO:GSE18301", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18301" } ] }, "title" : "Transcriptional profiling of the rat adipose tissue response to TCDD", "dateAssigned" : "2009-09-28T00:00:00.000-05:00", "summary" : "Rodents exposed to the environmental contaminant, TCDD, suffer from a number of acute and chronic toxicities, including lethality and a wasting syndrome. Hypothesizing that the wasting syndrome may be caused by changes in adipose tissue -- either in its hormonal regulation or in homeostatic effects -- we profiled the transcriptional response of rat white adipose to TCDD. We employed two separate rat strains: the Long-Evans strain is sensitive to TCDD toxicities while the Han/Wistar strain is over four orders of magnitude more resistant. One day after TCDD exposure few genes were altered in either strain, but after four days a modest number of transcriptional alterations were observed. Strikingly, TCDD had far fewer effects than did a feed-restriction protocol intended to mimic the wasting syndrome itself. Notably several classic TCDD-responsive genes were modulated at all time-points, including Cyp1a1, Cyp1b1, and Nqo1. We therefore concluded that rat adipose tissue is unlikely to be the primary driver of the wasting syndrome, and that another tissue is likely involved.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26232522" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18356" }, "primaryId" : "GEO:GSE18356", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18356" } ] }, "title" : "Network analysis of differentially expressed genes in a rat model of neonatal HI encephalopathy +/- antioxidant", "dateAssigned" : "2009-10-01T00:00:00.000-05:00", "summary" : "Neonatal hypoxic-ischemic (HI) encephalopathy can lead to severe brain damage, and is a common cause of neurological handicaps in adulthood. The modified Levine method (Rice model) has been widely used as an animal model of this condition, which can be rescued by the administration of an antioxidant such as 3-methyl-1-phenyl-2-pyrazolin-5-one (MCI-186). In the present study, by using the Rice model, we performed comprehensive gene expression and gene network analyses of neonatal HI brain insult with and without MCI-186 administration via a DNA microarray to help elucidate the molecular events responsible for the selective vulnerability of neurons to an HI insult and the underlying mechanisms of the effect of MCI-186 on the pathophysiological events. A large difference in gene expression was observed between the Rice model and the control. By performing a clustering analysis of the gene expression pattern after the HI brain insult, we found the following 3 clusters: (i) a cluster of strongly upregulated genes mainly consisting of genes related to immune responses; (ii) a cluster of mildly upregulated genes mainly consisting of genes related to cellular movement, growth and proliferation, and cell death; and (iii) a cluster of downregulated genes mainly consisting of genes related to neuronal activity. The effect of MCI-186 administration on gene expression was much less than and contrary to that of the HI brain insult. The genes upregulated and downregulated on MCI-186 administration were closely related to neuronal activity and immune responses, respectively, thereby reflecting the protective effect of MCI-186 on an HI brain insult.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20191329" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18687" }, "primaryId" : "GEO:GSE18687", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18687" } ] }, "title" : "Ventral striatal responses to reduced food intake in healthy animals and rats bearing small tumors", "dateAssigned" : "2009-10-22T00:00:00.000-05:00", "summary" : "Anorexia is frequently observed during cancer and associated with increased morbidity and mortality. Our previous work has shown the presence of transcription factors in the ventral striatum of anorectic tumor-bearing rats. The aim of the present study was, therefore, to assess expression of neuropeptides, neurotransmitter-synthesizing enzymes and receptors in this structure. Morris hepatoma 7777 cells injected subcutaneously in Buffalo rats provoked a 15% reduction in food intake and 10% lower body weight when the tumor represented 1-2% of body mass. Mircorarrays and real-time PCR revealed increased ventral striatal prostaglandin D synthase expression in food-restricted animals compared to anorectic tumor-bearing rats. These findings indicate that reduced ventral striatal prostaglandin D synthesis underlies cancer-associated anorexia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21334429" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18688" }, "primaryId" : "GEO:GSE18688", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18688" } ] }, "title" : "Hypothalamic responses to reduced food intake in healthy animals and rats bearing small tumors", "dateAssigned" : "2009-10-22T00:00:00.000-05:00", "summary" : "Anorexia is frequently observed during cancer and associated with increased morbidity and mortality. Our previous work has shown the presence of transcription factors in the hypothalamus of anorectic tumor-bearing rats. The aim of the present study was, therefore, to assess expression of neuropeptides, neurotransmitter-synthesizing enzymes and receptors in this structure. Morris hepatoma 7777 cells injected subcutaneously in Buffalo rats provoked a 15% reduction in food intake and 10% lower body weight when the tumor represented 1-2% of body mass. Real-time PCR showed that tumor-bearing rats did not display the increase in hypothalamic agouti-related peptide mRNA observed in food-restricted weight-matched animals. These findings indicate that blunted hypothalamic AgRp mRNA expression underlies cancer-associated anorexia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21334429" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18753" }, "primaryId" : "GEO:GSE18753", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18753" } ] }, "title" : "MOLECULAR MECHANISMS ASSOCIATED WITH MARKERS OF HEPATOCARCINOGENICITY DURING A 14 DAY DIETARY STUDY IN MALE FISCHER RAT", "dateAssigned" : "2009-10-27T00:00:00.000-05:00", "summary" : "To investigate the molecular mechanisms associated with initial dose-related events that are linked to the development of liver tumours: liver growth; cell proliferation; changes in histopathology such as hypertrophy", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20053287" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18803" }, "primaryId" : "GEO:GSE18803", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18803" } ] }, "title" : "Adult and Neonatal dorsal horn gene expression 7 day post sciatic nerve SNI injury", "dateAssigned" : "2009-10-29T00:00:00.000-05:00", "summary" : "Keywords: Two way analysis of differential regulation", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19923276" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18812" }, "primaryId" : "GEO:GSE18812", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18812" } ] }, "title" : "Comparative genome analysis of exosomal mRNA derived from Tspan8-overexpressing and Tspan8-negative rat pancreas tumors", "dateAssigned" : "2009-10-29T00:00:00.000-05:00", "summary" : "We recently described that tumor-derived exosomes containing the tetraspanin Tspan8 induce angiogenesis. However, not much is known about exosome-endothelial cell interactions and there are no clues on the role of tetraspanins, which are a constitutive component of exosomes. We used the stably Tspan8 expressing rat adenocarcinoma cell line AS-Tspan8, to explore how exosomal Tspan8 supports angiogenesis. Tspan8 contributed to a selective recruitment of proteins and mRNA into exosomes. A genome-wide microarray analysis revealed that both, AS- and AS-Tspan8-exosomes contain about 1500 transcripts, from which 285 are over 3 fold enriched in AS-Tspan8-exosomes. We confirmed high levels mRNA of transcription factors MycN and Spi-C, elongation factor B(SIII), TCEB-1, fibroblast growth factor binding protein 1 (FGFBP1) and growth and differentiation factor-3 (GDF3) in AS-Tspan8-exosomes compared to AS-exosomes and to the parental cells by RT-PCR. VEGF mRNA was not enriched in AS-Tspan8 cells or exosomes. Expression of CCL20, prothrombin, bone morphogenetic protein-2, several Ras and MAPK family members and a phosphatase2A subunit was below the detection level in exosomes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20124479" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18845" }, "primaryId" : "GEO:GSE18845", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18845" } ] }, "title" : "Rapamycin effect on gene expression: dependence on c-Myc", "dateAssigned" : "2009-11-02T00:00:00.000-06:00", "summary" : "This experiment utilized rat fibroblasts that are wild-type for c-Myc (TGR-1 cells) and null for c-Myc (HO15.19 cells). Both were treated treated with rapamycin for 24 hr (comparison group, vehicle control).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20140209" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18860" }, "primaryId" : "GEO:GSE18860", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18860" } ] }, "title" : "Regulation of neuronal gene and miRNA expression by the complement protein C1q associated with neuroprotection", "dateAssigned" : "2009-11-03T00:00:00.000-06:00", "summary" : "Use of the unbiased whole genome microarray approach to identify genes regulated by C1q.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21368058" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18945" }, "primaryId" : "GEO:GSE18945", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18945" } ] }, "title" : "Tonicity iduced changes in gene expression in IMCD cells and the effect of Cyclosporin A", "dateAssigned" : "2009-11-09T00:00:00.000-06:00", "summary" : "Cyclosporin A induces expression of proapoptotic factors when cells are challenged by increased tonicity", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21220920" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18998" }, "primaryId" : "GEO:GSE18998", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE18998" } ] }, "title" : "Gene expression microarray analysis of early oxygen-induced retinopathy (OIR)", "dateAssigned" : "2009-11-12T00:00:00.000-06:00", "summary" : "Different inbred strains of rats differ in their susceptibility to OIR, an animal model of human retinopathy of prematurity. We examined gene expression profiles in Fischer 344 (F344, resistant to OIR) and Sprague Dawley (SD, susceptible to OIR) rats at the early time point of day 3 to identifying gene pathways related to the underlying genetic cause of phenotypic differences between strains.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20157446" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19054" }, "primaryId" : "GEO:GSE19054", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19054" } ] }, "title" : "Small RNA expression and strain specificity in the rat", "dateAssigned" : "2009-11-17T00:00:00.000-06:00", "summary" : "Background Digital gene expression (DGE) profiling has become an established tool to study RNA expression. Here, we provide an in-depth analysis of small RNA DGE profiles from two different rat strains (BN-Lx and SHR) from six different rat tissues (spleen, liver, brain, testis, heart, kidney). We describe the expression patterns of known and novel micro (mi)RNAs and piwi-interacting (pi)RNAs. We confirmed the expression of 589 known miRNAs and identified 56 miRNAs homologous to known human or mouse miRNAs, as well as 45 new rat miRNAs. Furthermore, we confirmed specific A to I editing in brain for mir-376a/b/c and identified mir-377 as a novel editing target. In accordance with earlier findings, we observed a highly tissue-specific expression pattern for all tissues analyzed. The brain was found to express the highest number of tissue-specific miRNAs, followed by testis. Notably, our experiments also revealed robust strain-specific differential miRNA expression in the liver that is caused by genetic variation between the strains. Finally, we identified two types of germline-specific piRNAs in testis, mapping either to transposons or in strand-specific clusters. Taken together, the small RNA compendium described here advances the annotation of small RNAs in the rat genome. Strain and tissue-specific expression patterns furthermore provide a strong basis for studying the role of small RNAs in regulatory networks as well as biological process like physiology and neurobiology that are extensively studied in this model system.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20403161" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19057" }, "primaryId" : "GEO:GSE19057", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19057" } ] }, "title" : "Gene expression profile of liver tissue in low-dose, repeated diethylnitrosamine (DEN)-treated rat treated with erlotinib", "dateAssigned" : "2009-11-17T00:00:00.000-06:00", "summary" : "Keywords: Cirrhotic liver, Expression array, Illumina, Signatures, Outcome prediction", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24677197" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19058" }, "primaryId" : "GEO:GSE19058", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19058" } ] }, "title" : "Identification of cathepsin L as a potential sex-specific biomarker for renal damage", "dateAssigned" : "2009-11-17T00:00:00.000-06:00", "summary" : "The renin-angiotensin system is a well-known regulator of blood pressure and plays an important role in the pathogenesis of cardiovascular disease and renal damage. Genetic factors, including single nucleotide polymorphisms and sex, are increasingly recognized as potential risk factors for the development of cardiovascular disease. Double transgenic rats (dTGR), harboring human renin and angiotensinogen genes, were used in this study to investigate potential sex differences influencing renal function and renal gene expression. dTGR males and females had comparable increases in blood pressure, whereas body weight, albuminuria/proteinuria and urine flow rate were higher in males. At eight weeks of age renal plasma flow and glomerular filtration rate were proportionally lower in males, and renal vascular resistance tended to be higher. Males developed more severe tubulointerstitial and vascular lesions. By the end of week eight, 40% of the males, but none of the females had died. Genome expression studies were performed with RNA from kidneys of 7-week-old male and female dTGR and control rats to further investigate the sex-related differences on a molecular level. Forty-five genes showed sex-dependent expression patterns in dTGR that were significantly different compared to controls. Cathepsin L, one of the genes differentially expressed between the sexes, was shown to be also strongly associated with the degree of renal injury. In dTGR, urinary CTSL at week 7 was higher in males (ng/24 hours: M 512+/-163, F 132+/-70). These results reveal a potential new biomarker for the personalized diagnosis and management of chronic kidney disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21357272" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19106" }, "primaryId" : "GEO:GSE19106", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19106" } ] }, "title" : "Expression data from PDGF-BB-treated rat aortic smooth muscle cells", "dateAssigned" : "2009-11-19T00:00:00.000-06:00", "summary" : "We used whole-genome expression arrays to to identify genes associated with SMC phenotypic modulation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19926569" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19175" }, "primaryId" : "GEO:GSE19175", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19175" } ] }, "title" : "Differential gene expression in lactating rats compared against age matched virgin controls", "dateAssigned" : "2009-11-24T00:00:00.000-06:00", "summary" : "Lactation is a time of significantly increased energy demands imposed by the suckling young that requires a proportional adjustment in the ability of the lactating dam to absorb nutrients and to synthesize critical biomolecules to meet the dietary needs of both the offspring and the dam. We have shown an increase in the size and hydrophobicity of the bile acid pool during lactation [1], implying an increased absorption and disposition of lipids, sterols, nutrients, and xenobiotics. In order to investigate changes at the level of mRNA, we utilized an exon array and calculated gene level summaries to investigate changes in gene expression in the liver, duodenum, jejunum, and ileum of lactating dams when compared against age-matched virgin controls.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21291544" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19210" }, "primaryId" : "GEO:GSE19210", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19210" } ] }, "title" : "Transition from Compensated Hypertrophy to Systolic Heart Failure in the Spontaneously Hypertensive Rat", "dateAssigned" : "2009-11-26T00:00:00.000-06:00", "summary" : "Besides these individual transcripts, gene set enrichment analysis (GSEA) identified multiple enriched pathways with HF, most prominent of the altered signaling pathways involved TGF-ß and insulin signaling. GESA analysis additionally identified altered gene sets involving inflammation, oxidative stress, cell degradation and cell death, among others (all p<0.01). In contrast to diastolic HF where few transcripts are reported to be altered, our data indicate multiple genes and pathways involved in a variety of biological processes characterize the onset of systolic HF, consistent with many functional and structural changes present in the failing hypertensive heart.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20006699" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19250" }, "primaryId" : "GEO:GSE19250", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19250" } ] }, "title" : "Comparative Gene Expression Profiling of Olfactory Ensheathing Cells from Olfactory Bulb and Olfactory Mucosa", "dateAssigned" : "2009-12-01T00:00:00.000-06:00", "summary" : "The aim of this study was to use global gene expression profiling to define intrinsic molecular differences that distinguish olfactory ensheathing cells from mucosa (OM-OECs) from olfactory ensheathing cells from olfactory bulb (OB-OECs). 10,000 OECs from olfactory mucosa (OM) or olfactory bulb (OB) were isolated from 4 rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19277" }, "primaryId" : "GEO:GSE19277", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19277" } ] }, "title" : "Kainic acid-administered Rat brain: control vs Ketogenic diet-fed", "dateAssigned" : "2009-12-02T00:00:00.000-06:00", "summary" : "The ketogenic diet has long been used to treat epilepsy, but its mechanism is not yet clearly understood. To explore the potential mechanism, the changes in gene expression induced by the ketogenic diet in the rat kainic acid (KA) epilepsy model were analyzed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20635438" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19290" }, "primaryId" : "GEO:GSE19290", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19290" } ] }, "title" : "Cardiotoxicity of tubulin binders", "dateAssigned" : "2009-12-02T00:00:00.000-06:00", "summary" : "The use of tubulin binders (TBs) in oncology indications often is associated with cardiotoxicity, the mechanism of which has not been elucidated. We observed that a single administration of TBs to rats caused an increase in the number of mitotic figures in the myocardial interstitium after 24 hours. We therefore hypothesized that interstitial cells are the primary target of TBs. To test this hypothesis, we evaluated the acute effects of a single intravenous administration of 3 reference TBs, colchicine (0.2 and 2 mg/kg), vinblastine (0.5 and 3 mg/kg), and vincristine (0.1 and 1 mg/kg) 6 and 24 hours after dosing. Mitotic arrest was identified at 24 hours in all high-dose groups based on an increase in the number of mitotic figures in the interstitium coupled with a dramatic decrease in the number of Ki67-positive interstitial cells. Analysis of the myocardial transcriptomic data further supported G2/M cell cycle arrest 6 hours after dosing with the high-dose groups of all 3 compounds. Apoptotic figures and an increase in the number of cleaved caspase 3-positive cells were identified at 6 and 24 hours at the highest dose of each compound almost exclusively in interstitial cells; a few cardiomyocytes were affected as well. Transcriptomic data further suggested that some of the affected interstitial cells were endothelial cells based on the up-regulation of genes typically associated with vascular damage and down-regulation of Endothelial Cell-Specific Molecule 1 and Apelin. Taken together, these data identify endothelial cells of the myocardium as the primary target of the cardiotoxicity of TBs and identify cell cycle arrest as the mechanism of this toxicity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19292" }, "primaryId" : "GEO:GSE19292", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19292" } ] }, "title" : "Thiamine supplementation prevents obesity and obesity-associated metabolic disorders in OLETF rats.", "dateAssigned" : "2009-12-03T00:00:00.000-06:00", "summary" : "Thiamine prevents diabetic complications, and its deficiency, resulting from mutation of thiamine transporter gene SLC19A2 has been linked to diabetes mellitus. We previously found that thiamine mitigates metabolic disorders in spontaneous hypertensive rats, harboring defects in glucose and fatty acid metabolism. The current study extends our hypothesis that that thiamine intervention may impact metabolic abnormalities in polyphagia-induced Otsuka Long-Evans Tokushima Fatty (OLETF) rats that lack functional cholecystokinin A receptors. Male OLETF rats exhibit progressive obesity and metabolic disorders similar to human metabolic syndrome. Male OLETF rats (4-week-old) were given free access to water containing either 0.2 % or 0 % of thiamine for 51 weeks. At the end of treatment, blood parameters and cardiac functions were analyzed. After sacrifice, the organs were removed and weights of organs and histological findings were evaluated. In addition, differential gene expression in the liver was analyzed. Thiamine intervention averted obesity, mainly resulting from reduction of visceral adiposity, and prevented metabolic disorders in OLETF rats. Histological evaluation revealed that thiamine alleviated adipocyte hypertrophy, steatosis in the liver, heart, and skeletal muscle, interstitial fibrosis in the heart and kidney, fatty degeneration in the pancreas, thickening of the basement membrane of vasculature, and glomerulopathy and mononuclear cell infiltration in the kidney. Cardiac and renal functions were preserved in thiamine treatment. Seventy-six genes showed at least two-fold difference in hepatic expression with thiamine treatment. Several of them participated in carbohydrate metabolism (Hk1, Pygb, Slc2a8, Rtn4, Rhbdl1, and Tspan8), lipid metabolism (Pla2g15, Por, and Lmf1), vascular physiology (S1pr1, Epha8, Rtn4, Slc7a13, Cdh15, Itga9, Cd151, Cd40lg, Nid1 and Lamb1), and carcinogenesis (Lmo7, Fgfr3, and Dmbt1). Modification of transcript expression well accorded with the findings of blood parameters and organ morphologies. Thiamine prevented polyphagia-induced obesity and metabolic and functional disorders in OLETF rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19313" }, "primaryId" : "GEO:GSE19313", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19313" } ] }, "title" : "Comparative gene expression analysis of the rat gastrointestinal tract epithelia", "dateAssigned" : "2009-12-03T00:00:00.000-06:00", "summary" : "Background: The molecular basis of segment specific epithelial functions of the stomach and bowel has not been established. Regionally unique molecular properties of epithelial cells can be identified using cell-specific gene expression in each epithelial region by comparative mRNA analysis. Aim: To describe segment-specific epithelial mRNA content by comparative mRNA analysis of purified epithelial cell suspensions of stomach, small and large bowel. Results: 12% of all annotated genes show segment specific enrichment. The gastric (>3000 genes) and ileal (519 genes) mucosa show the most diverse expression profile. (a) Stomach: The gastric mucosa expresses the machinery for acid secretion, digestive enzyme release, and hormone release by gastric enteroendocrine cells. Associated with acid secretion is a specific set of K+, Cl-, and bicarbonate channels. Novel is a pathway for glucose and fatty acid sensing, iodine and glutamate uptake, and taurine synthesis. Specific sets of transcription factors control epithelial (Barx1, Runx) and enteroendocrine (FoxA2/N4) cell differentiation. (b) Small Bowel: This epithelium expresses genes coding for a unique fructose/glucose uptake and utilization mechanism. Enteroendocrine signalling to the gastric function is present. The upper portion expresses genes for iron uptake, bicarbonate secretion, and detoxification of food contents. Epithelial differentiation is transcriptionally controlled by Meis2/Pdx1 and Onecut 2. Expression of digestive enzymes, lipid/bile acid uptake and utilization increases distally. The ileal epithelium is also involved in innate and acquired immune defence, regulation of motility, and electrolyte and water re-absorption. Transcriptional regulation of enterocyte and goblet cell differentiation is mainly controlled by increasing expression of Cdx1 and 2. (c) Colon: This epithelium is mainly involved in Ca++-, K+, and water re-absorption, fatty acid uptake and sensing, and innate and acquired immune defence. Epithelial differentiation is controlled by Hox transcription factors in addition to Cdx1/2. Conclusion: This regional survey of gene expression by the GI tract epithelium reveals unique epithelial properties, raising several important questions as to the role of the proteins encoded in gut physiology.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21177383" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19354" }, "primaryId" : "GEO:GSE19354", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19354" } ] }, "title" : "Expression data for rno-miR-146a overexpressing cell line HSC-2", "dateAssigned" : "2009-12-07T00:00:00.000-06:00", "summary" : "We used Affymetrix rat genome RAT230 2.0 chip to monitor global transcriptome changes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19366" }, "primaryId" : "GEO:GSE19366", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19366" } ] }, "title" : "Genomic-Derived Markers for Early Detection of Calcineurin Inhibitor Immunosuppressant–Mediated Nephrotoxicity", "dateAssigned" : "2009-12-07T00:00:00.000-06:00", "summary" : "The use of calcineurin inhibitor (CI) immunosuppressants has significantly improved the early allograft survival rate in organ transplantation. However, CI therapy has been associated with chronic nephrotoxicity, which limits their long-term utility. In order to understand the mechanisms of the toxicity, we analyzed the gene expression changes that underlie the development of CI immunosuppressant-mediated nephrotoxicity, in male Sprague-Dawley (SD) rats dosed daily with cyclosporine (CsA), FK506 or rapamycin (Rapa) for 1 to 28 days. We identified a group of genes, whose expression in rat kidney is quantitatively correlated with CI-induced kidney injury as observed in changes in blood urea nitrogen (BUN) levels and kidney histopathology. These genes include both up-regulated genes, such as Ren1 and Klks3, and down-regulated genes, such as Calb1, Egf, NCC, and kidney specific Wnk1 (KS-Wnk1). Using the down-regulated genes alone we successfully predicted CI immunosuppressant-mediated kidney injury in rats following 7 days of treatment. Among these genes are two mechanism-related genes, NCC and KS-Wnk1, both of which are involved in the sodium transport in the distal nephrons. The down-regulation of both genes at the mRNA and protein level in rat kidney following CI treatment was confirmed by quantitative RT-PCR and immunohistochemical staining, respectively. We hypothesize that decreased expression of NCC may cause reduced sodium chloride reabsorption in the distal tubules, and contribute to the prolonged activation of the Renin-Angiotensin-System (RAS), a demonstrated contributor to the development of CI-induced nephrotoxicity in both animal models and clinical settings. Therefore, NCC and KS-Wnk1 could potentially be used as biomarkers for early detection and prevention of CI-related nephrotoxicity in clinical practice.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21865292" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19380" }, "primaryId" : "GEO:GSE19380", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19380" } ] }, "title" : "Gene expression from primary brain cell cultures and RNA mixtures.", "dateAssigned" : "2009-12-08T00:00:00.000-06:00", "summary" : "Keywords: Primary cell cultures", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21983921" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19394" }, "primaryId" : "GEO:GSE19394", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19394" } ] }, "title" : "Borna disease virus phosphoprotein expression affects glial functions in the C6 glioma cells", "dateAssigned" : "2009-12-09T00:00:00.000-06:00", "summary" : "Borna disease virus (BDV) is a highly neurotropic negative-strand RNA virus that belongs to the Mononegavirales. Many reports demonstrated that natural infection of BDV occurs worldwide in a variety of vertebrate species, suggesting that host range of this virus includes all warm-blooded animals. BDV persistently infects the central nervous system (CNS) of many animal species and causes neurobehavioral disorders resembling autism, such as anxiety, aggression, hyperactivity, abnormal play behavior, and cognitive deficits. We previously reported the generation of transgenic mice expressing BDV phosphoprotein (P) selectively in astrocytes. This transgenic mouse, P-Tg, showed striking neurobehavioral abnormalities resembling those in BDV-infected animals, such as enhanced intermale aggressiveness, hyperactivity and spatial reference memory deficit. To reveal the molecular mechanisms how glial cells induce these abnormalities, we performed microarray analysis using C6 rat glioma cells expressing either GFP (C6-GFP) or BDV P (C6-P). Sixty-eight genes are significantly affected in C6-P cells. The genes, whose products are localized at the extracellular region, were enriched in the differentially expressed genes in C6-P cells. Furthermore, gene ontology analysis revealed an emphasis on genes involved in morphogenesis. It is highly likely that the secretion of astrocyte factors may be widely dysregulated in the P-Tg, leading to the astrocyte hypofunction in the brain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21325425" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19460" }, "primaryId" : "GEO:GSE19460", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19460" } ] }, "title" : "Cyst formation in the PKD2 (1-703) transgenic rat precedes deregulation of proliferation-related pathways", "dateAssigned" : "2009-12-14T00:00:00.000-06:00", "summary" : "Polycystic Kidney Disease is characterized by the formation of large fluid-filled cysts that eventually destroy the renal parenchyma leading to end-stage renal failure. Although remarkable progress has been made in understanding the pathologic mechanism of the disease, the precise orchestration of the early events leading to cyst formation is still unclear. Abnormal cellular proliferation was traditionally considered to be one of the primary irregularities leading to cyst initiation and growth. Consequently, many therapeutic interventions have focused on targeting this abnormal proliferation, and some have even progressed to clinical trials. However, the role of proliferation in cyst development was primarily examined at stages where cysts are already visible in the kidneys and therefore at later stages of disease development. In this study we focused on the cystic phenotype since birth in an attempt to clarify the temporal contribution of cellular proliferation in cyst development. Using a PKD2 transgenic rat model (PKD2 (1-703)) of different ages (0-60 days after birth) we performed gene expression profiling and phenotype analysis by measuring various kidney parameters. Phenotype analysis demonstrated that renal cysts appear immediately after birth in the PKD2 transgenic rat model (PKD2 (1-703)). On the other hand, abnormal proliferation occurs at later stages of the disease as identified by gene expression profiling. Interestingly, other pathways appear to be deregulated at early stages of the disease in this PKD model. Our data suggest that cystogenesis precedes deregulation of proliferation-related pathways, suggesting that proliferation abnormalities may contribute in cyst growth rather than cyst formation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20813037" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19462" }, "primaryId" : "GEO:GSE19462", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19462" } ] }, "title" : "microRNA profiling in vitro activated primary hepatic stellate cells", "dateAssigned" : "2009-12-14T00:00:00.000-06:00", "summary" : "The miRNA was isolated at day 0 and 10 and hybridized onto the Ncode Multi-species miRNA microarray V2 from Invitrogen", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19524" }, "primaryId" : "GEO:GSE19524", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19524" } ] }, "title" : "Potential Molecular Basis for Impaired Collateral Artery Growth in the Spontaneously Hypertensive Rat", "dateAssigned" : "2009-12-17T00:00:00.000-06:00", "summary" : "Key words: arteriogenesis, microarray analysis, peripheral vascular disease, gene expression ", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19537" }, "primaryId" : "GEO:GSE19537", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19537" } ] }, "title" : "Identification of a Serum Induced Transcriptional Signature Associated with Type 1 Diabetes in the BioBreeding Rat", "dateAssigned" : "2009-12-17T00:00:00.000-06:00", "summary" : "Here we report that sera of both spontaneously diabetic BB DRlyp/lyp and diabetes inducible BB DR+/+ rats induce inflammatory signatures in healthy PBMC of non-diabetic Brown Norway (BN) rats, while allogeneic BN sera does not. Consistent with their common T1D susceptibility, transcriptional signatures of both BB sub-strains share identity, including cytokines, immune receptors and signaling molecules. However, like the human T1D signature, the DRlyp/lyp signature, which is associated with progression to diabetes, is differentiated from that of the DR+/+ by induction of many IL-1 regulated genes. Addition of IL-1RA to cultures significantly ablates the DRlyp/lyp signature. Daily treatment of DRlyp/lyp rats with human recombinant IL-1RA significantly delays onset and sera of treated animals do not induce the characteristic IL-1 signature. Consistent with the presence of immune regulation in DR+/+ rats is induction of a signature showing negative regulation of the NF¿B pathway. This study supports prior human investigations of serum that reflect disease processes associated with progression to T1D and add to a growing body of evidence implicating the balance of IL-1 and IL-1RA as key factors influencing the severity and outcome of inflammatory responses.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20682698" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19540" }, "primaryId" : "GEO:GSE19540", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19540" } ] }, "title" : "microRNA expression in rat lung receiving chemopreventive agents and attenuation of cigarette smoke-induced alterations", "dateAssigned" : "2009-12-17T00:00:00.000-06:00", "summary" : "Keywords: cancer chemoprevention, microRNA, environmental cigarete smoke (ECS), 5,6-benzoflavone (BF), Indole 3-carbinol (I3C),N-acetylcysteine (NAC), oltipraz (OPZ), Phenethyl isothiocyanate (PEITC).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20051373" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19589" }, "primaryId" : "GEO:GSE19589", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19589" } ] }, "title" : "Effect of odorant inhalation on hypothlamic gene expression profile exposed to restraint stress in rats", "dateAssigned" : "2009-12-21T00:00:00.000-06:00", "summary" : "As an attempt to assess physio-psychological effects elicited in odorant-inhaled rats, gene expression profiling in the central nervous system was carried out with rats housed under stressful conditions. (R)-(-)-linalool inhalation to rats during 2 h restraint significantly up-regulated the expression of genes in hypothalamus, which were found to be related to neuron differentiation and regulation of transcription as well as immediate early genes. The expressions of 104 among focused stress-regulated genes were significantly altered by the inhalation. The (R)-(-)-linalool inhalation significantly repressed the restraint-induced changes in the expression levels of 77 of the 104. It also promoted the expression of the remaining 27 genes including those related to anti-apoptotic heat shock proteins. The differences in their hypothalamic gene expressions revealed that the inhaled odorants actually influenced stress responses, based on the restraint-induced hypothalamic gene expressions related to apoptosis. These results indicate that the analysis of gene expression profiles in rats subjected to a stressful condition is useful to evaluate odorant-induced effects as shown by the particular results that (R)-(-)-linalool inhalation under only 2 h restraint- stressed condition induces neuron differentiation against apoptosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20536181" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19628" }, "primaryId" : "GEO:GSE19628", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19628" } ] }, "title" : "Liver toxicity induced by munitions compounds TNT, 2,6-DNT, 2,4-DNT, 4A-DNT, and 2A-DNT", "dateAssigned" : "2009-12-23T00:00:00.000-06:00", "summary" : "Here we describe to use an integrative systems biology approach including toxicology, pathology, transcriptomics, metabolomics, gene function classification, pathway analysis and gene network modeling to try to understand the mechanisms of toxicity of these compounds.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21073692" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19652" }, "primaryId" : "GEO:GSE19652", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19652" } ] }, "title" : "Effector T cells driving monophasic vs relapse/remitting experimental autoimmune uveitis show unique pathway signatures", "dateAssigned" : "2009-12-24T00:00:00.000-06:00", "summary" : "Keywords: Two group comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20727594" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19653" }, "primaryId" : "GEO:GSE19653", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19653" } ] }, "title" : "Temporal dysregulation of cortical gene expresssion in the isolation-reared Wistar rat", "dateAssigned" : "2009-12-24T00:00:00.000-06:00", "summary" : "Gene expression was assessed in social control and isolation reared rats at 4 increasing postnatal ages to relate gene expression dysregulation to behavioural and endophenotype emergence.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19658" }, "primaryId" : "GEO:GSE19658", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19658" } ] }, "title" : "Gene Profiling Male Fetal Rat Gubernaculum After Insulin-like 3 (Insl3) Exposure", "dateAssigned" : "2009-12-24T00:00:00.000-06:00", "summary" : "Insl3 is a testis-derived hormone that induces growth and differentiation of the fetal gubernaculum. The goal of this study was to identify genes showing altered expression in fetal gubernaculum following Insl3 exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24966393" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19662" }, "primaryId" : "GEO:GSE19662", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19662" } ] }, "title" : "Identification of biomarkers that distinguish chemical contaminants using a gradient feature selection method", "dateAssigned" : "2009-12-27T00:00:00.000-06:00", "summary" : "In this study, we divided 105 compounds plus vehicle control into 14 compound classes. On the basis of gene expression profiles of in vitro primary cultured hepatocytes, we comprehensively compared various normalization, feature selection and classification algorithms for the classification of these 14 class compounds. We found that normalization had little effect on the averaged classification accuracy. Two support vector machine methods LibSVM and SMO had better classification performance. When feature sizes were smaller, LibSVM outperformed other classification methods. Simple logistic algorithm also performed well. At the training stage, usually the feature selection method SVM-RFE performed the best, and PCA was the poorest feature selection algorithm. But overall, SVM-RFE had the highest overfitting rate when an independent dataset used for a prediction in this case. Therefore, we developed a new feature selection algorithm called gradient method which had a pretty high training classification as well as prediction accuracy with the lowest over-fitting rate. Through the analysis of biomarkers that distinguished 14 class compounds, we found a goup of genes that mainly invovled in cell cylce were significanly downregulated by the metal and inflammatory compounds, but were induced by anti-microbial, cancer related drugs, pesticides, and PXR mediators.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21073692" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19666" }, "primaryId" : "GEO:GSE19666", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19666" } ] }, "title" : "Genetic Influences on Asthma Susceptibility in Developing Lung", "dateAssigned" : "2009-12-28T00:00:00.000-06:00", "summary" : "Whole transcriptome assay of whole lung of rat from 3 genetic strains (Lewis, Fisher, Brown Norway) at 3 postnatal time points (postnatal days 1, 7, 14).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20118217" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19701" }, "primaryId" : "GEO:GSE19701", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19701" } ] }, "title" : "Time series gene expression data from adult rat tail MNs following spinal cord transection", "dateAssigned" : "2009-12-29T00:00:00.000-06:00", "summary" : "Gene expression changes were studied in motor neurones 0, 2, 7, 21 and 60 days after comlete spinal transection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20534130" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19710" }, "primaryId" : "GEO:GSE19710", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19710" } ] }, "title" : "Microarray analysis of rat pulmonary artery smooth muscle cells before or after exposure to S-nitrosoglutathione (GSNO)", "dateAssigned" : "2009-12-30T00:00:00.000-06:00", "summary" : "Nitric oxide (NO) regulated pulmonary vascular function and structure, in part, via its effect on gene expression. We used microarrays to determine the up- and downregulated genes in rat pulmonary artery smooth muscle cells exposed to the NO donor S-nitrosoglutathione (GSNO) for 1, 2, and 4 hours.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21642009" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19748" }, "primaryId" : "GEO:GSE19748", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19748" } ] }, "title" : "Gene expression screening during early granulation tissue formation (I)", "dateAssigned" : "2010-01-05T00:00:00.000-06:00", "summary" : "Hydroxyapatite-coated cellulose induces a quicker and stronger inflammatory response compared to uncoated cellulose. Furthermore, the coated cellulose increases the homing at circulating bone-marrow derived progenitor cells. For this reason, Illumina microarray was used to study the early gene expression of the forming granulation tissue in the hydroxyapatite-coated sponges.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21059732" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19749" }, "primaryId" : "GEO:GSE19749", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19749" } ] }, "title" : "Gene expression screening during early granulation tissue formation (II)", "dateAssigned" : "2010-01-05T00:00:00.000-06:00", "summary" : "Subcutaneous implantation of cellulose sponges has been used for decades to induce vital granulation tissue formation. Illumina microarray was done in order to study the early gene expression in the granulation tissue formation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21059732" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19771" }, "primaryId" : "GEO:GSE19771", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19771" } ] }, "title" : "Neonat cardiomyocytes_hypertrophy_HDAC4", "dateAssigned" : "2010-01-06T00:00:00.000-06:00", "summary" : "In order to identify targets for HDAC4, NRVM were infected with adenoviral vectors encoding beta-Galactosidase or Flag- HDAC4, and incubated in serum free or 10% fetal calf serum containing growth medium for 48 hrs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21464227" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19820" }, "primaryId" : "GEO:GSE19820", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19820" } ] }, "title" : "Expression data from rat pluripotent stem (PS) cells", "dateAssigned" : "2010-01-09T00:00:00.000-06:00", "summary" : "Various pluripotent stem (PS) cells can be isolated from early developing embryos in mouse. Among these, two kinds of PS cells were isolated from mouse blastocysts: conventional embryonic stem (ES) cells with domed morphology that are maintained with LIF and BMP for self-renewal, and FAB-ES cells with flat morphology that need bFGF, activinA and BIO for self-renewal. Here, we report a novel PS cell line from rat blastocysts, which is distinguishable from conventional ES cells but is morphologically similar to mouse epiblast stem cell (EpiSC) lines. We used microarrays to detail the global program of gene expression of rES and rPS.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21670743" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19830" }, "primaryId" : "GEO:GSE19830", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19830" } ] }, "title" : "Expression data from pure/mixed brain, liver and lung to test feasability and sensitivity of statistical deconvolution", "dateAssigned" : "2010-01-11T00:00:00.000-06:00", "summary" : "To test the relationship between measured gene expression in mixed samples and the expression of genes in the isolated pure subsets, we begin with a situation in which all factors are known. Tissue samples from the brain, liver and lung of a single rat were analyzed using expression arrays (Affymetrix) in triplicate. Homogenates of those three tissues were then mixed together at the cRNA level. We then measured the gene expression pattern of each mixed sample. Such mixtures mimic the common scenario in which biological samples in a dataset are heterogeneous and vary in the relative frequency of the component subsets from one another.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20208531" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19867" }, "primaryId" : "GEO:GSE19867", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19867" } ] }, "title" : "Whole brains and frontal lobes of rat offsprings exposed perinatally to low doses of 2,2',4,4'-tetrabromodiphenyl ether", "dateAssigned" : "2010-01-12T00:00:00.000-06:00", "summary" : "Analysis of developmental toxicity of environmental toxin 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) at the level of gene expression. Dams of Wistar rats were exposed to environmentaly relevant doses of BDE-47 at gestation and lactation. Gene expression in total brains and frontal lobes was analysed in offspring on postnatal day 10.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19868" }, "primaryId" : "GEO:GSE19868", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19868" } ] }, "title" : "Liver of rat offsprings exposed perinatally to low doses of 2,2',4,4'-tetrabromodiphenyl ether", "dateAssigned" : "2010-01-12T00:00:00.000-06:00", "summary" : "Background: Polybrominated diphenyl ethers are a group of flame-retardant chemicals appearing increasingly in the environment. Their health effects and mechanisms of toxicity are poorly understood.Objectives: We screened for the sensitive effects and mechanisms of toxicity of 2,2 ,4,4 -tetra-bromodiphenyl ether (BDE-47) by analyzing the gene expression profile in rats exposed to doses comparable to human exposure.Methods: Wistar dams were exposed to vehicle or BDE-47 (0.002 and 0.2 mg/kg body weight) every fifth day from gestation day 15 to postnatal day 20 by injections to caudal vein. Total RNA was extracted from the livers of pups and hybridized to the whole-genome RNA expression micro-arrays. The list of genes 2-fold differentially expressed was exported to PANTHER and Ingenuity Systems for analysis of enriched ontology groups and molecular pathways.Results: Oxidoreductase and transferase protein families were enriched in exposed rats as were these biological process categories: carbohydrate metabolism; electron transport; and lipid, fatty acid, and steroid metabolism. Four signaling pathways (cascades of activation of drug-metabolizing enzymes) and 10 metabolic pathways were significantly enriched. Drug-metabolizing enzymes appear to be regulated by BDE-47 through an aryl hydrocarbon receptorindependent mechanism. Direct interaction with retinoid X receptor or its upstream cascade may be involved. The main metabolic effects consisted of activation of metabolic pathways: alpha- and omega-oxidation of fatty acids, glycolysis, and starch hydrolysis.Conclusions: Altered expression of genes involved in metabolic and signaling pathways and functions of the organism occurs after perinatal exposure of rat offspring to BDE-47 at doses relevant for the general population.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20056577" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19877" }, "primaryId" : "GEO:GSE19877", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19877" } ] }, "title" : "Effects of dietary obesity in fathers on gene expression of islets in the female offspring", "dateAssigned" : "2010-01-13T00:00:00.000-06:00", "summary" : "The global prevalence of obesity is increasing across age and gender. The rising burden of obesity in young people contributes to the early emergence of type 2 diabetes. Having one parent obese is an independent risk factor for childhood obesity. While the detrimental impact of diet-induced maternal obesity on offspring is well established, the extent of the contribution of obese fathers is unclear, as is the role of non-genetic factors in the casual pathway. Here we show that paternal high fat diet exposure programmed ß-cell ‘dysfunction’ in their F1 female offspring. Chronic high fat diet consumption in Sprague Dawley fathers led to increased body weight, adiposity, impaired glucose tolerance and insulin sensitivity. Relative to controls, their female offspring had lower body weight at day-1, increased pubertal growth rate, impaired insulin secretion and glucose tolerance, in the absence of obesity or increased adiposity. Paternal high fat diet was observed to alter gene expression of pancreatic islet genes in adult female offspring (P < 0.001); affected functional clusters includes calcium ion binding, insulin, apoptosis, Wnt and cell cycle organ/system development. This is the first reported study in mammals describing non-genetic, intergenerational transmission of metabolic sequelae of high fat diet from father to offspring. These findings support a role of fathers in metabolic programming of offspring and form a framework for further studies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20962845" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19890" }, "primaryId" : "GEO:GSE19890", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19890" } ] }, "title" : "miRNA expression after moderate Spinal Cord Injury in Rats", "dateAssigned" : "2010-01-14T00:00:00.000-06:00", "summary" : "Expression changes were analyzed 1, 3 and 7 days after injury and compared to expression of control (untreated) and sham (laminectony but no contusion) individuals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19909" }, "primaryId" : "GEO:GSE19909", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19909" } ] }, "title" : "Tissue Factor Pathway Inhibitor-2 is Induced by Fluid Shear Stress in Vascular Smooth Muscle", "dateAssigned" : "2010-01-15T00:00:00.000-06:00", "summary" : "Results: Microarrays identified tissue-pathway inhibitor-2 (TFPI-2) as the most differentially expressed gene by FSS in cultured SMCs. The regulatory effect of FSS on the expression of TFPI-2 was confirmed by RT-PCR and immunobloting demonstrating a more than 400-fold increase in TFPI-2 expression in SMCs exposed to FSS compared to static controls and a consistent upregulation at the protein level. Functionally, SMC proliferation was decreased by FSS and recombinant TFPI-2 was found to inhibit SMC proliferation and induce SMC apoptosis as indicated by activation of caspase-3. In vivo, TFPI-2 expression was found to be up-regulated 5, 10 and 20 h after rat carotid balloon-injury and immunohistochemistry demonstrated TFPI-2 protein in luminal SMCs exposed to FSS in rat carotid intimal hyperplasia 10 days after balloon-injury. Conclusion: FSS strongly influence gene expression in cultured SMCs and induce TFPI-2 expression, which is also expressed after rat carotid balloon injury in luminal SMCs exposed to FSS. Functionally, TFPI-2 may play an important role in vessel wall repair by regulating SMC proliferation and survival. Further studies are needed to elucidate the mechanisms by which TFPI-2 control SMC function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20537494" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19948" }, "primaryId" : "GEO:GSE19948", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19948" } ] }, "title" : "Molecular basis for vulnerability to mitochondrial and oxidative stress in an insulinoma cell line", "dateAssigned" : "2010-01-19T00:00:00.000-06:00", "summary" : "CONCLUSIONS/SIGNIFICANCE: The molecular profile presented here will enable identification of individual genes or gene clusters that shape vulnerability to mitochondrial dysfunction and thus represent potential therapeutic targets for diabetes and neurodegenerative diseases. In addition, the newly identified CRI-G1-RS cell line represents a new experimental model for investigating how endogenous antioxidants affect glucose sensing and insulin release by pancreatic ß cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21249230" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19950" }, "primaryId" : "GEO:GSE19950", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE19950" } ] }, "title" : "Multinucleated Tartrate Resistant Acid Phosphatase Positive Cells with Macrophage and Osteoclast Phenotypes in Bone", "dateAssigned" : "2010-01-19T00:00:00.000-06:00", "summary" : "Prothrombin (PT) and osteopontin (OPN) promotes adhesion of different TRAP-positive multinucleated cells isolated from rat long bone (Hu et al. Exp Cell Res. 2008; 314: 638-50). The PT-adhering cell could represent either an immature precursor to the OPN-adherent osteoclast or constitute a distinct multinucleated cell population with a unique role in bone. Herein, phenotypic differences between PT- and OPN- cells were investigated with microarray- expression analysis. Characteristic for PT-cells was expression of innate immune response genes and scavenger receptors whereas OPN-cells expressed typical osteoclast proteins such as collagenases implicated in bone degradation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21195739" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20037" }, "primaryId" : "GEO:GSE20037", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20037" } ] }, "title" : "cdr2 siRNA knockdown during passage through mitosis: HeLa cells, Rat1 wild type and c-myc null cells", "dateAssigned" : "2010-01-26T00:00:00.000-06:00", "summary" : "[Rat1a wild type and myc null cells]: We performed cdr2 knockdown using a pool of 4 cdr2-specific siRNAs to test whether cdr2 may regulate c-myc target genes as cells passage through mitosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20383333" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20102" }, "primaryId" : "GEO:GSE20102", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20102" } ] }, "title" : "Profiling of copy-number variation between BN and SHR rats", "dateAssigned" : "2010-01-29T00:00:00.000-06:00", "summary" : "We used Nimblegen HD aCGH to detect copy-number variants between genomes of BN and SHR rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20430781" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20149" }, "primaryId" : "GEO:GSE20149", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20149" } ] }, "title" : "Microarray studies on effect of Pneumocystis carinii infection on global gene expression in alveolar macrophages", "dateAssigned" : "2010-02-02T00:00:00.000-06:00", "summary" : "With a filter of false-discovery rate less than 0.1 and fold change greater than 1.5, 115 genes were found to be up- and 137 were down-regulated in alveolar macrophages during Pneumocystis carinii infection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20377877" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20214" }, "primaryId" : "GEO:GSE20214", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20214" } ] }, "title" : "Gene expression profiling of pancreatic islets in BioBreeding rats", "dateAssigned" : "2010-02-05T00:00:00.000-06:00", "summary" : "DRlyp/lyp and DR+/+ rats possess characteristics that make them ideal for the identification of pathways relevant to the development of T1D since they possess absolute or conditional susceptibility to T1D. The Gimap-/- Iddm2 locus conveys upon DRlyp/lyp rats a deficiency in immune regulatory capacity and the spontaneous T1D phenotype. Consistent with the concept that autoimmunity involves both a lack of self-tolerance as well as target organ-specific factors, we have discovered that DRlyp/lyp and DR+/+ (BB) rats share an islet specific stress. This is reflected by the expression of immune mediators, including the chemokine eotaxin that recruits eosinophils, certain T cell subsets, dendritic cells, and mast cells, by islet ß cells early in life, before infiltration of immune cells into the islet (insulitis). While BB and WF rats share Iddm1 (RT1u/u MHC), islet eotaxin expression in not observed in WF islets and thus is associated with the T1D susceptibility of BB rats. Further supporting the hypothesis that additional genetic factors, perhaps those working at the level of the pancreatic ß cell, are necessary for the development of T1D are the observations that 1) The generation Fischer 344 (F344) rats either homozygous for Gimap5-/- or homozygous for both RT1u/u and Gimap5-/- fail to develop T1D; and 2) genetic crosses between BB rats and non diabetic strains have identified numerous Iddm loci independent of Iddm1 and Iddm2.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23111281" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20219" }, "primaryId" : "GEO:GSE20219", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20219" } ] }, "title" : "Effects of Long-term Pioglitazone Treatment on Peripheral and Central Markers of Aging", "dateAssigned" : "2010-02-07T00:00:00.000-06:00", "summary" : "Keywords: hippocampus, rat, young or aged, control or pioglitazone-treated", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20454453" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20245" }, "primaryId" : "GEO:GSE20245", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20245" } ] }, "title" : "Alterations in the developing testis transcriptome following embryonic vinclozolin exposure", "dateAssigned" : "2010-02-09T00:00:00.000-06:00", "summary" : "For Samples 17-20: We used microarrays to determine genes expressed differentially between control and in vitro Flutamide treated rat E13 cultured testis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20566332" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20246" }, "primaryId" : "GEO:GSE20246", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20246" } ] }, "title" : "Effect of Runx2 Knockdown by siRNA in granulosa cell cultures.", "dateAssigned" : "2010-02-09T00:00:00.000-06:00", "summary" : "LH-indced RUNX2 expression is important for luteal gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20197312" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20259" }, "primaryId" : "GEO:GSE20259", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20259" } ] }, "title" : "Phylogenetic & expression analysis of the bHLH transcription factor family: genomic approach to cellular differentiation", "dateAssigned" : "2010-02-10T00:00:00.000-06:00", "summary" : "We used microarrays to determine bHLH expression in 20d rat Sertoli cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18557763" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20324" }, "primaryId" : "GEO:GSE20324", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20324" } ] }, "title" : "Gene Bionetwork Analysis of Ovarian Primordial Follicle Development", "dateAssigned" : "2010-02-13T00:00:00.000-06:00", "summary" : "For GSM510028-65: We used microarrays to determine genes expressed differentially between control and growth factors treated P4 ovary and co-expressed in the same manner for P4 ovaries treated with 8 growth factors AMH, BMP4, GDNF, FGF2, FGF7, KITLG, LIF, PDGFab.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20661288" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20344" }, "primaryId" : "GEO:GSE20344", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20344" } ] }, "title" : "Expression data from the basolateral amygdala of Long-Evans rats with a history of limited intermittent sucrose snacks", "dateAssigned" : "2010-02-16T00:00:00.000-06:00", "summary" : "To study the molecular mediators of naturally rewarding effects of palatable food we used a model of palatable “snacking” (Ulrich-Lai et al., 2007) in which rats are given chronic, brief access to a limited amount of sucrose solution (30%). Single housed, male Long-Evans rats (250g) (n=12 per group) from Harlan Labs (Indianapolis, IN) received normal rat chow (Harlan Teklad) and water ad libitum for the duration of the experiment. After a one-week period of acclimation, rats were randomly assigned to drink treatment groups of either 30% sucrose solution or water. Rats received a 14-day regimen of twice daily (9:30 and 15:30) brief (maximum of 30 minutes) limited (up to 4 mL) access of their assigned drink solution. Drink solutions were delivered via a graduated sipper placed onto the cage top in addition to the existing water bottle and sippers were immediately removed when the animal had consumed 4mL or after the 30-minute access period, whichever occurred first. Drink intake, food intake, and body weight were monitored throughout the experiment to verify that the rats learned to drink sucrose, that they adjusted chow intake for calories consumed from sucrose (~10%), and that there was no effect on body weight gain as is normally seen with this model (Ulrich-Lai et al., 2007). Drink treatment terminated on day 14 and at 8:00 on the morning of day 15, the rats were sacrificed by rapid decapitation. BLA tissue was dissected, RNA extracted, and gene expression changes between water and sucrose groups were accessed by microarray.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21059919" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20358" }, "primaryId" : "GEO:GSE20358", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20358" } ] }, "title" : "Neurotrophin NT3 promotes ovarian primordial to primary follicle transition", "dateAssigned" : "2010-02-16T00:00:00.000-06:00", "summary" : "We used microarrays to determine genes expressed differentially between control and NT3 (neurotrophin-3) treated P4 ovary.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19584175" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20375" }, "primaryId" : "GEO:GSE20375", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20375" } ] }, "title" : "Liver sinusoidal endothelium: a microenvironment-dependent differentiation program in rat including the novel junctional protein liver endothelial differentiation-associated protein-1", "dateAssigned" : "2010-02-17T00:00:00.000-06:00", "summary" : "Liver sinusoidal endothelium (LSEC) is a prime example for organ-specific microvascular differentiation and functions. Disease-associated capillarization of LSEC in vivo and dedifferentiation of LSEC in vitro indicate the importance of the hepatic microenvironment. To identify the LSEC-specific molecular differentiation program in the rat, we used a two-sided gene expression profiling approach comparing LSEC freshly isolated ex vivo with both lung microvascular endothelial cells (LMEC) and with LSEC cultured for 42h. The LSEC signature consisted of 48 genes both down-regulated in LMEC and in LSEC upon culture (FC>7 in at least one comparison); qRT-PCR confirmation of these genes included numerous family members and signalling pathway-associated molecules. The LSEC differentiation program comprised distinct sets of growth (wnt2, Fzd4, 5, 9, wls, VEGFR1, 2, 3, Nrp2) and transcription factors (Gata4, Lmo3, Tcfec, Maf) as well as endocytosis-related (Stabilin-1/2, Lyve1 and Ehd3) and cytoskeleton-associated molecules (Rnd3/RhoE). Specific gene induction in cultured LSEC versus freshly isolated LSEC as well as LMEC (Esm-1, Aatf) and up-regulation of gene expression to LMEC levels (CXCR4, Apelin) confirmed true transdifferentiation of LSEC in vitro. In addition, our analysis identified a novel 26 kDa single-pass transmembrane protein, liver endothelial differentiation-associated protein (Leda)-1, that was selectively expressed in all liver endothelial cells and preferentially localized to the abluminal cell surface. Upon forced over-expression in MDCK cells, Leda-1 was sorted baso-laterally to E-cadherin-positive adherens junctions suggesting functional involvement in cell adhesion and polarity. Conclusion: Comparative microvascular analysis in rat identified a hepatic microenvironment-dependent LSEC-specific differentiation program including the novel junctional molecule Leda-1.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20578158" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20388" }, "primaryId" : "GEO:GSE20388", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20388" } ] }, "title" : "Expression Profiling of a Genetic Animal Model of Depression", "dateAssigned" : "2010-02-17T00:00:00.000-06:00", "summary" : "We profiled two independent cohorts of Flinders animals derived from the same colony six months apart, each cohort statistically powered to allow independent as well as combined analysis. Using this approach, we were able to validate using real-time-PCR a core set of gene expression differences that showed statistical significance in each of the temporally distinct cohorts, representing consistently maintained features of the model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20830301" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20498" }, "primaryId" : "GEO:GSE20498", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20498" } ] }, "title" : "Gene expression in hepatocytes and bile ducts from ANIT-treated rats", "dateAssigned" : "2010-02-23T00:00:00.000-06:00", "summary" : "Acute toxic responses to a single 50 mg/kg oral dose of 1-napthylisothiocyanate (ANIT) were evaluated by microarray analysis of laser capture-microdissected rat biliary epithelium or hepatic parenchyma at 2 and 6 hours post-dose. Selective and dramatic differences between the biliary epithelium and the hepatic parenchyma were evident as soon as 2 hours at which time 375 genes were altered in biliary epithelium, but only a nominal 38 genes were altered in the hepatic parenchyma. Gene expression analysis revealed increased expression of genes involved in the unfolded protein response and ER stress in biliary epithelial cells, but no alteration of these genes in hepatocytes. By 6 hours post dose, 620 genes showed altered expression in biliary epithelium while there were only 32 genes altered in hepatic parenchyma. At this timepoint, analysis of the biliary epithelium revealed decreased expression of genes involved in the unfolded protein response compared to the 2 hour time point, and increased expression at 6 hours of genes involved in protein degradation such as proteasome-ubquination pathways, and genes associated with cell death. Our analysis revealed early loss of biliary epithelial integrity and attempts at repair of damage with subsequent activation of protein degradation and cell fate decisions leading to death pathways within a 6 hour time course. During this same time interval, hepatic parenchymal gene expression changed little and mainly reflected a decrease in enterohepatic circulation of bile acids and an increase in ribosomal proteins which may signal an adaptive change to reduced bile acid delivery to the liver and an increased demand for bile acids and glutathione-mediated transport of ANIT. This versatile approach provides a precise evaluation of distinct cell populations, biliary epithelium and hepatic parenchyma, in situ. (Cullen et.al., Toxicologic Pathology 2010)", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20521" }, "primaryId" : "GEO:GSE20521", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20521" } ] }, "title" : "Vascular Permeability and Apoptosis are Separable Processes in Retinal Ischemia-Reperfusion Injury", "dateAssigned" : "2010-02-24T00:00:00.000-06:00", "summary" : "Ischemia and reperfusion injury provides an acute model of ischemic retinopathy that includes neurodegeneration and VEGF-dependent vascular permeability and is amenable to rapid drug testing. The distinct effects of ischemic preconditioning and bevacizumab demonstrate that the apoptotic and vascular responses to ischemia may be separated and that VEGF expression is not neuroprotective following ischemic-reperfusion.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20554620" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20528" }, "primaryId" : "GEO:GSE20528", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20528" } ] }, "title" : "Gene expression in response to axotomy in organotypical slices co-cultures", "dateAssigned" : "2010-02-25T00:00:00.000-06:00", "summary" : "Keywords: organotypic slice cultures; axonal lession; gene expression", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20374426" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20550" }, "primaryId" : "GEO:GSE20550", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20550" } ] }, "title" : "A high resolution analyis of c-Myc-regulated gene expression dynamics.", "dateAssigned" : "2010-02-26T00:00:00.000-06:00", "summary" : "In this dataset, we included the expression data hourly for the first 6 h, then every 2 or 4 hours over a total of 24 h for 4-hydoxytamoxifen activated cells, and expression data from control samples (no 4-hydroxytamoxifen activation) at 8, 16 and 24 h.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21623162" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20601" }, "primaryId" : "GEO:GSE20601", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20601" } ] }, "title" : "Sex-different hepatic glycogen content, glucose and amino acid output in rats.", "dateAssigned" : "2010-03-02T00:00:00.000-06:00", "summary" : "Keywords: Hepatic gene expression, sex-differences", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20863371" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20603" }, "primaryId" : "GEO:GSE20603", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20603" } ] }, "title" : "MicroRNA miR-16 is anti-proliferative in enterocytes and exhibits diurnal rhythmicity in intestinal crypts", "dateAssigned" : "2010-03-02T00:00:00.000-06:00", "summary" : "This is the first report to document circadian rhythmicity of specific microRNAs in rat jejunum. Our data provide a link between the anti-proliferative microRNA miR-16 and the intestinal proliferation rhythm and point to miR-16 as an important regulator of proliferation in jejunal crypts. This function may be essential to match proliferation and absorptive capacity with nutrient availability.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20633552" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20635" }, "primaryId" : "GEO:GSE20635", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20635" } ] }, "title" : "Circadian regulation in rat abdominal adipose tissue", "dateAssigned" : "2010-03-04T00:00:00.000-06:00", "summary" : "Circadian rhythms are oscillations with a periodicity of 24 hours that are controlled by an endogenous clock and are observed in virtually all aspects of mammalian function from expression of genes to complex physiological processes. The master clock is present in the suprachiasmatic nucleus (SCN) in the anterior part of the hypothalamus and controls peripheral clocks present in other parts of the body. Although much is known about the mechanism of the central clock in the SCN, the regulation of clocks present in peripheral tissues is still unclear. This study is designed to examine fluctuations in gene expression in abdominal white adipose tissue within the 24 hour circadian cycle in normal animals. The objectives of this study is to identify and analyze circadian oscillation in gene expression in white adipose tissue, and to identify the role of circadian regulation in coordinating the functioning of this dynamic tissue.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20682845" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20659" }, "primaryId" : "GEO:GSE20659", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20659" } ] }, "title" : "A Comparative Study of Genome Wide Transcriptional Profiles of Primary Hepatocyte in In Vitro Cultures", "dateAssigned" : "2010-03-05T00:00:00.000-06:00", "summary" : "The liver is one of most important organs in our bodies. It performs many essential functions including metabolism, synthesis, secretion, detoxification, and storage. Hepatocytes are the principal cell type in the liver and are involved in multiple liver-specific functions. There have been several efforts to develop in vitro culture systems capable of maintaining hepatocyte-specific phenotype over long time periods. In hepatic tissue engineering, two commonly used culture systems are the collagen sandwich and monolayers of cells. In this study, genome-wide gene expression profiles of primary hepatocytes were measured over an 8-day period for each cell culture system using Affymetrix GeneChips and analyzed via Gene Set Enrichment Analysis (GSEA), which is a powerful method to elicit biologically meaningful information from microarray data at the level of gene sets. Results indicate that the gene expression in hepatocytes in collagen sandwich cultures gradually diverges from that in monolayer cultures. Gene sets up-regulated in collagen sandwich cultures include those associated with liver metabolic and synthetic functions. These functions are associated with lipid, amino acid, carbohydrate, and alcohol metabolism and bile acid synthesis. Nuclear receptors are up-regulated in collagen sandwiches 24 hours after seeding. Signals transmitted from these receptors may cause the up-regulation of other processes in subsequent days. Cytochrome-P450 monooxygenase expression was initially down-regulated but exhibited up-regulation after 72 hours. Our results provide a baseline for further explorations into the systems biology of engineered liver mimics as well as 2D and 3D co-cultures of primary hepatocytes and non-parenchymal cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21245926" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20714" }, "primaryId" : "GEO:GSE20714", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20714" } ] }, "title" : "Broad epigenetic signature of maternal care in the brain of adult rats (DNA methylation and H3K9 acetylation profiles)", "dateAssigned" : "2010-03-09T00:00:00.000-06:00", "summary" : "Maternal care is associated with long-term effects on behavior and epigenetic programming of the NR3C1 (GLUCOCORTICOID RECEPTOR) gene in the hippocampus of both rats and humans. However, epigenetic changes at a single gene promoter are unlikely to account for the range of responses to the early life environment and the persistent change in expression of hundreds of additional genes in adult rats in response to differences in maternal care. Here we show that natural variations in maternal care are associated with coordinate changes in DNA methylation, chromatin, and gene expression spanning over a hundred kilobase pairs in the hippocampus of adult rats. The offspring of high compared to low maternal care mothers show epigenetic changes in promoters, exons, and gene ends and higher transcriptional activity across many genes, suggesting that a broad epigenetic regulation of gene expression may form part of a coordinated response to early maternal care.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21386994" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20717" }, "primaryId" : "GEO:GSE20717", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20717" } ] }, "title" : "Broad epigenetic signature of maternal care in the brain of adult rats (expression)", "dateAssigned" : "2010-03-09T00:00:00.000-06:00", "summary" : "Maternal care is associated with long-term effects on behavior and epigenetic programming of the NR3C1 (GLUCOCORTICOID RECEPTOR) gene in the hippocampus of both rats and humans. However, epigenetic changes at a single gene promoter are unlikely to account for the range of responses to the early life environment and the persistent change in expression of hundreds of additional genes in adult rats in response to differences in maternal care. Here we show that natural variations in maternal care are associated with coordinate changes in DNA methylation, chromatin, and gene expression spanning over a hundred kilobase pairs in the hippocampus of adult rats. The offspring of high compared to low maternal care mothers show epigenetic changes in promoters, exons, and gene ends and higher transcriptional activity across many genes, suggesting that a broad epigenetic regulation of gene expression may form part of a coordinated response to early maternal care.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21386994" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20885" }, "primaryId" : "GEO:GSE20885", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20885" } ] }, "title" : "Gene expression changes in the medial prefrontal cortex and nucleus accumbens following abstinence from cocaine self-administration", "dateAssigned" : "2010-03-15T00:00:00.000-05:00", "summary" : "Results: Whole-genome expression analysis was conducted on a rat cocaine binge-abstinence model that has previously been demonstrated to engender increased drug seeking and taking with abstinence. Gene expression changes in two mesolimbic terminal fields (mPFC and NAc) were identified in a comparison of cocaine-naïve rats with rats after 10 days of cocaine selfadministration followed by 1, 10, or 100 days of enforced abstinence (n=6-11 per group). A total of 1,461 genes in the mPFC and 414 genes in the NAc were altered between at least two time points (ANOVA, p<0.05; ±1.4 fold-change). These genes can be subdivided into: 1) changes with cocaine self-administration that do not persist into periods of abstinence, 2) changes with cocaine self-administration that persist with abstinence, 3) and those not changed with cocaine self-administration, but changed during enforced abstinence. qPCR analysis was conducted to confirm gene expression changes observed in the microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20187946" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20886" }, "primaryId" : "GEO:GSE20886", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20886" } ] }, "title" : "Multi-modal proteomic target discovery and orthogonol confirmation of preclinical diabetic retinopathy drug development biomarkers", "dateAssigned" : "2010-03-15T00:00:00.000-05:00", "summary" : "The aim of this study was to identify proteomic alterations associated with functional dysregulation of the retina with diabetes that could eventually be used as surrogate endpoints in preclinical drug testing studies. A multi-modal approach of antibody (Luminex)-, electrophoresis (2-DIGE)-, and LC-MS (iTRAQ)-based quantitation methods was used to provide broad coverage of the retinal proteome. Transcriptional profiling through microarray analysis was also included to increase coverage and provide insight into potential regulation of protein expression changes at the mRNA level. The different technologies proved complementary, with limited coverage overlap between methods.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20894" }, "primaryId" : "GEO:GSE20894", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20894" } ] }, "title" : "Gene expression and gene ontology analysis of the transcriptional changes occurring in spinal cord from the G93A SOD1 gene mutant rat", "dateAssigned" : "2010-03-15T00:00:00.000-05:00", "summary" : "We have investigated the process of disease-induced functional perturbation and the related transcriptional changes occurring in thoraco-lumbar spinal cord extracted from Sprague-Dawley rats heterozygous for the G93A SOD1 gene mutation (Emerging Model 2148 Het Male, Taconic USA; Wyeth and Amyotrophic Lateral Sclerosis Association 2002) using spinal cord from wild type females littermates as reference tissues. Rats were obtained from a breeding project at Taconic Breeding Services (USA). We have applied large-scale gene expression analysis to define the pattern or transcriptional changes occurring in spinal cord from the G93A SOD1 rat model from a pre-symptomatic stage, at disease onset and at end-stage disease, using Bead Array analysis (Illumina, San Diego, USA). We have pooled spinal cord from N:5 transgenic rats for each of the time points considered, using the same pools of spinal cord from sex and age-matched WT rats as reference. In this specific project, the aim was to obtain a gene ontology (GO) pathway analysis of the transcriptional changes induced by the G93A SOD1 mutation in rat spinal cord. Hence, we have opted for a sample pooling strategy, well aware that in so doing, we would not obtaineed information about individuals genes variation across the samples in study but an overall view of the activation of multi-genes molecular signals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20895" }, "primaryId" : "GEO:GSE20895", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20895" } ] }, "title" : "mRNA-seq with Agnostic Splice Site Discovery for CNS Transcriptomics Tested in Chronic Pain", "dateAssigned" : "2010-03-15T00:00:00.000-05:00", "summary" : "The study pursued dual goals: To advance mRNA-seq bioinformatics towards unbiased transcriptome capture and to demonstrate its potential for discovery in neuroscience by applying the approach to an in vivo model of neurological disease. We found that 12.4% of known genes were induced and 7% were suppressed in the dysfunctional (but anatomically intact) L4 dorsal root ganglion (DRG) 2 weeks after L5 spinal Nerve Ligation (SNL). A new algorithm for agnostic mapping of pre-mRNA splice junctions (SJ) achieved a precision of 97%.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20452967" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20907" }, "primaryId" : "GEO:GSE20907", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20907" } ] }, "title" : "Intrinsic response of thoracic propriospinal neurons to axotomy", "dateAssigned" : "2010-03-16T00:00:00.000-05:00", "summary" : "Analysis of expression changes in prelabeled laser-microdissected thoracic propriospinal neurons at different times after low-thoracic spinal cord transection in adult rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20525361" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20935" }, "primaryId" : "GEO:GSE20935", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20935" } ] }, "title" : "Gene expression in NKR-P1B+ versus Ly49s3+ rat NK cells", "dateAssigned" : "2010-03-17T00:00:00.000-05:00", "summary" : "Here, we performed a global gene expression profiling of sorted, single-positive NKR-P1B+ or Ly49s3+ splenic NK cells in order to get an overview of differences in expressed genes between the NKR-P1B+ and Ly49s3+ NK cell subsets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20395458" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20952" }, "primaryId" : "GEO:GSE20952", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20952" } ] }, "title" : "Discriminating reprotoxic and non-reprotoxic phthalates by transcriptomics analysis of rat testis", "dateAssigned" : "2010-03-18T00:00:00.000-05:00", "summary" : "Male rats were treated with a single dose of either reprotoxic or non-reprotoxic phthalates and sacrificed 24h thereafter. Subsequently, histopathological and gene-expression profiling analyses were performed. Despite ambiguous histopathological observations, we were able to distinguish the reprotoxic from the non-reprotoxic phthalates based on differential gene expression. This shows that differences in gene expression indicative for the type of exposure can be detected earlier, or at lower doses, than phenotypic tissue damage. These findings are promising for ’early warning’ biomarker analyses and for using toxicogenomics in a category approach.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20967" }, "primaryId" : "GEO:GSE20967", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20967" } ] }, "title" : "Gene expression profiling of vasoregression in the retina", "dateAssigned" : "2010-03-19T00:00:00.000-05:00", "summary" : "we used microarray techniques to define gene expression profiles related to vasoregression in a rat ciliopathy model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21379381" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20980" }, "primaryId" : "GEO:GSE20980", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20980" } ] }, "title" : "Temporal Gene Expression Profiling of Bone Repair in a Rat Calvarial Defect", "dateAssigned" : "2010-03-19T00:00:00.000-05:00", "summary" : "Microarray analysis of gene expression was performed in the healing and non-healing calvarial defects of 12-week old male rats during various stages of bone repair: 1, 3, 5, 7, 10, 14, and 21 days post surgery.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20982" }, "primaryId" : "GEO:GSE20982", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20982" } ] }, "title" : "Murine small intestinal crypt cell line IEC-6: control vs. TGF-beta stimulated", "dateAssigned" : "2010-03-19T00:00:00.000-05:00", "summary" : "microRNA profiling of rat small intestinal crypt cell IEC-6. Comparing control untreated with cells treated with transforming growth factor-beta (TGF-beta). TGF-beta stimulated cell differentiation, as observed in the stimulation of intestinal epithelial cell markers (alkaline phophotase, villin, aminopeptidase N, etc.).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20997" }, "primaryId" : "GEO:GSE20997", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE20997" } ] }, "title" : "High and low exercise responders", "dateAssigned" : "2010-03-22T00:00:00.000-05:00", "summary" : "Aerobic exercise capacity is a strong predictor of disease and survivability but the utility of exercise intervention is largely dependent on how one’s genome interacts with an exercise-training environment. A newly developed rat model selectively bred for inherited differences in response to aerobic exercise training shows to be a useful resource to sort out the networks of genes responsible for signalling exercise-induced changes that benefit cardiac function.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21006" }, "primaryId" : "GEO:GSE21006", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21006" } ] }, "title" : "Pheochromocytoma in rats with multiple endocrine neoplasia (MENX) shares gene expression patterns with human pheochromocytoma", "dateAssigned" : "2010-03-22T00:00:00.000-05:00", "summary" : "We here report that hyperplasia and tumor have similar gene expression profiles, suggesting an early determination of the tumorigenic signature. Overexpressed genes in rat adrenal lesions are especially enriched in development/differentiation-associated genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20937862" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21007" }, "primaryId" : "GEO:GSE21007", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21007" } ] }, "title" : "Whole-genome gene expression profiling of dorsal root ganglion neurons after nerve damage", "dateAssigned" : "2010-03-22T00:00:00.000-05:00", "summary" : "We generated whole-genome gene expression profiles of dorsal root ganglion (DRG) neurons following nerve damage. DRG neurons extend one peripheral axon into the spinal nerve and one central axon into the dorsal root. The peripheral axon regenerates vigorously, while in contrast the central axon has little regenerative capacity. For this study, two groups of animals were subjected either to sciatic nerve (SN) or dorsal root (DR) crush, and at 12, 24, 72 hours and 7 days after the crush, lumbar DRGs L4, L5 and L6 were dissected and total RNA was extracted.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21422075" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21021" }, "primaryId" : "GEO:GSE21021", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21021" } ] }, "title" : "Myocardial contractile response to physiological stress improves with high saturated fat feeding in heart failure", "dateAssigned" : "2010-03-23T00:00:00.000-05:00", "summary" : "Impaired myocardial contractile function is a hallmark of heart failure (HF) which may present under resting conditions and/or during physiological stress. Previous studies reported that high fat feeding in HF is associated with improved myocardial contractile function at baseline. Our goal was to determine whether myocardial function is compromised in response to physiological stress and to evaluate the global gene expression profile of rats fed high dietary fat following infarction. Male Wistar rats underwent ligation or sham surgery and were fed normal (10% kcal fat) (SHAM+NC, HF+NC) or high fat (60% kcal saturated fat) (SHAM+SAT, HF+SAT) for 8 weeks. Myocardial contractile function was assessed using a Millar pressure-volume (PV) conductance catheter at baseline, during inferior vena caval occlusions and dobutamine (DOB) stress. Steady state indices of systolic function, left ventricular (LV)+dP/dtmax, stroke work and maximal power were increased in HF+SAT vs HF+NC; HF+NC were reduced vs SHAM+NC. Preload-recruitable measures of contractility [end systolic PV relationship, maximal elastance, preload recruitable SW and peak+dP/dtmax to end diastolic volume] were decreased in HF+NC but not HF+SAT. ß-adrenergic responsiveness (delta-LV+dP/dtmax and delta-cardiac output DOB 0-10 µg•kg-1•min-1) was reduced in HF, but high fat feeding did not further impact contractile reserve in HF. Contractile reserve was reduced by high fat in SHAM+SAT. Microarray gene expression analysis reveals the majority of significantly altered pathways identified to contain multiple gene targets correspond to cell signaling pathways and energy metabolism. These findings suggest that high saturated fat improves myocardial function at rest and during physiological stress in infarcted hearts, but may negatively impact contractile reserve under non-pathological conditions. Furthermore, high fat feeding-induced alterations in gene expression related to energy metabolism and specific signaling pathways reveal promising targets through which high saturated fat potentially mediates cardioprotection in heart failure/LV dysfunction.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21023" }, "primaryId" : "GEO:GSE21023", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21023" } ] }, "title" : "Bioinformatic profiling of the transcriptional response of adult rat cardiomyocytes to distinct fatty acids", "dateAssigned" : "2010-03-23T00:00:00.000-05:00", "summary" : "Diabetes mellitus, obesity, and dyslipidemia increase risk for cardiovascular disease, and expose the heart to high plasma fatty acid (FA) levels. Recent studies suggest that distinct FA species are cardiotoxic (e.g., palmitate), while others are cardioprotective (e.g., oleate), although the molecular mechanisms mediating these observations are unclear. The purpose of the present study was to investigate the differential effects of distinct FA species (varying carbon length and degree of saturation) on adult rat cardiomyocyte (ARC) gene expression. ARCs were initialy challenged with 0.4 mM octanoate (8:0), palmitate (16:0), stearate (18:0), oleate (18:1), or linoleate (18:2) for 24 h. Microarray analysis revealed differential regulation of gene expression by the distinct FAs; the order regarding the number of genes whose expression was influenced by a specific FA was octanoate (1,188) . stearate (740) . palmitate (590) . oleate (83) . linoleate (65). In general, cardioprotective FAs (e.g., oleate) increased expression of genes promoting FA oxidation to a greater extent than cardiotoxic FAs (e.g., palmitate), whereas the latter induced markers of endoplasmic reticulum and oxidative stress. Subsequent RT-PCR analysis revealed distinct time- and concentration-dependent effects of these FA species, in a gene-specific manner. For example, stearate- and palmitate-mediated ucp3 induction tended to be transient (i.e., initial high induction, followed by subsequent repression), whereas oleate-mediated induction was sustained. These findings may provide insight into why diets high in unsaturated FAs (e.g., oleate) are cardioprotective, whereas diets rich in saturated FAs (e.g., palmitate) are not.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18387886" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21068" }, "primaryId" : "GEO:GSE21068", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21068" } ] }, "title" : "Estrogen-mediated Epigenetic Repression of Large Chromosomal Regions through DNA Looping", "dateAssigned" : "2010-03-25T00:00:00.000-05:00", "summary" : "The current concept of epigenetic repression is based on one repressor unit corresponding to one silent gene. This notion, however, cannot adequately explain concurrent silencing of multiple loci observed in large chromosome regions. The long-range epigenetic silencing (LRES) can be a frequent occurrence throughout the human genome. To comprehensively characterize the influence of estrogen signaling on LRES, we analyzed transcriptome, methylome, and estrogen receptor alpha (ESR1)-binding datasets from normal breast epithelia and breast cancer cells. This ?omics? approach uncovered 11 large repressive zones (range: 0.35~5.98 megabases), including a 14-gene cluster located on 16p11.2. In normal cells, estrogen signaling induced transient formation of multiple DNA loops in the 16p11.2 region by bringing 14 distant loci to focal ESR1-docking sites for coordinate repression. However, the plasticity of this free DNA movement was reduced in breast cancer cells. Together with the acquisition of DNA methylation and repressive chromatin modifications at the 16p11.2 loci, an inflexible DNA scaffold may be a novel determinant used by breast cancer cells to reinforce estrogen-mediated repression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20442245" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21075" }, "primaryId" : "GEO:GSE21075", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21075" } ] }, "title" : "Gene expression data from liver of rat fed a high-fat diet without/with mulberry leaves", "dateAssigned" : "2010-03-25T00:00:00.000-05:00", "summary" : "Microarray analysis revealed that mulberry leaves up-regulated the genes involved in alpha-, beta-, and omega-oxidation of fatty acids, mainly relating to peroxisome proliferator-activated receptor signaling pathway, and down-regulated the gene expression involved in lipogenesis. Furthermore, the genes relating to response to oxidative stress were up-regulated in rats administrated mulberry leaves.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21150120" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21098" }, "primaryId" : "GEO:GSE21098", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21098" } ] }, "title" : "Coculture with lin-/c-kit+ Stem Cells leads to a Paracrine Mediated Inhibition of Apoptosis in Cardiomyocytes", "dateAssigned" : "2010-03-29T00:00:00.000-05:00", "summary" : "Conclusion: Our results provide evidence that coculture of SC with NRVCM leads to an upregulation of antiapoptotic genes and a paracrine-mediated increase in the phosphorylation of AKT. This results in less apoptotis in cocultured NRVCM. We therefore conclude, that cell-cell interactions lead to a modified gene expression in SC that may in part explain the cardioprotective effects of stem cell therapy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22672705" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21136" }, "primaryId" : "GEO:GSE21136", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21136" } ] }, "title" : "Genome response to tissue plasminogen activator in experimental ischemic stroke", "dateAssigned" : "2010-03-30T00:00:00.000-05:00", "summary" : "Forty-two Sprague-Dawley rats were subjected to: 2 hours of middle cerebral artery occlusion (MCAO); a permanent-MCAO; or were used as controls. tPA was administered to half of the rats in each group at 3hours. Whole blood was drawn at 24 hours, and isolated RNA levels measured on Affymetrix Rat Genome 230 2.0 GeneChip microarrays to examine the entire RNA transcriptome.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21150" }, "primaryId" : "GEO:GSE21150", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21150" } ] }, "title" : "High fat diet effects on mammary epithelium of OP and OR rats", "dateAssigned" : "2010-03-31T00:00:00.000-05:00", "summary" : "Conclusion: Our findings indicate that consumption of high fat safflower diet enhances mammary carcinogenesis in an OR rat strain through increased proliferation of mammary epithelium at the time of exposure, but not in the OP rat strain. Thus, the diet-induced increase in sensitivity was strain-specific and independent of weight gain or obesity level.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21210" }, "primaryId" : "GEO:GSE21210", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21210" } ] }, "title" : "Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic Acid on rat kidneys", "dateAssigned" : "2010-04-05T00:00:00.000-05:00", "summary" : "RNA-Seq has been increasingly used for the quantification and characterization of transcriptomes. The ongoing development of the technology promises the more accurate measurement of gene expression. However, its benefits over widely accepted microarray technologies have not been adequately assessed, especially in toxicogenomics studies. The goal of this study is to enhance the scientific community's understanding of the advantages and challenges of RNA-Seq in the quantification of gene expression by comparing analysis results from RNA-Seq and microarray data on a toxicogenomics study. A typical toxicogenomics study design was used to compare the performance of an RNA-Seq approach (Illumina Genome Analyzer II) to a microarray-based approach (Affymetrix Rat Genome 230 2.0 arrays) for detecting differentially expressed genes (DEGs) in the kidneys of rats treated with aristolochic acid (AA), a carcinogenic and nephrotoxic chemical most notably used for weight loss. We studied the comparability of the RNA-Seq and microarray data in terms of absolute gene expression, gene expression patterns, differentially expressed genes, and biological interpretation. We found that RNA-Seq was more sensitive in detecting genes with low expression levels, while similar gene expression patterns were observed for both platforms. Moreover, although the overlap of the DEGs was only 40-50%, the biological interpretation was largely consistent between the RNA-Seq and microarray data. RNA-Seq maintained a consistent biological interpretation with time-tested microarray platforms while generating more sensitive results. However, there is clearly a need for future investigations to better understand the advantages and limitations of RNA-Seq in toxicogenomics studies and environmental health research.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25633159" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21239" }, "primaryId" : "GEO:GSE21239", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21239" } ] }, "title" : "Transcriptional profiling of lung tissue of rat pretreated with cobalt in normoxic and hypoxic conditions and comapring with saline treated normoxic and hypoxic lung tissue in different time interval", "dateAssigned" : "2010-04-07T00:00:00.000-05:00", "summary" : "The goal of the study was to examine the effect of hypoxic preconditioning with cobalt on global gene profiling in lung tissues.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21258" }, "primaryId" : "GEO:GSE21258", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21258" } ] }, "title" : "Transcript Profiling of Spinal Dorsal Horn in Response to Electroacupuncture on Rats at 1h", "dateAssigned" : "2010-04-08T00:00:00.000-05:00", "summary" : "Keywords: Transcriptome analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25346229" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21326" }, "primaryId" : "GEO:GSE21326", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21326" } ] }, "title" : "Pro-inflammatory rat macrophage mediators", "dateAssigned" : "2010-04-13T00:00:00.000-05:00", "summary" : "R11 macrophages had reduced pro-inflammatory mediators after stimulation", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20505148" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21329" }, "primaryId" : "GEO:GSE21329", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21329" } ] }, "title" : "Multi-tissue, selective PPAR¿ modulation of insulin sensitivity and metabolic pathways in obese rats", "dateAssigned" : "2010-04-13T00:00:00.000-05:00", "summary" : "Male Zucker fatty (fa/fa) and lean (fa/+) rats (Charles River, Wilmington, MA) were received at 6 weeks of age. Fatty rats were weight-matched upon arrival and randomly divided into one of five experimental groups. The fatty rat groups varied by the type of chow they were fed - normal chow alone or with a PPAR¿ ligand admixture: normal chow (fatty control, FC), rosiglitazone-treated (Rosi), pioglitazone-treated (Pio), troglitazone-treated (Tro), or AG035029-treated (AG). Lean control (LC) rats were all fed normal chow. Rats groups were maintained on the diets for 21 days.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20959535" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21335" }, "primaryId" : "GEO:GSE21335", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21335" } ] }, "title" : "Rat life cycle liver gene expression", "dateAssigned" : "2010-04-14T00:00:00.000-05:00", "summary" : "Age- and sex-related susceptibility to adverse drug reactions is a key concern in understanding drug safety and disease progression. We hypothesize that the underlying suite of hepatic genes expressed at various developmental and life-cycle stages will impact susceptibility to adverse drug reactions. Thus, understanding the basal expression patterns of genes throughout the life span of the rat model species in both sexes will inform our assessments of adverse drug reactions. The liver plays a central role in the metabolism and biotransformation of drugs via key cellular pathways. Untreated, male and female F344 rats were sacrificed at 2, 5, 6, 8, 15, 21, 52, 78, and 104 weeks of age. Liver tissues were collected for histology and gene expression analysis. Whole-genome rat microarrays (44,000 features) were used to query global expression profiles. An initial list of active genes was selected using a 2-way ANOVA with a p-value cutoff of 0.05 and 1.5 fold-change difference from mean expression. Three dimensional principal component analyses revealed notable expression profile divergence between males and females after 5 weeks with greatest differences observed at 21 and 52 weeks before converging again at 104 weeks. Furthermore, k-means clustering identified groups of genes that displayed specific developmental and age-related patterns of expression. Various adult aging-related clusters included genes involved in pathways related to susceptibility to adverse drug effects such as xenobiotic metabolism, DNA damage repair, and oxidative stress. These results suggest an underlying role for genes in these specific clusters in potentiating age- and sex-related susceptibilities to adverse health effects.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21118493" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21387" }, "primaryId" : "GEO:GSE21387", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21387" } ] }, "title" : "Array CGH between GK and Wistar Rats for Detecting Copy Number Variations", "dateAssigned" : "2010-04-19T00:00:00.000-05:00", "summary" : "This array CGH experiment can detect loci which show different copy numbers (genotype) between GK and Wistar rats. These loci serve as a valuable repository for mining candidates contributing to the pathogenesis of T2D.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21124896" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21403" }, "primaryId" : "GEO:GSE21403", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21403" } ] }, "title" : "Effect of IL-1b treatment on cultured rat aortic smooth muscle cells", "dateAssigned" : "2010-04-20T00:00:00.000-05:00", "summary" : "IL-1 plays an important role in atherosclerosis, and alters expression of a number of genes involved in atherosclerotic plaque development and progression. Smooth muscle cells play important roles in atherosclerotic plaque formation and stability, so this study was undertaken to determine the global effects of IL-1b on gene expression in smooth muscle cells in vitro.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22201681" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21405" }, "primaryId" : "GEO:GSE21405", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21405" } ] }, "title" : "MicroRNA Profiling in Ischemia-Reperfusion Injury of the Gracilis Muscle in Rats (miRNA data)", "dateAssigned" : "2010-04-20T00:00:00.000-05:00", "summary" : "Following 4 h of ischemia and subsequent reperfusion for 4 h of the gracilis muscles, the specimens were analyzed with an Agilent rat miRNA array to detect the expressed miRNAs in the experimental muscles compared to those from the sham-operated controls.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21406" }, "primaryId" : "GEO:GSE21406", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21406" } ] }, "title" : "Potential Target Genes of MicroRNA-21 In Ischemia-Reperfusion Injury Of The Gracilis Muscle In Rats", "dateAssigned" : "2010-04-20T00:00:00.000-05:00", "summary" : "Following 4 h of ischemia and subsequent reperfusion for 4 h of the gracilis muscles, three miRNAs (miR-21, miR-200c, and miR-205) of 350 tested rat miRNAs were found to have an increased expression in the miRNA array.The expression of the mRNA in the muscle specimens after 4 h of ischemia and reperfusion for 1, 3, 7, and 14 d were detected with the Agilent Whole Rat Genome 4 × 44 k oligo microarray. A combined approach using a computational prediction algorithm that included miRanda, PicTar, TargetScanS, MirTarget2, RNAhybrid, and the whole genome microarray experiment was performed by monitoring the mRNA:miRNA association to identify potential target genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21417" }, "primaryId" : "GEO:GSE21417", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21417" } ] }, "title" : "Hepatic gene expression profile in persimmon peel extract administrated GK rat", "dateAssigned" : "2010-04-20T00:00:00.000-05:00", "summary" : "Persimmon (Diospyros kaki L. f.) is a most popular fruit in Asian countries but its peels are totally wasted despite of containing a plenty of antioxidants such as carotenoids and polyphenols. We prepared a fat-soluble extract from a persimmon peel (PP) fraction and fed type 2 diabetic Goto-Kakizaki (GK) rats with a PP extract-containing AIN-93G diet (PP diet) for 12 weeks. Compared with the control AIN-93G diet, the feeding of the PP diet reduced the plasma glutamic-pyruvate transaminase activity significantly, with accumulation of ß-cryptoxanthin in the liver. A DNA microarray analysis revealed that the PP diet altered the hepatic gene expression profiles. In particular, insulin signaling pathway-related genes were significantly enriched in differentially expressed gene sets. Moreover, Western blotting analysis actually showed the promotion of IRß tyrosine phosphorylation. All these data suggest that the PP extract administration to the GK rats improves their insulin resistance.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21370910" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21476" }, "primaryId" : "GEO:GSE21476", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21476" } ] }, "title" : "Comparison of Mineralizing Synchronous UMR106-01 cells with UMR106-01 cells treated with Mineralization Inhibitor AEBSF", "dateAssigned" : "2010-04-22T00:00:00.000-05:00", "summary" : "UMR106-01 osteoblastic cells are a model for studying bone mineralization. We have shown that mineralization is temporally synchronized within cultures grown under defined conditions . Cells are plated at time zero and differentiate into osteoblastic phenotype by 64 h later. If an exogenous phosphate source is added to the cultures, the cells form and deposit hydroxyapatite mineral within distinct extracellular supramolecular lipid protein complexes termed biomineralization foci (BMF) starting 12 h later. Mineralization is largely complete by 24 h later (88 h after plating). We have also shown that AEBSF, covalent serine protease inhibitor, blocks mineralization within BMF and inhibits the fragmentation of several proteins related to biomineralization. The present experiment was designed to test whether AEBSF treatment for 12 h has an effect on transcription by UMR106-01 osteoblastic cells. AEBSF is known to inactivate several serine proteases including SKI-1 (site 1, subtilisin kexin protease-1).SKI-1 functions intracellularly to activate transmembrane bound transcription factor precursors releasing the transcriptionally active N-terminal portions to imported into the nucleus. Thus, if AEBSF blocks transcription of mineralization related genes, it would support a role for SKI-1 in gene regulation in mineralizing UMR106-01 osteoblastic cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21075843" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21573" }, "primaryId" : "GEO:GSE21573", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21573" } ] }, "title" : "Effect of BMPR2 mutation on vascular smooth muscle gene expression", "dateAssigned" : "2010-04-28T00:00:00.000-05:00", "summary" : "BMPR2 mutation is the cause of most hereditary pulmonary arterial hypertension, but the common molecular consequence of different types of BMPR2 mutation is still not known. The goal of this study was to determine the common molecular consequences of three different classes of patient-derived BMPR2 mutation in vascular smooth muscle gene expression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21600" }, "primaryId" : "GEO:GSE21600", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21600" } ] }, "title" : "Time course study of experimental cardiac hypertrophy in rat", "dateAssigned" : "2010-04-29T00:00:00.000-05:00", "summary" : "Factor analysis was used to study correlation over time.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20417270" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21640" }, "primaryId" : "GEO:GSE21640", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21640" } ] }, "title" : "Gene expression analysis of cardiomyocytes treated with a clinically relevant concentration of DEHP (50 ug/mL)", "dateAssigned" : "2010-05-03T00:00:00.000-05:00", "summary" : "We used microarrays to expression profile cardiomyocytes from neonatal Sprague-Dawley rats treated with 50 ug/mL DEHP and control (0.1% DMSO) to identify changes in gene expression related to connexin-43 expression, calcium handling, arrhythmogenesis and mechanical motion.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20920545" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21641" }, "primaryId" : "GEO:GSE21641", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21641" } ] }, "title" : "Dose-dependent gene expression analysis of cardiomyocytes treated with DEHP (1-50 ug/mL)", "dateAssigned" : "2010-05-03T00:00:00.000-05:00", "summary" : "We used microarrays to expression profile cardiomyocytes from neonatal Sprague-Dawley rats treated with 1 to 50 ug/mL DEHP and control (0.1% DMSO) to identify changes in gene expression related to connexin-43 expression, calcium handling, arrhythmogenesis and mechanical motion.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20920545" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21681" }, "primaryId" : "GEO:GSE21681", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21681" } ] }, "title" : "Expression data from aged, calorically restricted rat hippocampal regions CA1, CA3, and DG", "dateAssigned" : "2010-05-05T00:00:00.000-05:00", "summary" : "Aging is associated with a decline in hippocampal mediated learning and memory, a process wich can be ameliorated by dietary (caloric) restriction. We used Affymetrix gene expression analysis to monitor changes in three regions of the hippocampus (CA1, CA3, DG) of middle aged (18 months) and old (28 month) rats that were exposed to dietary restriction. Old rats were determined to be good performers (GP) or poor performers (PP) in behavioral tests to assess thier hippocampal function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21055414" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21682" }, "primaryId" : "GEO:GSE21682", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21682" } ] }, "title" : "Gene expression study of macrophages during early foreign body reaction", "dateAssigned" : "2010-05-05T00:00:00.000-05:00", "summary" : "Searching for mechanisms potentially useful to overcome these complications, we have established the signaling role of macrophages in the development of FBR. This study profiles gene expression of in vitro fibrinogen activated macrophages as well as that of freshly isolated macrophages from 3-days implants, against a background of unactivated macrophages/monocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20886081" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21686" }, "primaryId" : "GEO:GSE21686", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21686" } ] }, "title" : "Comparison of thymic epithelial cells and hair follicle stem cells", "dateAssigned" : "2010-05-05T00:00:00.000-05:00", "summary" : "Keywords: Cell type comparison", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20725041" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21693" }, "primaryId" : "GEO:GSE21693", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21693" } ] }, "title" : "Rat & M. fortis - lung and liver", "dateAssigned" : "2010-05-05T00:00:00.000-05:00", "summary" : "More than 40 kinds of mammals in China are known to be naturally infected with Schistosoma japonicum (S. japonicum); Microtus fortis (M. fortis), a species of vole, is the only mammal in which the schistosomes cannot mature or cause significant pathogenic changes. In the current study, we compared the differences in pathology by Hematoxylin-eosin staining and in changes in the T cell subsets with flow cytometry as well as gene expression using genome oligonucleotide microarrays in the lung and liver, before challenge and 10 days post-infection with schistosomes in a S. japonicum-susceptible mouse model of infection, a non-susceptible rat model and the non-permissive host, M. fortis. The results demonstrated that S. japonicum promoted a more intensive immune response and more pathological lesions in M. fortis and rats than in mice. Hematoxylin-eosin staining revealed that the immune effector cells involved were mainly eosinophilic granulocytes supplemented with heterophilic granulocytes and macrophages. The analysis of splenic T cell subsets showed that CD4+ T cell subsets and the CD4+/CD8+ ratio were increased while the CD8+ T cell subsets decreased remarkably in rats; whereas the CD8+ T cell subsets were increased but the CD4+/CD8+ ratio was decreased significantly in mice. The analysis of the pattern of gene expression suggested that some immune-associated genes and apoptosis-inducing genes upregulated while some development-associated genes were downregulated in the infected M. fortis compared to the uninfected controls; the three different hosts have different response mechanisms to schistosome infection. The results of this study will be helpful for identifying the key molecules in the immune response to S. japonicum in M. fortis and for understanding more about the underlying mechanism of the response, as well as for elucidating the interaction between S. japonicum and its hosts.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20976156" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21733" }, "primaryId" : "GEO:GSE21733", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21733" } ] }, "title" : "Transcript Profiling of Spinal Dorsal Horn in Response to Electroacupuncture on Rats at 24h", "dateAssigned" : "2010-05-07T00:00:00.000-05:00", "summary" : "Keywords: Transcriptome analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25346229" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21771" }, "primaryId" : "GEO:GSE21771", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21771" } ] }, "title" : "Raloxifene Attenuates Gas6 and Apoptosis in Experimental Aortic Valve Disease in Renal Failure", "dateAssigned" : "2010-05-10T00:00:00.000-05:00", "summary" : "Introduction: Renal failure is associated with aortic valve calcification. Using our rat model of uraemia-induced reversible aortic valve calcification, we assessed the role of apoptosis and survival pathways in aortic valve calcification. We also explored the effects of raloxifene - an estrogen receptor modulator on valvular calcification. Methods: Gene array analysis was performed in aortic valves obtained from 3 groups of rats (n=7 each): calcified valves from rats fed with uremic diet -high-adenine (0.75%), high-phosphate diet (1.5%), valves after calcification resolution following diet cessation (reversibility) and control. In addition, four groups of rats (n=10 each) were used in order to evaluate the effect of raloxifene in aortic valve calcification: three groups as mentioned above and a fourth group fed with the uremic diet which also received daily raloxifene. Evaluation of these groups included imaging, histology and antigen expression analysis. Results: Gene array results showed that the majority of the expressed genes that were altered were from the diet group valves. Most apoptosis-related genes were changed in a pro-apoptotic direction in calcified valves. Apoptosis and decrease in several survival pathways were confirmed in calcified valves. Resolution of aortic valve calcification was accompanied by decreased apoptosis and upregulation of these ant-apoptotic pathways. Imaging and histology demonstrated that raloxifene significantly decreased aortic valve calcification. Conclusion: Downregulation of several survival pathways and apoptosis are involved in the pathogenesis of aortic valve calcification. The beneficial effect of raloxifene in valve calcification is related to apoptosis modulation. This novel observation is important for developing remedies for aortic valve calcification in patients with renal failure. Introduction: Renal failure is associated with aortic valve calcification. Using our rat model of uraemia-induced reversible aortic valve calcification, we assessed the role of apoptosis and survival pathways in aortic valve calcification. We also explored the effects of raloxifene - an estrogen receptor modulator on valvular calcification. Methods: Gene array analysis was performed in aortic valves obtained from 3 groups of rats (n=7 each): calcified valves from rats fed with uremic diet -high-adenine (0.75%), high-phosphate diet (1.5%), valves after calcification resolution following diet cessation (reversibility) and control. In addition, four groups of rats (n=10 each) were used in order to evaluate the effect of raloxifene in aortic valve calcification: three groups as mentioned above and a fourth group fed with the uremic diet which also received daily raloxifene. Evaluation of these groups included imaging, histology and antigen expression analysis. Results: Gene array results showed that the majority of the expressed genes that were altered were from the diet group valves. Most apoptosis-related genes were changed in a pro-apoptotic direction in calcified valves. Apoptosis and decrease in several survival pathways were confirmed in calcified valves. Resolution of aortic valve calcification was accompanied by decreased apoptosis and upregulation of these ant-apoptotic pathways. Imaging and histology demonstrated that raloxifene significantly decreased aortic valve calcification. Conclusion: Downregulation of several survival pathways and apoptosis are involved in the pathogenesis of aortic valve calcification. The beneficial effect of raloxifene in valve calcification is related to apoptosis modulation. This novel observation is important for developing remedies for aortic valve calcification in patients with renal failure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21335463" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21791" }, "primaryId" : "GEO:GSE21791", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21791" } ] }, "title" : "Zucker Diabetic Fatty (ZDF) Rat Study - Diaphragm vs. Sternohyoid", "dateAssigned" : "2010-05-12T00:00:00.000-05:00", "summary" : "Type 2 diabetes differs from type 1 diabetes in its pathogenesis. Type 1 diabetic diaphragm has altered gene expression which includes lipid and carbohydrate metabolism, ubiquitination and oxidoreductase activity. The objectives of the present study were to assess respiratory muscle gene expression changes in type 2 diabetes and to determine whether they are greater for the diaphragm than an upper airway muscle. Diaphragm and sternohyoid muscle from Zucker diabetic fatty (ZDF) rats were analyzed with Affymetrix gene expression arrays. The two muscles had 97 and 102 genes, respectively, with at least ±1.5-fold significantly changed expression with diabetes, and these were assigned to gene ontology groups based on over-representation analysis. Several significantly changed groups were common to both muscles, including lipid metabolism, carbohydrate metabolism, muscle contraction, ion transport and collagen, although the number of genes and the specific genes involved differed considerably for the two muscles. In both muscles there was a shift in metabolism gene expression from carbohydrate metabolism toward lipid metabolism, but the shift was greater and involved more genes in diabetic diaphragm than diabetic sternohyoid muscle. Groups present in only diaphragm were blood circulation and oxidoreductase activity. Groups present in only sternohyoid were immune & inflammation and response to stress & wounding, with complement genes being a prominent component. In conclusion, type 2 diabetes-induced gene expression changes in respiratory muscles has both similarities and differences relative to previous data on type 1 diabetes gene expression. Furthermore, the diabetic alterations in gene expression differ between diaphragm and sternohyoid.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21806" }, "primaryId" : "GEO:GSE21806", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21806" } ] }, "title" : "Testicular lumicrine factors regulate ERK, STAT and NFKB pathways in the initial segment of the rat epididymis to prevent apoptosis", "dateAssigned" : "2010-05-13T00:00:00.000-05:00", "summary" : "The initial segment of the epididymis is vital for male fertility, therefore, it is important to understand the mechanisms that regulate this important region. Deprival of testicular luminal fluid factors/lumicrine factors from epididymis, a subset of cells within the initial segment undergo apoptosis. In this study, microarray analyses was used to examine early changes in the downstream signal transduction pathways following the loss of lumicrine factors, and we discovered the following cascade of events leading to loss of protection and eventual apoptosis. First, mRNA expression of several key components of ERK pathway decreased sharply after 6 hours of loss protection from testicular lumicrine factors. After 12 hours, the levels of mRNA expression of STAT and NF-¿B pathways components increased, mRNA expression of genes encoding cell cycle inhibitors increased. After 18 hours of loss protection from testicular lumicrine factors, apoptosis was observed in the initial segment. In conclusion, testicular lumicrine factors protect the cells of the initial segment by activating ERK pathway, repressing STAT and NF-¿B pathways, and preventing a cascade of reactions leading to apoptosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21311037" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21843" }, "primaryId" : "GEO:GSE21843", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21843" } ] }, "title" : "Three Major salivary glands", "dateAssigned" : "2010-05-14T00:00:00.000-05:00", "summary" : "The aim of this study is characterize the gene expression of rat parotid, submandibular and sublingual glands, providing basic information for the salivary marker proteins.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21901" }, "primaryId" : "GEO:GSE21901", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21901" } ] }, "title" : "Striatal microRNA controls cocaine intake through CREB signalling", "dateAssigned" : "2010-05-19T00:00:00.000-05:00", "summary" : "To identify potential targets for miR-212, we transfected cells with a vector to overexpress miR-212 or an empty vector. We then analyzed profiled gene expression using Affymetrix arrays.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20613834" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21937" }, "primaryId" : "GEO:GSE21937", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21937" } ] }, "title" : "Germ-free and anti-biotic treated rats", "dateAssigned" : "2010-05-20T00:00:00.000-05:00", "summary" : "The objective of the study was identify hepatic genes with expression by deprivation of gut flora. Two models were used: model 1 (study 1443KR) examined germ-free Sprague Dawley and model 2 (1512KR) examined antibiotic treated Han Wistar rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20837534" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21938" }, "primaryId" : "GEO:GSE21938", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE21938" } ] }, "title" : "Phosphatidylinositol 3-kinase modulation of trophoblast cell differentiation", "dateAssigned" : "2010-05-20T00:00:00.000-05:00", "summary" : "Microarray analysis of stem, differentiated and differentiated Rcho-1 trophoblast stem cells treated with the PI3K inhibitor LY294002.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20840781" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22024" }, "primaryId" : "GEO:GSE22024", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22024" } ] }, "title" : "Next Gen(etics): targeted genome enrichment and next-generation sequencing enhances phenotype-driven forward genetics and gene-driven reverse genetics", "dateAssigned" : "2010-05-27T00:00:00.000-05:00", "summary" : "Targeted genomic enrichment followed by next-generation sequencing dramatically increased the efficiency of mutation discovery in human genomes. Here we demonstrate that these techniques also revolutionize traditional genetic approaches in model systems. We developed a two-step protocol utilizing a traditional bulk-segregant analysis (BSA) approach for positional cloning mutants in phenotype-driven forward genetic screens. First, BSA pools are 'light' sequenced for rough mapping, followed by targeted enrichment and deep-sequencing of the mutant BSA pool for the linked genomic region to fine-map and discover candidate mutations. We applied this method successfully to three Arabidopsis mutants and show that it can be scaled by multiplexing. Similarly, we applied these techniques to a gene-driven reverse genetics method (chemical driven target-selected mutagenesis or TILLING) that is used for generating gene knockouts in a wide range of organisms, including plants, invertebrates and vertebrates. We developed an efficient multiplexed genomic enrichment protocol for pre-barcoded samples. As a proof-of-principle, 770 genes were screened for induced mutations in 30 rats, which identified all but one known variants (30) as well as a large series of novel knockout and missense alleles. Mutations were retrieved at the expected frequency with a the false-positive rate of less than 1 in 6 million basepairs, which is much lower as compared to traditional mutation discovery approaches. Both methods are largely independent of the genome size due to the targeted enrichment and can thus be applied to any genetic model system of interest.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20953175" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22096" }, "primaryId" : "GEO:GSE22096", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22096" } ] }, "title" : "Induction of Ovarian Primordial Follicle Assembly by Connective Tissue Growth Factor CTGF", "dateAssigned" : "2010-06-02T00:00:00.000-05:00", "summary" : "We used microarrays to determine genes expressed differentially between control and CTGF (connective tissue growth factor) treated P0 ovary", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20886044" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22118" }, "primaryId" : "GEO:GSE22118", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22118" } ] }, "title" : "Effect of iodine on early stage thyroid autonomy", "dateAssigned" : "2010-06-03T00:00:00.000-05:00", "summary" : "Iodine slows TSH effects on thyroid growth stimulation and this effect is more pronounced in thyrocytes with constitutive cAMP activation i.e. in thyroid autonomy. Iodine induced growth alteration in early stage thyroid autonomy is conferred by induction of apoptosis and G2/M arrest. Transcriptome analysis revealed significant modulation of gene networks relevant to cell adhesion, cadherin signalling and ion binding with more pronounced effects in constitutively active FRTL-5 cells compared to normal FRTL-5 cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21035537" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22157" }, "primaryId" : "GEO:GSE22157", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22157" } ] }, "title" : "Target of Ascl1 in CG4 cell", "dateAssigned" : "2010-06-04T00:00:00.000-05:00", "summary" : "To identify the downstream targets of transcription factor Ascl1, transcriptional profiling of rat glial cell line, CG4 cell, transfected with either Ascl1 or mock control was performed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22161" }, "primaryId" : "GEO:GSE22161", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22161" } ] }, "title" : "Comparative gene expression analysis of thoracic spinal cord from G93A SOD1 mutant rats and from wild type littermates following mild compression injury", "dateAssigned" : "2010-06-04T00:00:00.000-05:00", "summary" : "In this study we investigate how the molecular response to a mechanical stress applied to the spinal cord can be modified by a G93A SOD1 gene mutation, a genetic defect known to cause an invariably fatal form of motor neuron disease. In a 7-day post-injury time period, we perform a 4 time points gene expression profiling of injured spinal cords obtained from pre-symptomatic rats over-expressing the G93A SOD1 gene mutation and from wild type (WT) littermates. The hypothesis tested in this investigation is that the presence of a known genetic defect in a pre-symptomatic rat with a macroscopically normal spinal cord modifies the molecular response to mechanical stress as part of an increase genetically-induced vulnerability to this kind of stress. A better understanding of the molecular mechanisms underlying this susceptibility to trauma may open the way to the uncovering of molecular events which are crucially linked to neurodegenerastion.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22181" }, "primaryId" : "GEO:GSE22181", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22181" } ] }, "title" : "Entrapment Neuropathy Results in Different MicroRNAs Expression Patterns from Denervation Injury in Rats", "dateAssigned" : "2010-06-07T00:00:00.000-05:00", "summary" : "The experimental soleus muscles and dorsal root ganglions (DRGs) from each experimental group (sham control, denervation, entrapment, and decompression) were analyzed with an Agilent® rat miRNA array to detect dysregulated miRNAs", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22218" }, "primaryId" : "GEO:GSE22218", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22218" } ] }, "title" : "Alteration of the expression and 17, 20 lyase activity of cytochrome P450 17-hydroxylase/17, 20 lyase and of the expression of other Leydig cells genes in the rat fetal testis directly exposed to Mono-ethyl hexyl phthalate in culture.", "dateAssigned" : "2010-06-08T00:00:00.000-05:00", "summary" : "This study aimed to investigate the direct mechanism(s) of action ofMono-(Ethyl-Hexyl) phthalate (MEHP) on the rat fetal testis with particular emphasis to Leydig cell steroidogenesis, by means of an in vitro system based on culture for 3 days of fetal testes from 14.5 days post-coïtum old rats. We first confirmed that an exposure to MEHP led to a dose-dependent decrease of testosterone and demonstrated that dihydrotestosterone (DHT) production was also inhibited. We then demonstrated that in 10µM MEHP-exposed testis basal 17alpha-hydroxy-progesterone (17OHP) production was increased (+40%) while androstenedione levels decreased (-55%). Furthermore, the addition of the latter steroid but none of the other precursors rescued testosterone thus establishing further that MEHP specifically blocked steroidogenesis at the level of the 17,20 lyase activity of the P450c17 enzyme (CYP17), which converts 17OHP to androstenedione. Furthermore and accordingly, both levels of testicular CYP17 protein (western blot) and cyp17a1 gene (qPCR, microarrays) were found to decrease under MEHP exposure. The microarray analysis also showed that among the few other testicular genes cyp17a1 whose expression was inhibited by MEHP were the genes encoding for the Leydig cell insulin-like peptid 3 (INSL3), involved in the control of testicular descent, and for inhibin A (INHA), that regulates follicular-stimulating hormone secretion.Under in vitro conditions where MEHP is not metabolized and remains at low intratesticular concentration, our findings show in particular that this phthalate directly inhibits several important Leydig cell factors involved in testis development and function.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22263" }, "primaryId" : "GEO:GSE22263", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22263" } ] }, "title" : "Effect of 52 weeks of chronic exposure to TCDD AND PCB126 on hepatic gene expression", "dateAssigned" : "2010-06-09T00:00:00.000-05:00", "summary" : "This study investigates the effects of the aryl hydrocarbon receptor (AhR) ligands TCDD and PCB126 on hepatic gene expression in female sprague dawley rats. Rats were treated with toxicological equivalent doses of TCDD (100ng/kg/day) (Toxic equivalence factor (TEF) = 1.0), PCB126 (30ng, 300ng or 1000ng/kg/day) (TEF = 0.1) or a vehicle control of corn oil:acetone (99:1) 5 days a week for 52 weeks.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20959002" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22286" }, "primaryId" : "GEO:GSE22286", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22286" } ] }, "title" : "Gene expression patterns in bone following mechanical loading", "dateAssigned" : "2010-06-10T00:00:00.000-05:00", "summary" : "The advent of high-throughput measurements of gene expression and bioinformatics analysis methods offers new ways to study gene expression patterns. The primary goal of this study was to determine the time sequence for gene expression in a bone subjected to mechanical loading, during key periods of the bone formation process, including expression of matrix-related genes, the appearance of active osteoblasts, and bone desensitization. A standard model for bone loading was employed in which the right forelimb was loaded axially for three minutes per day, while the left forearm served as a non-loaded, contralateral control. We evaluated loading-induced gene expression over a time course of 4 hours to 32 days after the first loading session. Six distinct, time-dependent patterns of gene expression were identified over the time course and categorized into three primary clusters: genes upregulated early in the time course, genes upregulated during matrix formation, and genes downregulated during matrix formation. Genes were then grouped based on function and/or signaling pathways. Many gene groups known to be important in loading-induced bone formation were identified within the clusters, including AP-1-related genes in the early response cluster, matrix-related genes in the upregulated gene clusters, and Wnt/ß-catenin signaling pathway inhibitors in the downregulated gene clusters. Several novel gene groups were identified as well, including chemokine-related genes which were upregulated early but downregulated later in the time course, solute carrier genes which were both up- and downregulated, and muscle-related genes which were primarily downregulated.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20658561" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22299" }, "primaryId" : "GEO:GSE22299", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22299" } ] }, "title" : "Role of the Yersinia pestis Virulence Plasmid in Evading a Protective Polymorphonuclear Leukocyte Response During the Early Stages of Bubonic Plague", "dateAssigned" : "2010-06-10T00:00:00.000-05:00", "summary" : "A delay in the mammalian inflammatory response is a prominent feature of infection with Yersinia pestis, the agent of bubonic and pneumonic plague. Y. pestis factors have been identified that either do not stimulate a normal inflammatory response, or actively suppress it. Prominent among these are components of the Type III secretion system that is encoded on the Yersinia virulence plasmid (pYV). We used a rat model of bubonic plague to characterize the kinetics and extent of the mammalian transcriptomic response to infection with wild-type or pYV-negative Y. pestis in the draining lymph node. Remarkably, dissemination and multiplication of wild-type Y. pestis during the bubonic stage of disease did not induce any detectable gene expression response by host lymph node cells. This was followed, however, by an extensive transcriptomic response, including upregulation of several cytokine, chemokine, and other immune response genes, after systemic spread during septicemic plague. Matched lymph node samples used for histopathology and extracellular cytokine measurements, combined with the microarray data set, broadly outlined the mammalian immune response to Y. pestis and how it is influenced by pYV-encoded factors. The results indicate that both WT and pYV– Y. pestis induce primarily a Th17 response, and not a Th1 or Th2 response. In the absence of pYV, a sustained recruitment of polymorphonuclear leukocytes, the major Th17 effector cell, to the lymph node resulted in clearance of infection. Thus, the ability to counteract a Th17- driven PMN response in the lymph node appears to be a major function of the Y. pestis virulence plasmid. In contrast, classic markers of the proinflammatory response and macrophage activation, such as TNF-á and IFN-ã, were not induced at all by pYV– Y. pestis, and appeared only late in infection with WT Y. pestis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20876291" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22321" }, "primaryId" : "GEO:GSE22321", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22321" } ] }, "title" : "Temporal Gene Expression Profiling during Rat Femoral Marrow Ablation-Induced Intramembranous Bone Regeneration", "dateAssigned" : "2010-06-14T00:00:00.000-05:00", "summary" : "These data present the first temporal gene expression profiling analysis of the rat genome during intramembranous bone regeneration induced by femoral marrow ablation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20957030" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22364" }, "primaryId" : "GEO:GSE22364", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22364" } ] }, "title" : "Cumulative low doses of the organic pesticide rotenone in the adult rat substantia nigra pars compacta", "dateAssigned" : "2010-06-15T00:00:00.000-05:00", "summary" : "Adult male Sprague Dawley rats (5 month-old at the beginning of the study) were subcutaneously exposed to 0.5 mg.kg/d rotenone or the corresponding solvent (PEG/DMSO, 1/1) for 28 days. At the end of the experiment, animals were sacrificed by decapitation and brains were rapidly taken out within 30-40 s. Total RNA was prepared from laser-capture microdissected rat substantia nigra pars compacta (Snpc). Changes in transcript abundance within SNpc were analyzed on samples from solvent and rotenone-exposed groups (n = 3 per group) using CodeLink™ Rat Whole Genome bioarrays containing 34,000 transcripts and EST probes (GE Healthcare, Amersham, Saclay, France).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22456" }, "primaryId" : "GEO:GSE22456", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22456" } ] }, "title" : "low and high aerobic capacity rats exposed to cigarette smoke, lung tissue", "dateAssigned" : "2010-06-18T00:00:00.000-05:00", "summary" : "Low aerobic exercise capacity increases susceptibility to smoking-induced inflammation and tissue damage", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22489" }, "primaryId" : "GEO:GSE22489", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22489" } ] }, "title" : "Thrombopoietin (TPO) protects against heart damage induced infarction in rat model", "dateAssigned" : "2010-06-22T00:00:00.000-05:00", "summary" : "In order to examine the mechanism of TPO on cardiac protection against myocardial infarction damage (MI), we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to delineate the TPO cardioprotective mechanism against infarction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22770769" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22515" }, "primaryId" : "GEO:GSE22515", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22515" } ] }, "title" : "DEFINING A RAT BLOOD PRESSURE QUANTITATIVE TRAIT LOCUS TO A <81.8KB CONGENIC SEGMENT: COMPREHENSIVE SEQUENCING AND RENAL TRANSCRIPTOME ANALYSIS.", "dateAssigned" : "2010-06-22T00:00:00.000-05:00", "summary" : "Evidence from multiple linkage and genome-wide association studies suggest that human chromosome 2 (HSA2) contains alleles that influence blood pressure (BP). Homologous to a large segment of HSA2 is rat chromosome 9 (RNO9), to which a BP quantitative trait locus (QTL) was previously mapped. The objective of the current study was to further resolve this BP QTL. Eleven congenic strains with introgressed segments spanning <81.8kb to <1.33Mb were developed by introgressing genomic segments of RNO9 from the Dahl salt-resistant (R) rat onto the genome of the Dahl salt-sensitive (S) rat and tested for BP. The congenic strain with the shortest introgressed segment spanning <81.8kb significantly lowered BP of the hypertensive S rat by 25 mm Hg and significantly increased its mean survival by 45 days. In contrast, two other congenic strains had increased BP compared with the S. We focused on the <81.8kb congenic strain which represents the shortest genomic segment to which a BP QTL has been definitively mapped to date in any species. Sequencing of this entire region in both S and R rats detected 563 variants. The region did not contain any known or predicted rat protein coding genes. Further, a whole genome renal transcriptome analysis between S and the <81.8kb S.R congenic strain revealed alterations in several critical genes implicated in renal homeostasis. Taken together, our results provide the basis for future studies to examine the relationship between the candidate variants within the QTL region and the renal differentially expressed genes as potential causal mechanisms for BP regulation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20716646" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22531" }, "primaryId" : "GEO:GSE22531", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22531" } ] }, "title" : "A Sphingosine 1-Phosphate 1 Receptor Agonist Modulates Brain Death-Induced Neurogenic Pulmonary Injury", "dateAssigned" : "2010-06-23T00:00:00.000-05:00", "summary" : "Lung transplantation remains the only viable therapy for patients with end-stage lung disease; however, full utilization of this treatment strategy is severely compromised by the lack of donor lung availability. For example, the vast majority of donor lungs available for transplantation are obtained from brain death (BD) individuals. Unfortunately, the autonomic storm which accompanies BD often results in neurogenic pulmonary edema (NPE), thereby either producing irreversible lung injury or leading to primary graft dysfunction following lung transplantation. We previously demonstrated that sphingosine 1-phosphate (S1P), a phospholipid angiogenic factor and major barrier-enhancing agent, as well as S1P analogues serve to reduce vascular permeability and ischemia/reperfusion (I/R) lung injury in rodents via ligation of the S1P1 receptor, S1PR1. As primary lung graft dysfunction is induced by lung vascular endothelial cell barrier dysfunction, we hypothesized that SEW-2871, a S1PR1 agonist, may attenuate NPE when administered to the donor shortly after BD. Significant lung injury was observed 4h after BD in a rat BD model with ~60% increases in BAL total protein, BAL cell counts, and lung tissue W/D weight ratios. In contrast, rats receiving SEW-2871 (0.1 mg/kg) 15 minutes after the induction of BD and assessed 4h later exhibited significant lung protection (~50% reduction, p=0.01) reflected by reduced BAL total protein, BAL cytokines concentrations, BAL albumin, BAL total cell count and lung tissue wet/dry (W/D) weights ratio. Microarray analysis at 4hrs revealed a global impact of both BD and SEW on lung gene expression with differential expression of a subclass of genes enriched in immune/inflammation response pathways across the 4 experimental groups. Overall, SEW served to attenuate the BD-mediated ie gene expression upregulation. Two potentially useful biomarkers, Tnf and Ccrl2, exhibited gene dysregulation by microarray analysis, which was validated by qPCR. We conclude that SEW-2871 significantly attenuates BD-induced lung injury and may serve as a potential candidate to improve human lung donor availability and transplantation outcomes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21617203" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22537" }, "primaryId" : "GEO:GSE22537", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22537" } ] }, "title" : "Gene expression changes in response to doxycyline-induced expression of proinsulin (C96Y)-GFP in an INS-1 insulinoma cell line", "dateAssigned" : "2010-06-23T00:00:00.000-05:00", "summary" : "A doxycyline-inducible INS-1 insulinoma cell line expressing proinsulin (C96Y)-GFP was engineered. Addition of doxycyline causes the production of the proinsulin (C96Y)-GFP, which is retained in the endoplasmic reticulum. This study analyzes the gene expression changes that occur after doxycyline-induced expression of proinsulin (C96Y)-GFP for 24h, 48h and 5 days. Expression changes were compared between control un-induced cells and cells treated with doxycyline. Three replicates (experiments) were performed for each time point.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20659334" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22540" }, "primaryId" : "GEO:GSE22540", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22540" } ] }, "title" : "Nutritional programming of the metabolic syndrome is associated with long-lasting changes in nutrient sensing and energy homeostasis in the hypothalamus as revealed by genome-wide DNA microarray analysis", "dateAssigned" : "2010-06-23T00:00:00.000-05:00", "summary" : "Nutrient deficiency during perinatal development is associated with an increased risk to develop obesity, diabetes and hypertension in adulthood. However, the molecular mechanisms underlying the developmental programming of the metabolic syndrome remain largely unknown. Given the essential role of the hypothalamus in the integration of nutritional, endocrine and neuronal cues, here we have analyzed the profile of the hypothalamus transcriptome in 180-day-old rats born to dams fed either a control (200 g/kg) or a low-protein (80 g/kg) diet throughout pregnancy and lactation. From a total of 26,209 examined genes, 688 were up-regulated and 309 down-regulated (P<0.003) by early protein restriction. Based on the hypothesis that variations in gene expression levels often reflect changes in gene’s activity and that transcriptional networks are at the heart of physiological functions, we identified two gene clusters regulating common cellular processes whose expression is coordinately regulated by perinatal protein restriction. The first one is constituted by several genes of the insulin signaling pathway which, additionally, act as gatekeeper genes for regulation of nutrient sensing. The second cluster encompasses a functional network of nuclear receptors and co-regulators of transcription involved in the detection and use of lipid nutrients as fuel which, in addition, link temporal and nutritional cues to metabolism through their tight interaction with the circadian clock. Collectively, these results indicate that the programming of the hypothalamic circuits regulating energy homeostasis is a key step in the development of obesity associated with malnutrition in early life and provide a valuable starting point for the direct and systematic experimental analysis of the role of the hypothalamus in the physiopathological disturbances associated with the programming of the metabolic syndrome.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20975839" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22545" }, "primaryId" : "GEO:GSE22545", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22545" } ] }, "title" : "Mammary gland development: cross-species analysis of the mammary gland transcriptome in pregnant or lactating wild type female Sprague Dawley rats.", "dateAssigned" : "2010-06-24T00:00:00.000-05:00", "summary" : "Cross-species hybridization analysis of mammary glands during pregnancy and lactation. Results provide insight into putative conserved molecular mechanisms regulating mammary gland development. This study was performed to identify orthologous transcripts that are differentially co-expressed in the mammary gland at 2 stages of development (pregnancy and lactation) in wild type Sprague-Dawley rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24288657" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22553" }, "primaryId" : "GEO:GSE22553", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22553" } ] }, "title" : "Cardiac Effects of Rosiglitazone in Male Wistar Rats", "dateAssigned" : "2010-06-24T00:00:00.000-05:00", "summary" : "Rosiglitazone, a peroxisome proliferator-activated receptor g (PPARg) agonist of the thiazolidinedione class, is a major insulin-sensitizing drug widely used to treat type-2 diabetes. Rosiglitazone causes myocardial hypertrophy in rodents and increases the risk of cardiac events in man. To better characterize its cardiac effects, male Wistar rats were orally administered 0, 10 or 80 mg/kg/day rosiglitazone.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22622" }, "primaryId" : "GEO:GSE22622", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22622" } ] }, "title" : "Neurotoxin tetrodotoxin TTX withdrawal induced neuronal activity: RNA Pol II is poised for rapid induction of arc and other neuronal VF-IEGs", "dateAssigned" : "2010-06-29T00:00:00.000-05:00", "summary" : "Transcription of immediate early genes (IEGs) in neurons is exquisitely sensitive to neuronal activity, but the mechanism underlying the earliest of these transcription events is largely unknown. Here we demonstrate that very fast IEGs (VF-IEGs) such as arc/arg3.1 are poised for rapid transcription by the stalling of RNA Polymerase II (Pol II) just downstream of the transcription start site. RNAi-depletion of two subunits of a mediator of Pol II stalling, Negative Elongation Factor, reduces Pol II occupancy of the arc promoter and compromises rapid induction of arc and other VF-IEGs. In contrast, reduction of Pol II stalling did not prevent expression of other fast IEGs (F-IEGs). These F-IEGs are expressed with comparatively slower kinetics and largely lack promoter proximal Pol II stalling. Taken together, our data strongly indicate that very fast kinetics of neuronal IEG expression require poised Pol II and suggest a role for this mechanism in transcription-dependent learning and memory.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21623364" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22631" }, "primaryId" : "GEO:GSE22631", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22631" } ] }, "title" : "Whole-genome gene expression profiling of F11 dorsal root ganglion (DRG)-like cells stimulated with forskolin", "dateAssigned" : "2010-06-30T00:00:00.000-05:00", "summary" : "We generated whole-genome gene expression profiles of F11 dorsal root ganglion (DRG)-like neuroblastoma cells stimulated with the adenylate cyclase activator forskolin for 0, 2, 4, 24 and 48 hours.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21112399" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22638" }, "primaryId" : "GEO:GSE22638", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22638" } ] }, "title" : "Global transcriptome analysis reveals differences between embryonic and adult dorsal root ganglion axonal mRNAs that are implicated in axonal growth and pain", "dateAssigned" : "2010-06-30T00:00:00.000-05:00", "summary" : "Local protein synthesis in sensory neuron axons is necessary for axonal regeneration with the efficiency of regeneration decreasing with age. Because the full repertoire of transcripts in embryonic and adult rat sensory axons is unknown we asked how the pool of mRNAs dynamically changes during ageing. We isolated mRNA from pure axons and growth cones devoid of non-neuronal or cell body contamination. Genome-wide microarray analysis reveals that a previously unappreciated number of transcripts are localised in sensory axons and that this repertoire changes during development toward adulthood. Embryonic sensory axons are enriched in transcripts encoding cytoskeletal-related proteins with a role in axonal outgrowth. Surprisingly, adult axons are highly enriched in mRNAs encoding immune molecules with a role in nociception. To validate our experimental approach we show that Tubulin-beta3 mRNA is present only in embryonic axons where it is locally synthesised. In summary, we show that the population of axonal mRNAs dynamically changes during development, which may partly contribute to the intrinsic capacity of axons at different ages to regenerate after injury and to modulate pain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21098654" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22647" }, "primaryId" : "GEO:GSE22647", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22647" } ] }, "title" : "Adenosine 5’ monophosphate-activated protein kinase regulates metabolic actions of glucocorticoids by phosphorylating the glucocorticoid receptor through p38 mitogen-activated protein kinase.", "dateAssigned" : "2010-06-30T00:00:00.000-05:00", "summary" : "Glucocorticoids play central roles in the regulation of energy metabolism by shifting it toward catabolism, while AMPK is the master regulator of energy homeostasis, sensing energy depletion and stimulating pathways of increasing fuel uptake and saving on peripheral supplies. We showed here that AMPK regulates glucocorticoid actions on carbohydrate metabolism by targeting the glucocorticoid receptor (GR) and modifying transcription of glucocorticoid-responsive genes in a tissue- and promoter-specific fashion. Activation of AMPK in rats reversed glucocorticoid-induced hepatic steatosis and suppressed glucocorticoid-mediated stimulation of glucose metabolism. Transcriptomic analysis in the liver suggested marked overlaps between the AMPK and glucocorticoid signaling pathways directed mostly from AMPK to glucocorticoid actions. AMPK accomplishes this by phosphorylating serine 211 of the human GR indirectly through phosphorylation and consequent activation of p38 MAPK and by altering attraction of transcriptional coregulators to DNA-bound GR. In human peripheral mononuclear cells, AMPK mRNA expression positively correlated with that of glucocorticoid-responsive GILZ, which correlated also positively with the body mass index of subjects. These results indicate that the AMPK-mediated energy control system modulates glucocorticoid action at target tissues. Since increased action of glucocorticoids is associated with development of metabolic disorders, activation of AMPK could be a promising target for developing pharmacologic interventions to these pathologies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20660302" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22655" }, "primaryId" : "GEO:GSE22655", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22655" } ] }, "title" : "MicroRNAs and Their Predicted TargetMessenger RNAs are Deregulated by Exposure to a Carcinogenic Dose of Comfrey in Rat Liver", "dateAssigned" : "2010-07-01T00:00:00.000-05:00", "summary" : "MicroRNAs (miRNAs) are small non-coding RNAs that function as regulators of gene expression to control cell growth and differentiation. MiRNA levels are substantially altered in various types of tumors and have been used as biomarkers in defining malignant status. However, studies on responses of miRNA expression to carcinogen insults in their target tissues are rare. In this study, we analyzed miRNA expression in the livers of rats treated with carcinogenic dose of comfrey (Symphytum officinale), a rat botanical carcinogen.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22770" }, "primaryId" : "GEO:GSE22770", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22770" } ] }, "title" : "Comparison of rat mammary carcinomas induced by pre- and postpubertal irradiation", "dateAssigned" : "2010-07-06T00:00:00.000-05:00", "summary" : "Childhood exposure to carcinogens renders a higher risk of breast cancer. The molecular mechanisms underlying cancer development after such exposure are not, however, well understood. Here we examined how the mechanism of cancer development relates to the age at exposure to ionizing radiation (IR) or the carcinogen 1-methyl-1-nitrosourea (MNU). Pre- and postpubertal (3- and 7-week-old, respectively) female Sprague-Dawley rats were whole-body gamma-irradiated (2 Gy), injected intraperitoneally with MNU (20 mg/kg) or left untreated and were autopsied at 50 weeks of age. Mammary carcinomas were examined for estrogen receptor (ER) alpha, progesterone receptor (PR) and ErbB ligand expression and for expression microarrays. Early histological changes of the ovaries were also evaluated. The incidence of mammary cancer was higher after postpubertal, rather than prepubertal, IR exposure; the inverse was true for MNU. Most cancers were positive for both ER alpha and PR except for the prepubertal IR group. Interestingly, cancers of the prepubertal IR group expressed a different set of ErbB ligands from those of the other groups and did not overexpress Areg, which encodes an estrogen-regulated ErbB ligand, or other developmentally related genes including those for hormonally regulated mammary gland development. Prepubertal IR exposure resulted in ovarian dysfunction as revealed by a reduced follicular pool. Evidence thus suggests that mammary carcinogenesis induced by prepubertal IR exposure is independent of ovarian hormones but requires certain ErbB ligands; induction by postpubertal exposure depends on ovarian hormones and different ErbB ligands. In contrast, MNU-induced carcinogenesis was less influenced by the age at exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21374731" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22791" }, "primaryId" : "GEO:GSE22791", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22791" } ] }, "title" : "Microarray analysis of expression of cell death-associated genes in rat spinal cord cells exposed to cyclic tensile stresses in vitro", "dateAssigned" : "2010-07-07T00:00:00.000-05:00", "summary" : "We investigated the effect of cyclic tensile stresses on cultured spinal cord cells from E15 Sprague-Dawley rats, using the FX3000® Flexercell Strain Unit. We examined cell morphology and viability over a 72 hour time course. Microarray analysis of gene expression was performed using the Affymetrix GeneChip System®, where categorization of identified genes was performed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) systems.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20663127" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22818" }, "primaryId" : "GEO:GSE22818", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22818" } ] }, "title" : "Comparison of Saffron and Photobiomodulation on the light damaged rat retina.", "dateAssigned" : "2010-07-08T00:00:00.000-05:00", "summary" : "Conclusions: Given alone, saffron and (more prominently) PBM both regulated significant numbers of genes and ncRNAs. Given prior to retinal exposure to damaging light, thus while exerting their neuroprotective action, they regulated much larger numbers of entities, among which ncRNAs were prominent. Further, the downregulation of known genes and of ncRNAs was prominent in the protective actions of both neuroprotectants. These comparisons provide an overview of gene expression induced by two neuroprotectants and provide a basis for more focused study of their mechanisms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21571681" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22878" }, "primaryId" : "GEO:GSE22878", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22878" } ] }, "title" : "Rapid transcription of arc/arg3.1 and other very fast immediate early genes in response to neuronal activity is mediated by a stalled RNA polymerase II mechanism", "dateAssigned" : "2010-07-12T00:00:00.000-05:00", "summary" : "Transcription of immediate early genes (IEGs) in neurons is exquisitely sensitive to neuronal activity, but the mechanism underlying the earliest of these transcription events is largely unknown. Here we demonstrate that very fast IEGs (VF-IEGs) such as arc/arg3.1 are poised for rapid transcription by the stalling of RNA Polymerase II (Pol II) just downstream of the transcription start site. RNAi-depletion of two subunits of Negative Elongation Factor, a mediator of Pol II stalling, reduces the Pol II occupancy of the arc promoter and compromises the rapid induction of arc and other VF-IEGs. In contrast, reduction of Pol II stalling did not prevent expression of fast IEGs (F-IEGs). These F-IEGs are expressed with comparatively slower kinetics and largely lack promoter proximal Pol II stalling. Taken together, our data strongly indicate that very fast kinetics of neuronal IEG expression require poised Pol II and suggest a role for this mechanism in transcription-dependent learning and memory.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21623364" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22894" }, "primaryId" : "GEO:GSE22894", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22894" } ] }, "title" : "NRSF mediated epigenetic mechanisms of ion channel dysfunction in experimental temporal lobe epilepsy [Control vs. Kainate, NRSE ODNs]", "dateAssigned" : "2010-07-12T00:00:00.000-05:00", "summary" : "Oligodeoxynucleotides used to prevent NRSF binding to NRSE containing genes were utilized to prevent many kainate induced status epilepticus changes in gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25117540" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22896" }, "primaryId" : "GEO:GSE22896", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22896" } ] }, "title" : "NRSF mediated epigenetic mechanisms of ion channel dysfunction in experimental temporal lobe epilepsy [Control vs. Kainate, scrambled ODNs]", "dateAssigned" : "2010-07-12T00:00:00.000-05:00", "summary" : "Oligodeoxynucleotides used to prevent NRSF binding to NRSE containing genes were utilized to prevent many kainate induced status epilepticus changes in gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25117540" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22897" }, "primaryId" : "GEO:GSE22897", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22897" } ] }, "title" : "NRSF mediated epigenetic mechanisms of ion channel dysfunction in experimental temporal lobe epilepsy [Kainate, NRSE ODNs vs. Kainate, scrambled ODNs]", "dateAssigned" : "2010-07-12T00:00:00.000-05:00", "summary" : "Oligodeoxynucleotides used to prevent NRSF binding to NRSE containing genes were used to prevent many kainate induced status epilepticus changes in gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25117540" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22977" }, "primaryId" : "GEO:GSE22977", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE22977" } ] }, "title" : "Rat hepatocytes: Advanced cirrhosis vs Control liver, Advanced cirrhosis vs Early cirrhosis", "dateAssigned" : "2010-07-16T00:00:00.000-05:00", "summary" : "Gene profiling of hepatocytes in early and advanced cirrhotic Rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22109844" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23004" }, "primaryId" : "GEO:GSE23004", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23004" } ] }, "title" : "Gene expression profiles in rat mesenteric lymph nodes upon supplementation with conjugated linoleic acid during gestation and suckling", "dateAssigned" : "2010-07-19T00:00:00.000-05:00", "summary" : "Diet plays a role in the development of the immune system, and polyunsaturated fatty acids can modulate the expression of a variety of genes. Human milk contains conjugated linoleic acid (CLA), a fatty acid that seems to contribute to immune development. Indeed, recent studies carried out in our group in suckling animals have shown that the immune function is enhanced after feeding 80:20 isomer mix of c9,t11 and t10,c12 CLA, respectively. However, little work has been done on the effects of CLA on gene expression, and even less regarding immune system development in early life. With all these concepts in mind, we determined the expression profile of Mesentheric Lymph Nodes (MLN) from animals supplemented with CLA during gestation and suckling through dam’s milk (Group A) or by oral gavage (Group B), supplemented just during suckling (Group C) and control animals (Group D) with the aid of the specific GeneChip ® Rat Genome 230 2.0 (Affymettrix). Bioinformatic analyses were performed using the GeneSpring GX software package v10.0.2 and lead to the identification of 123 genes differentially expressed in all three dietary approaches. Generation of a Biological Association Network (BAN) evidenced several genes, such as connective tissue growth factor (Ctgf), tissue inhibitor of metalloproteinase 1 (Timp1), galanin (Gal), synaptotagmin 1 (Syt1), growth factor receptor bound protein 2 (Grb2) actin gamma 2 (Actg2) and smooth muscle alpha actin (Acta2), as highly interconnected nodes of the resulting network. Gene underexpression was confirmed by Real-Time RT-PCR. We conclude that Ctgf, Timp1, Gal and Syt1, among others, are genes modulated by CLA supplementation that may have a role on lymphoproliferation and mucosal immune responses in early life.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21481241" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23037" }, "primaryId" : "GEO:GSE23037", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23037" } ] }, "title" : "Estrogens and selective estrogen receptor modulators regulate gene and protein expression in the mesenteric arteries", "dateAssigned" : "2010-07-20T00:00:00.000-05:00", "summary" : "Estrogen is a reproductive steroid hormone that has both beneficial and detrimental effects on the cardiovascular system. Selective estrogen receptor modulators (SERMs) exhibit partial estrogen agonist/antagonist activity in estrogen target tissues. Since we still have an incomplete picture of the gene targets of estrogen in the vasculature, and our understanding of SERM gene targets in the vasculature is even less well-developed, it is important to broaden the available information on this subject. The present study tested the hypothesis that estrogens (ethinyl estradiol, estradiol benzoate, and equilin) and SERMs (tamoxifen and raloxifene) cause differential gene and protein expression in the vasculature. DNA microarray and real-time RT-PCR were used to investigate gene expression in the mesenteric arteries of estrogen and SERM treated ovariectomized rats. The genes shown to be differentially expressed included stearoyl-CoA desaturase (SCD), soluble epoxide hydrolase (sEH), secreted frizzled related protein-4 (SFRP-4), insulin-like growth factor-1 (IGF-1), phospholipase A2 group 1B (PLA2-G1B), and fatty acid synthase (FAS). Western blot further confirmed the differential expression of sEH, SFRP-4, FAS, and SCD protein. These results reveal that estrogens and SERMs cause differential gene and protein expression in the mesenteric artery. Consequently, the use of these agents may be associated with a unique profile of functional and structural changes in the mesenteric arterial circulation. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21658471" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23079" }, "primaryId" : "GEO:GSE23079", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23079" } ] }, "title" : "Global gene expression profiling in early-stage polycystic kidney disease in the Han:SPRD Cy rat identifies a role for RXR signaling", "dateAssigned" : "2010-07-22T00:00:00.000-05:00", "summary" : "Han:SPRD Cy is a spontaneous rat model of polycystic kidney disease (PKD) caused by a missense mutation in Pkdr1. Cystogenesis in this model is not clearly understood. In the current study, we performed global gene expression profiling in early-stage PKD cyst development in Cy/Cy kidneys and normal (+/+) kidneys, at 3 and 7 days of postnatal age. Expression profiles were determined by microarray analysis, followed by validation with real-time RT-PCR. Genes were selected with over 1.5 fold expression changes compared with age-matched +/+ kidneys for canonical pathway analysis. We found 9 pathways in common between 3-day and 7-day Cy/Cy kidneys. Three significantly changed pathways were designated 'VDR/RXR Activation,' 'LPS/IL-1 Mediated Inhibition of RXR Function,' and 'LXR/RXR Activation'. These results suggest that RXR mediated signaling is significantly altered in developing kidneys with mutated Pkdr1. In gene ontology analysis, the functions of these RXR-related genes were found to be involved in regulating cell proliferation and organ morphogenesis. With real-time RT-PCR analysis, the up-regulation of Ptx2, Alox15b, OSP and PCNA, major markers of cell proliferation associated with the RXR pathway, were confirmed in 3- and 7-day Cy/Cy kidneys compared with 3-day +/+ kidneys. The increased RXR protein was observed both in nuclei and cytoplasm of cystic epithelial cells in early-stage Cy/Cy kidneys, and the RXR-positive cells were strongly positive for PCNA staining. Taken together, cell proliferation and organ morphogenesis signals transduced by RXR mediated pathways may have important roles for cystogenesis in early-stage PKD in this Pkdr1-mutated Cy rat.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20926632" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23093" }, "primaryId" : "GEO:GSE23093", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23093" } ] }, "title" : "Using Oligo Array Analysis to Determine Genes of Importance in the Meninges and Associated Vasculature Function and their Sensitivity to Amphetamine Toxicity", "dateAssigned" : "2010-07-22T00:00:00.000-05:00", "summary" : "Oligo array analysis with bioinformatics tools identified genes with very high expression levels in the meninges, arachnoid and pial membranes, and associated vasculatures (MAV) which are potentially important and unique to these tissues functional capabilities in rat. It was also determined if these genes were more sensitive to expression changes after a neurotoxic exposure to environmentally induced hyperthermia (EIH) or amphetamine (AMPH). Gene expression in the MAV was compared to the neuronal rich tissues of the striatum and parietal cortex. In controls, 1,116 genes differed by more than 5-fold when comparing MAV to both striatum and parietal cortex. Genes specifically identified with the blood-brain barrier (BBB) were also expressed at high levels indicating they may help form tight junctions in MAV. The more than 300 genes having a 15-fold or greater expression in MAV compared to striatum and cortex were deemed of potential uniqueness and importance to MAV function. Many of these genes are abundant in different types of epithelial tissue and function in binding, transport or metabolism of ions and solute, and may help MAV regulate cerebrospinal fluid. Many others with high expressions are involved in immune system function possibly serving to facilitate lymphocyte and macrophage trafficking in vasculature and cerebrospinal fluid. Genes in MAV with a higher expression (relative to striatum and cortex) were affected in greater numbers than expected by EIH and AMPH. Many expression increases evoked by AMPH and EIH in MAV relate to reactive oxidative stress and inflammation. However, AMPH induced more robust alterations in the expression of genes related to ion/solute transport (Slc15a1), lipid metabolism (Fst), bacterial infection (Lbp) and oddly pancreatitis (Reg3a, Reg3b). Expression of the BBB-related genes Sox18 and Cldn5 decreased in all regions with AMPH and EIH but even more so in MAV. Esam increased with AMPH in all regions while Angpt2 was only affected in striatum and parietal cortex. It is not known how these changes affect MAV, striatum or parietal cortex tight junction function/BBB and integrity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23183685" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23152" }, "primaryId" : "GEO:GSE23152", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23152" } ] }, "title" : "Gene expression during first day of collagen gel culture of rat aortic rings", "dateAssigned" : "2010-07-26T00:00:00.000-05:00", "summary" : "We used microarrays to detail the pattern of gene expression underlying initial 24 hours of growth, prior to the sprouting of visible neovessles, and identified distinct classes of up-regulated genes during this process.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21372301" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23153" }, "primaryId" : "GEO:GSE23153", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23153" } ] }, "title" : "Gene expression in TNF treated rat aortic rings cultured in collagen or fibrin gels.", "dateAssigned" : "2010-07-26T00:00:00.000-05:00", "summary" : "We used microarrys to examine the effects of TNF-alpha on gene expression in both fibrin and collagen gels during the first 48 hours or culture.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21372301" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23179" }, "primaryId" : "GEO:GSE23179", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23179" } ] }, "title" : "Gene expression microarray analysis of rat nasal tissue with time and dose following formaldehyde inhalation", "dateAssigned" : "2010-07-27T00:00:00.000-05:00", "summary" : "Formaldehyde (FA), an endogenous cellular aldehyde, is a rat nasal carcinogen. In this study, concentration- and exposure-duration transitions in FA mode of action (MOA) were examined with pharmacokinetic (PK) modeling for tissue formaldehyde acetal (FAcetal) and glutathione (GSH) and with histopathology and gene expression studies for tissue responses in nasal epithelium from rats exposed to 0, 0.7, 2, 6, 10 or 15 ppm FA 6 hr/day for 1, 4 or 13 weeks. The study had two goals. The first goal was to develop a basic PK model to estimate various forms of tissue formaldehyde and tissue glutathione (GSH). The second goal was to compare histopathology and gene expression changes in nasal tissues caused by inhalation of FA with changes in tissue FAcetal and free GSH calculated from the PK model. Patterns of gene expression varied with concentration and with duration. At 0.7 and 2 ppm, sensitive response genes (SRGs) - associated with cellular stress, thiol transport/reduction, inflammation, and cell proliferation - were similarly upregulated at all exposure durations. At 6 ppm and greater, gene expression changes showed enrichment of pathways involved in cell cycle, DNA repair, and apoptosis processes. ERBB, EGFR, WNT, TGF-ß, Hedgehog, and Notch signaling were also enriched in differentially expressed genes. Benchmark doses (BMDs) for genes in significantly enriched pathways were lower at 13 weeks than at 1 or 4-week. The transcriptional and histological changes corresponded to PK model-predicted changes in free GSH at 0.7 and 2 ppm and in FAcetal at 6 ppm. DNA-replication stress, enhanced proliferation, metaplasia, and stem cell-niche activation appear to be associated with FA carcinogenesis at 6 ppm and above. Dose dependencies in MOA, the presence of high physiological FAcetal, and non-linear FAcetal/GSH tissue kinetics indicate that FA concentrations below 150 ppb (and probably any concentrations below irritant levels, i.e., ~ 1 ppm) would not increase cancer risks of inhaled FA in the nose or any other tissue. Closer examination of dose response relationships for endogenous compound toxicity could help guide biologically relevant approaches for chemical risk assessment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20884683" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23207" }, "primaryId" : "GEO:GSE23207", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23207" } ] }, "title" : "Transcriptome analysis of MENX-associated rat pituitary adenomas identifies novel molecular mechanisms involved in the pathogenesis of human pituitary gonadotroph adenomas", "dateAssigned" : "2010-07-27T00:00:00.000-05:00", "summary" : "Gonadotroph adenomas comprise 15–40 % of all pituitary tumors, are usually non-functioning and are often large and invasive at presentation. Surgery is the first-choice treatment, but complete resection is not always achieved, leading to high recurrence rates. As gonadotroph adenomas poorly respond to conventional pharmacological therapies, novel treatment strategies are needed. Their identification has been hampered by our incomplete understanding of the molecular pathogenesis of these tumors. Recently, we dem¬onstrated that MENX-affected rats develop gonadotroph adenomas closely resembling their human counterparts. To discover new genes/pathways involved in gonadotroph cells tumorigenesis, we performed transcriptome profiling of rat tumors versus normal pituitary. Adenomas showed overrep¬resentation of genes involved in cell cycle, development, cell differentiation/proliferation, and lipid metabolism. Bioinfor¬matic analysis identified downstream targets of the transcrip¬tion factor SF-1 as being up-regulated in rat (and human) adenomas. Meta-analyses demonstrated remarkable similari¬ties between gonadotroph adenomas in rats and humans, and highlighted common dysregulated genes, several of which were not previously implicated in pituitary tumorigenesis. Two such genes, CYP11A1 and NUSAP1, were analyzed in 39 human gonadotroph adenomas by qRT-PCR and found to be up-regulated in 77 and 95 % of cases, respectively. Immunohistochemistry detected high P450scc (encoded by CYP11A1) and NuSAP expression in 18 human gonado¬troph tumors. In vitro studies demonstrated for the first time that Cyp11a1 is a target of SF-1 in gonadotroph cells and promotes proliferation/survival of rat pituitary adenoma pri¬mary cells and cell lines. Our studies reveal clues about the molecular mechanisms driving rat and human gonadotroph adenomas development, and may help identify previously unexplored biomarkers for clinical use.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23756599" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23328" }, "primaryId" : "GEO:GSE23328", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23328" } ] }, "title" : "Expression data from seven rat tissues at multiple ages", "dateAssigned" : "2010-07-29T00:00:00.000-05:00", "summary" : "This study sampled seven tissues at four ages in rats to measure genome-scale gene expression, which allows global insight into coordination, specificity and/or commonness among different tissues with aging progress.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21912663" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23432" }, "primaryId" : "GEO:GSE23432", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23432" } ] }, "title" : "Indian Hedgehog Signaling in the Postnatal Growth Plate", "dateAssigned" : "2010-08-05T00:00:00.000-05:00", "summary" : "In order to characterize mRNA expression in the growth plate, we microdissected postnatal rat growth plates into their constituent zones and used microarray analysis to assess the abundences of individual transcripts. Expression patterns of PTHrP and Ihh-related genes were confirmed using real-time PCR. Using a gli1-lacZ mouse, Gli1 expression, presumably representing Ihh signaling, was visualized during pre- and postnatal development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21642420" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23559" }, "primaryId" : "GEO:GSE23559", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23559" } ] }, "title" : "The role of dietary leucine and dairy protein on hepatic gene expression", "dateAssigned" : "2010-08-11T00:00:00.000-05:00", "summary" : "The primary aims of this study were: (i) to compare the effects of diets with protein derived from casein, casein supplemented with leucine, and complete dairy on body composition and insulin sensitivity; and (ii) to determine if there is a synergistic effect of dietary Ca and protein source on body composition and insulin sensitivity. Secondarily, we used microarray analysis to examine the effect of casein, leucine, or complete dairy containing diets on the expression of hepatic genes related to lipid and glucose metabolism.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23643" }, "primaryId" : "GEO:GSE23643", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23643" } ] }, "title" : "Cardiac transcriptome profiles of S.LEW congenic strain compared with the hypertensive Dahl S rat", "dateAssigned" : "2010-08-16T00:00:00.000-05:00", "summary" : "Despite inheritance of hypertension in families, identifying genetic mechanisms predisposing individuals to hypertension has remained challenging. The effects of single genes contributing to the development of hypertension may not be readily detected in individuals whose genomes also contain other genetic factors that resist hypertension. By using a highly permissive rat genome for inherited hypertension, we demonstrate that increased expression of one such gene, Rififylin (Rffl), is a novel inherited risk factor for hypertension and increased mortality. Animals overexpressing Rffl demonstrated delayed endocytic recycling, accumulated polyubiquitinated proteins, increased beats/min of neonatal cardiomyocytes, had shorter QT-intervals and developed salt-insensitive hypertension very early in their life (50-52 days). Thus, the discovery of a physiological link between overexpression of rififylin and the development of hypertension constitutes a novel mechanism that could be targeted for rectifying normal QT-interval and preventing hypertension.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21357277" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23648" }, "primaryId" : "GEO:GSE23648", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23648" } ] }, "title" : "Sciatic nerve FAIRE-chip and ChIP-Chip with Egr2/Krox20 and Sox10", "dateAssigned" : "2010-08-16T00:00:00.000-05:00", "summary" : "This experiment includes a custom ChIP-chip design incorporating many genes that are dynamically regulated during peripheral nerve myelination. Two antibodies were used for Egr2, Abcam and Covance PRB-236P.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21653862" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23651" }, "primaryId" : "GEO:GSE23651", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23651" } ] }, "title" : "Global transcriptomic profiling of permanent focal ischemia in an in vivo rat model", "dateAssigned" : "2010-08-16T00:00:00.000-05:00", "summary" : "Focal ischemia is triggered by the sudden significant reduction of blood supply to the brain, as a result of either the rupture or occlusion by thrombus/embolism of a blood vessel in the brain. Permanent focal ischemia occurred when blood supply to a specific part of the brain is impeded without reperfusion. Despite major steps achieved in the elucidation of the patho-physiology of cerebral ischemia, the available therapeutic avenues for acute ischemic stroke remain scarce. Cell cycle re-activation has been revealed as a novel signaling pathway during permanent focal ischemia. As such, non-specific aurora kinase inhibitor ZM447439, has been injected intracranial-ventricularly30min post-ischemia induction to determine its efficacy in reduction of neuronal damage in terms of infarct volume.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23653" }, "primaryId" : "GEO:GSE23653", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23653" } ] }, "title" : "Comparative global transcriptomic profiling of mild and severe neurotrauma in an in vitro neuronal model", "dateAssigned" : "2010-08-16T00:00:00.000-05:00", "summary" : "Traumatic brain injury is one of the common cause of adult permanent disability. As its physio-pathological mechanism has yet to be elucidated, by adopting microarray technique we hope to decipher the novel signaling cascades involved, and if different severity of injury would induce any form of neuronal regeneration.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23668" }, "primaryId" : "GEO:GSE23668", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23668" } ] }, "title" : "A small molecule accelerates neuronal differentiation in the adult rat", "dateAssigned" : "2010-08-17T00:00:00.000-05:00", "summary" : "Adult neurogenesis occurs in mammals and provides a mechanism for continuous neural plasticity in the brain.However, little is known about the molecular mechanisms regulating hippocampal neural progenitor cells (NPCs) and whether their fate can be pharmacologically modulated to improve neural plasticity and regeneration. Here, we report the characterization of a unique small molecule (KHS101) that selectively induces a neuronal differentiation phenotype. Mechanism of action studies revealed a link of KHS101 to cell cycle exit and specific binding to the TACC3 protein, whose knockdown in NPCs recapitulates the KHS101-induced phenotype. Upon systemic administration, KHS101 distributed to the brainandresulted in a significant increase in neuronal differentiation in vivo. Our findings indicate that KHS101 accelerates neuronal differentiation by interaction with TACC3 and may provide a basis for pharmacological intervention.directed at endogenous NPCs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20823227" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23696" }, "primaryId" : "GEO:GSE23696", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23696" } ] }, "title" : "MicroRNA array analysis during the regenerative peak following rat liver resection", "dateAssigned" : "2010-08-18T00:00:00.000-05:00", "summary" : "The liver has the unique capacity to regenerate after surgical resection. However, the regulation of liver regeneration is not completely understood. We performed miRNA microarray analyses of liver tissue from Wistar rats at different time points after 70% partial hepatectomy (0, 2, 6, 12, 24, 48 hours, and 5 days) and after sham laparotomy (12, 24, and 48 hours). We demonstrate that miRNA expression patterns changed during liver regeneration and that these changes were most evident during the peak of DNA replication at 24 hours after resection. Expression of 13 miRNAs, including five members of the let-7 family, was significantly reduced 12-48 hours after resection, whereas 3 miRNAs were significantly upregulated (> 25% change). We provide a temporal miRNA expression dataset of the regenerating rat liver, which indicates a primary function for miRNA during the peak of DNA replication. These data will assist further functional studies on the role of miRNAs during liver regeneration.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21430077" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23728" }, "primaryId" : "GEO:GSE23728", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23728" } ] }, "title" : "Effect of Maternal Separation on DOI-induced transcriptome", "dateAssigned" : "2010-08-20T00:00:00.000-05:00", "summary" : "While several molecular mechanisms have been hypothesized to mediate the long lasting effects of MS, the serotonin 2a receptor is an attractive candidate, given its role in regulating anxiety-like behavior. So we set out to ask if Maternal Separation alters the 5HT2a responses. In order to assay if MS alters the transcriptional targets of the 5Ht2a receptor, we use a drug that stimulates the 5Ht2a receptor, DOI. The experiment involves injecting both control and MS animals with DOI and looking at the transcriptome induced by DOI under control and MS conditions. This would help understand how the adverse early life experience MS, alters the transcriptional response of an adult rat to stimulation at the 5HT2a receptor, which is physiologically seen in conditions of stress.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23740" }, "primaryId" : "GEO:GSE23740", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23740" } ] }, "title" : "Effect of probiotic Lactobacillus casei Zhang on liver gene expression of hypercholesterolemic rats", "dateAssigned" : "2010-08-21T00:00:00.000-05:00", "summary" : "The hypocholesterolemic effect of probiotics has been observed, but the molecular mechanism of probiotic-host interaction is still obscure. In this study, DNA microarray technology was used to explore the gene expression profile of liver of hypercholesterolemic rats caused by administration of probiotic Lactobacillus casei Zhang, which can decrease the serum triglyceride, low-density lipoprotein cholesterol, hepatic cholesterol and triglyceride of hypercholesterolemic rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23748" }, "primaryId" : "GEO:GSE23748", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23748" } ] }, "title" : "Tofu decreases serum lipid levels and modulates hepatic gene expression involved in lipid metabolism in rats", "dateAssigned" : "2010-08-23T00:00:00.000-05:00", "summary" : "The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21721588" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23808" }, "primaryId" : "GEO:GSE23808", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23808" } ] }, "title" : "Molecular studies on sex-different control of the hepatic metabolism in relations to insulin sensitivity (set 1)", "dateAssigned" : "2010-08-25T00:00:00.000-05:00", "summary" : "In this study we have analyzed gene expression and metabolite levels in the livers of male and female Zucker diabetic fatty (ZDF) rats. We speculated that the sex different development of diabetes in the ZDF animals presents the opportunity to relate gender to diabetes (since only males become diabetic on normal diet). In this model one can search for parameters that distinguish females fed normal diet compared to high fat diet (i.e. components that vary with the development of diabetes) and evaluate if such changes can be related to components that characterize male diabetic animals..", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21673048" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23809" }, "primaryId" : "GEO:GSE23809", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23809" } ] }, "title" : "Molecular studies on sex-different control of the hepatic metabolism in relations to insulin sensitivity (set 2)", "dateAssigned" : "2010-08-25T00:00:00.000-05:00", "summary" : "In this study we have analyzed gene expression and metabolite levels in the livers of male and female Zucker diabetic fatty (ZDF) rats. We speculated that the sex different development of diabetes in the ZDF animals presents the opportunity to relate gender to diabetes (since only males become diabetic on normal diet). In this model one can search for parameters that distinguish females fed normal diet compared to high fat diet (i.e. components that vary with the development of diabetes) and evaluate if such changes can be related to components that characterize male diabetic animals..", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21673048" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23895" }, "primaryId" : "GEO:GSE23895", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23895" } ] }, "title" : "Selenium toxicity but not deficient or super-nutritional selenium status vastly alters the transcriptome in rodents", "dateAssigned" : "2010-08-31T00:00:00.000-05:00", "summary" : "Selenoprotein levels in rats increase sigmoidally with increasing dietary Se and reach defined plateaus at the Se requirement, making them sensitive biomarkers for Se deficiency, but not high for Se status. Biomarkers for high Se status are needed as super-nutritional Se intakes are associated with beneficial and adverse health outcomes, but conventional biomarkers are not especially useful above the Se requirement. To characterize Se regulation of the transcriptome, we conducted 3 microarray experiments in weanling mice and rats fed Se-deficient diets supplemented with levels of Se up to 5 µg Se/g diet.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21226930" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23941" }, "primaryId" : "GEO:GSE23941", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23941" } ] }, "title" : "Leptin dependent control of testosterone regulated hepatic lipid metabolism", "dateAssigned" : "2010-09-02T00:00:00.000-05:00", "summary" : "Results: Array analysis revealed that many hepatic lipogenic genes were increased in male ZDF rat livers treated with TU. Interestingly, SREBP-1c, a key transcriptional activator of lipogenic genes and PGC-1 , an activator of SREBP-1c were induced while small heterodimer partner, a transcriptional inhibitor of lipogenic genes was suppressed by TU treatment. Exploring signaling pathways for these effects, we observed that the hepatic activated forms of STAT3 and AMPK, two known inhibitors of hepatic lipogenesis, were decreased in TU treated rat. Moreover, we observed that DHT could block the induction of STAT3 and AMPK phosphorylation in treated primary human hepatocytes. Preliminarily, in the leptin receptor positive zucker diabetic lean male rats, we observed that TU treatment has an oppose effect on the hepatic lipogenic genes, suggesting that hepatic leptin signaling may influence androgen signaling. Further insight into the relationship between androgen deficiency and the leptin system may help improve treatment of the metabolic syndrome. Population based studies have established that androgen deficiency in males correlates with type 2 diabetes, visceral adiposity, and metabolic syndrome. Androgen therapy has been investigated as a possible treatment regime to combat these disorders. However, the molecular mechanism of androgen effects on these diseases still remain poorly understood. The zucker diabetic fatty (ZDF) rat, containing a mutation in the leptin receptor, is a well-investigated model of obesity and type 2 diabetes. Male rats are characterized as androgen deficient and spontaneously develop obese, hyperlipidemia, hyperglycemia and hyperinsulinemia. In this study, we used ZDF male rats as a model of metabolic syndrome to investigate the effects of testosterone administration on the development of the metabolic conditions.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23954" }, "primaryId" : "GEO:GSE23954", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23954" } ] }, "title" : "CONVERGENT GENESIS OF AN ADULT NEURAL CREST-LIKE DERMAL STEM CELL FROM DISTINCT DEVELOPMENTAL ORIGINS", "dateAssigned" : "2010-09-02T00:00:00.000-05:00", "summary" : "Skin-derived precursors (SKPs) are multipotent dermal stem cells that reside within a hair follicle niche and that share properties with embryonic neural crest precursors. Here, we have asked whether SKPs and their endogenous dermal precursors originate from the neural crest or whether, like the dermis itself, they originate from multiple developmental origins. To do this, we used two different mouse Cre lines that allow us to perform lineage tracing: Wnt1-cre, which targets cells deriving from the neural crest, and Myf5-cre, which targets cells of a somite origin. By crossing these Cre lines to reporter mice, we show that the endogenous follicle-associated dermal precursors in the face derive from the neural crest, and those in the dorsal trunk derive from the somites, as do the SKPs they generate. In spite of these different developmental origins, SKPs from these two locations are functionally similar, even with regard to their ability to differentiate into Schwann cells, a cell type only thought to be generated from the neural crest. Analysis of global gene expression using microarrays confirmed that facial and dorsal SKPs exhibit a very high degree of similarity, and that they are also very similar to SKPs derived from ventral dermis, which has a lateral plate origin. However, these developmentally-distinct SKPs also retain differential expression of a small number of genes that reflect their developmental origins. Thus, an adult neural crest-like dermal precursor can be generated from a non-neural crest origin, a finding with broad implications for the many neuroendocrine cells in the body.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20848654" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23983" }, "primaryId" : "GEO:GSE23983", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE23983" } ] }, "title" : "Short-term exposure to effluent from bulk drug industries", "dateAssigned" : "2010-09-07T00:00:00.000-05:00", "summary" : "The Patancheru area near Hyderabad in India is recognized as a key link in the global supply chain for many bulk drugs. A central treatment plant receives wastewater from about 90 different manufacturers and the resulting complex effluent has contaminated surface, ground and drinking water in the region. Ecotoxicological testing of the effluent has shown adverse effects for several organisms, including aquatic vertebrates. In an attempt to start investigating how exposure to effluent-contaminated water may affect humans and other terrestrial vertebrates, rats were tube-fed effluent. Results from microarray and quantitative polymerase chain reaction assays indicated, however, no marked effects on hepatic gene expression after five days exposure. Neither did a clinical analysis of blood serum constituents used as biomarkers for human disease reveal any significant changes, nor were there any effects on weight gain. Taken together, we could not find evidence for any acute toxicity in the rat; however, we cannot rule out that higher doses of effluent or a longer exposure time may still be associated with risks for terrestrial vertebrates.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24047" }, "primaryId" : "GEO:GSE24047", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24047" } ] }, "title" : "Gene expression profiles after traumatic brain injury", "dateAssigned" : "2010-09-09T00:00:00.000-05:00", "summary" : "We used microarray to elucidate relationship between the alteration of gene expression levels and the progression of brain damages following traumatic brain injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20950674" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24104" }, "primaryId" : "GEO:GSE24104", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24104" } ] }, "title" : "Vitamin A nutritional status and retinoic acid as regulators of gene expression in rat liver", "dateAssigned" : "2010-09-13T00:00:00.000-05:00", "summary" : "Vitamin A (retinol) is an essential precursor for the production of retinoic acid (RA), which in turn is a major regulator of gene expression, affecting cell differentiation throughout the body. Understanding how vitamin A nutritional status, as well as therapeutic retinoid treatment, regulates the expression of retinoid homeostatic genes is important for improving dietary recommendations and therapeutic strategies using retinoids. This study investigated genes central to processes of retinoid uptake and storage, release to plasma, and oxidation in the liver of rats under steady-state conditions after different exposures to dietary vitamin A (deficient, marginal, adequate and supplemented), and acutely after administration of a therapeutic dose of all-trans-RA. Over a very wide range of dietary vitamin A, lecithin:retinol acyltransferase (LRAT) as well as multiple cytochrome P450s (CYP26A1, CYP26B1, and CYP2C22) differed by diet and were highly correlated with one another and with vitamin A status assessed by liver retinol concentration (all correlations, P<0.05). After acute treatment with RA, the same genes were rapidly and concomitantly induced, preceding RARß, a classical direct target of RA. CYP26A1 mRNA exhibited the greatest dynamic range (change of log26 in 3 h). Moreover, CYP26A1 increased more rapidly in the liver of RA-primed rats than naïve rats. By in situ hybridization, CYP26A1 mRNA was strongly regulated within hepatocytes, closely resembling RBP4 in location. Overall, whether RA is produced endogenously from retinol or administered exogenously, changes in retinoid homeostatic gene expression simultaneously favor both retinol esterification and RA oxidation, with CYP26A1 exhibiting the greatest dynamic change.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21045116" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24110" }, "primaryId" : "GEO:GSE24110", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24110" } ] }, "title" : "Regression of Cardiac Hypertrophy and Attenuation of Progression to Heart Failure by Paricalcitol Therapy in Rats", "dateAssigned" : "2010-09-13T00:00:00.000-05:00", "summary" : "Conclusions: PC treatment resulted in both the regression of pre-existing cardiac hypertrophy, and the attenuation of the progression to heart failure, compared to improvement in progression to heart failure by EP alone. These beneficial findings in the heart were associated with inhibition of PKCe activation, and reversal of gene alterations.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21565836" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24194" }, "primaryId" : "GEO:GSE24194", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24194" } ] }, "title" : "Identification and characteristics of microRNAs in rat abdominal aortic aneurysms", "dateAssigned" : "2010-09-17T00:00:00.000-05:00", "summary" : "Abdominal aortic aneurysm (AAA) is a lethal disease, occurring mostly in men more than 65 years of age. Until recently, the pathogenesis of AAA remains poorly understood. MicroRNAs (miRNAs) are a novel class of endogenous small noncoding RNAs that play important roles in diverse biological and pathological processes and was more recently investigated in cardiovascular physiology and pathology. In this study, we employed microarray to detect and compare miRNA expressions of AAAs in rats. Four miRNAs were validated using real time RT-PCR. Functional annotations of putative targets of deregulated miRNAs via bioinformatics approaches revealed that predicted targets were highly enriched and involved in several signaling pathways important for AAA formation. Our results indicate that miRNAs are extensively involved in rat AAA formation and provide a global view of AAA miRNA profiles, which is expected to provide new clues to develop targeted therapies against this calamitous disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21030819" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24213" }, "primaryId" : "GEO:GSE24213", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24213" } ] }, "title" : "Expression profiling of rat heart and blood after amiodarone treatment", "dateAssigned" : "2010-09-18T00:00:00.000-05:00", "summary" : "In the present study, an oligonucleotide microarray platform was used to compare expression profiles of heart and blood in rats treated with amiodarone against respective controls. Male Sprague-Dawley (CD) rats, which were 10 weeks old and weighed 290-320 grams at the beginning of the study, have been treated for ten days with amiodarone by oral route at a dose of 300mg/Kg/die. The study has been constituted by a control group, which received the vehicle (methylcellulose 1%, w/v), and by a treatment group (10 animals for both groups). For each tissue sample, total RNA has been individually extracted and evaluated. For each tissue, three pools/group (2 pools composed of 3 animals and the last one by 4) have been used for microarray analysis. A modulation of 600 genes in heart and 8300 genes in blood has been obtained.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25580480" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24233" }, "primaryId" : "GEO:GSE24233", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24233" } ] }, "title" : "Transcriptome profiling in 6-hydroxydopamine hemiparkinsonian rats reveals methamphetamine-mediated dopamine-independent changes in striatal gene expression.", "dateAssigned" : "2010-09-20T00:00:00.000-05:00", "summary" : "Unilateral injections of 6-hydroxydopamine into the medial forebrain bundle (MFB) is used extensively as a model of Parkinson’s disease. The present experiments examined whether a single injection of methamphetamine (METH) (2.5 mg/kg) could still influence striatal gene expression after 6-hydroxydopamine (DA)-induced destruction of the nigrostriatal dopaminergic pathway in the rat. Unilateral injections of 6-hydroxydopamine into the MFB resulted in total striatal dopamine depletion on the lesioned side. This injection also caused decreased striatal serotonin (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels. DA depletion was associated with increases in 5-HIAA/5-HT ratios which were potentiated by the METH injection. Microarray analyses revealed changes (+ 1.7-fold, p < 0.025) in the expression of 67 genes on the lesioned side in comparison to the intact side of the saline-treated hemiparkinsonian animals. These include follistatin, neuromedin U, and tachykinin 2 which were up-regulated. METH administration caused increases in the expression of several genes including c-fos, Egr1, and NOR-1 on the intact side. On the DA-depleted side, METH administration also increased the expression of 61 genes including Pdgfd and COX-2. There were METH-induced changes in 16 genes that were common in the DA-innervated and DA-depleted sides. These include c-fos and NOR-1 which show greater changes on the normal DA side. The present study documents METH-mediated DA-independent transcriptional alterations of several genes in the DA-denervated striatum. Our results also implicate serotonin as an important player in METH-induced gene expression because the METH injection also caused significant increases in 5-HIAA/5-HT ratios on the DA-depleted side.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24252" }, "primaryId" : "GEO:GSE24252", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24252" } ] }, "title" : "miRNA profiling in adult rat cardiomyocytes and myocyte-derived progenitor cells", "dateAssigned" : "2010-09-21T00:00:00.000-05:00", "summary" : "TLDA miRNA profiling on purified rat cardiomyocytes (Myo) (Ctl) and myocyte-derived progenitor cells (MDCs) demonstrated significant dedifferentiation of myocytes and identity of stemness, cell cycle progression and proliferation in MDCs after continuous culture in mitogen-rich medium for about 2 weeks.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20838637" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24255" }, "primaryId" : "GEO:GSE24255", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24255" } ] }, "title" : "Wide-genome analysis of hepatocytes isolated from male and female rats treated with glucocorticoid.", "dateAssigned" : "2010-09-21T00:00:00.000-05:00", "summary" : "Glucocorticoids are widely used therapeutically to suppress inflammatory/immune responses and most of their effects are produced either by altering transcription of specific genes directly, or by altering the expression of transcription factors that subsequently alter the expression of downstream genes. Relevant data from previous studies indicate that the number of genes regulated by glucocorticoid receptor exceeds 4000 in cells and that 358 different genes are regulated in the liver of adrenalectomized males rats treated with a chronic infusion of methylprednisolone for up to 1 week . However, differences in gene expression between males and females in response to glucocorticoid treatment in isolated hepatocytes are not known.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20940427" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24363" }, "primaryId" : "GEO:GSE24363", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24363" } ] }, "title" : "MAQC-II Project: NIEHS data set", "dateAssigned" : "2010-09-24T00:00:00.000-05:00", "summary" : "The NIEHS data set (endpoint C) was provided by the National Institute of Environmental Health Sciences (NIEHS) of the National Institutes of Health (Research Triangle Park, NC, USA). The study objective was to use microarray gene expression data acquired from the liver of rats exposed to hepatotoxicants to build classifiers for prediction of liver necrosis. The gene expression compendium data set was collected from 418 rats exposed to one of eight compounds (1,2-dichlorobenzene, 1,4-dichlorobenzene, bromobenzene, monocrotaline, N-nitrosomorpholine, thioacetamide, galactosamine, and diquat dibromide). All eight compounds were studied using standardized procedures, i.e. a common array platform (Affymetrix Rat 230 2.0 microarray), experimental procedures and data retrieving and analysis processes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20676074" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24377" }, "primaryId" : "GEO:GSE24377", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24377" } ] }, "title" : "Gene expression data from liver of rat fed a high-fat diet and high-fructose water without/with Eucommia ulmoides leaves", "dateAssigned" : "2010-09-27T00:00:00.000-05:00", "summary" : "Microarray analysis revealed that Eucommia ulmoides leaves up-regulated the gene expression involved in alpha-, beta-, and omega-oxidation of fatty acids, mainly relating to peroxisome proliferator-activated receptor signaling pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21815167" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24423" }, "primaryId" : "GEO:GSE24423", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24423" } ] }, "title" : "Transcriptomic characterization of the diabetic retinal response to chronic insulin treatment", "dateAssigned" : "2010-09-28T00:00:00.000-05:00", "summary" : "The aim of this study was to identify alterations associated with diabetes-induced functional dysregulation of the retina and the effects of chronic insulin therapy. Transcriptional profiling through microarray analysis was analyzed to find mRNA targets of interest in diabetic samples, as well as in the insulin treated group. Verification of targets shown to be unrecovered in the insulin group was validated.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21575160" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24430" }, "primaryId" : "GEO:GSE24430", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24430" } ] }, "title" : "Ischemic Pre- and Post Conditioning has pronounced effects on Gene Expression Profiles in the Rat Liver after Ischemia/Reperfusion", "dateAssigned" : "2010-09-29T00:00:00.000-05:00", "summary" : "Ischemia/reperfusion injuries is a known complication to hepatic surgery. Ischemic pre- (IPC) and postconditioning (IPO) protects the liver against ischemia/reperfusion-injuries. Expression profiling were performed on liver biopsies seeking to identify molecular mediators of the protective properties.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22679003" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24431" }, "primaryId" : "GEO:GSE24431", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24431" } ] }, "title" : "Evaluation of phenoxybenzamine in the CFA model of pain following gene expression studies and connectivity mapping", "dateAssigned" : "2010-09-29T00:00:00.000-05:00", "summary" : "Background: We have previously used the rat 4 day Complete Freund's Adjuvant (CFA) model to screen compounds with potential to reduce osteoarthritic pain. The aim of this study was to identify genes altered in this model of osteoarthritic pain and use this information to infer analgesic potential of compounds based on their own gene expression profiles using the Connectivity Map approach. Results: Using microarrays, we identified differentially expressed genes in L4 and L5 dorsal root ganglia (DRG) from rats that had received intraplantar CFA for 4 days compared to matched, untreated control animals. Analysis of these data indicated that the two groups were distinguishable by differences in genes important in immune responses, nerve growth and regeneration. This list of differentially expressed genes defined a “CFA signature”. We used the Connectivity Map approach to identify pharmacologic agents in the Broad Institute Build02 database that had gene expression signatures that were inversely related (‘negatively connected’) with our CFA signature. To test the predictive nature of the Connectivity Map methodology, we tested phenoxybenzamine (an alpha adrenergic receptor antagonist) – one of the most negatively connected compounds identified in this database - for analgesic activity in the CFA model. Our results indicate that at 10mg/kg, phenoxybenzamine demonstrated analgesia comparable to that of Naproxen in this model. Conclusion: Evaluation of phenoxybenzamine-induced analgesia in the current study lends support to the utility of the Connectivity Map approach for identifying compounds with analgesic properties in the CFA model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20846436" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24440" }, "primaryId" : "GEO:GSE24440", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24440" } ] }, "title" : "Sprouting transcriptome in cortical neurons: young", "dateAssigned" : "2010-09-29T00:00:00.000-05:00", "summary" : "Selective isolation of total RNA and then whole genome expression analysis of sprouting neurons in peri-infarct cortex of the adult rat after stroke, compared to adjacent neurons that have not sprouted a new connection, in young adult (2 months) and aged (2 years) animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21057507" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24441" }, "primaryId" : "GEO:GSE24441", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24441" } ] }, "title" : "Sprouting transcriptome in cortical neurons: aged", "dateAssigned" : "2010-09-29T00:00:00.000-05:00", "summary" : "Selective isolation of total RNA and then whole genome expression analysis of sprouting neurons in peri-infarct cortex of the adult rat after stroke, compared to adjacent neurons that have not sprouted a new connection, in young adult (2 months) and aged (2 years) animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21057507" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24515" }, "primaryId" : "GEO:GSE24515", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24515" } ] }, "title" : "Deep Sleep and Parietal Cortex Gene Expression Changes are Related to Cognitive Deficits with Age", "dateAssigned" : "2010-10-04T00:00:00.000-05:00", "summary" : "KEYWORDS: frontal cortex, rat, young or aged", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21483696" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24600" }, "primaryId" : "GEO:GSE24600", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24600" } ] }, "title" : "Expression profiles dysplastic and neoplastic rat liver lesions", "dateAssigned" : "2010-10-08T00:00:00.000-05:00", "summary" : "Predisposition to hepatocarcinogenesis is under polygenic control. We analyzed gene expression patterns of dysplastic liver nodules (DN) and hepatocellular carcinoma (HCC) chemically-induced in F344 and BN rats, respectively susceptible and resistant to hepatocarcinogenesis, to evaluate effector mechanisms of predisposition genes, and commonalties between transcription signatures of rat and human liver lesions. Gene expression profiles were determined by microarray analysis and validated by quantitative RT-PCR and Western blot. Cluster analysis revealed two distinctive gene expression patterns, the first of which included normal liver of F344 and BN rats and BN rat nodules, and the second one F344 nodules and HCC of both strains. Expression of 91 and 55 genes of DN and HCC, respectively, showed significant interstrain differences. Considering genes mostly associated with cell proliferation we identified a signature predicting DN evolution to HCC. Notably, expression of oncosuppressors Csmd1, Dmbt, Dusp1, and Gnmt ,in DN, and Bhmt, Dmbt1, Dusp1, Gadd45g, Gnmt, Napsa, Pp2ca, and Ptpn13, in HCC, was higher in BN than F344 rats. Comparative genomics approach, using gene expression data from rat lesions, and human HCC with different prognosis (based on survival length), revealed expression patterns of BN and F344 lesions close to those of human HCCs with better and poorer prognosis, respectively, suggesting that similar molecular events contribute to create a phenotype prone to progression in rats and human lesions. In conclusion, we identified a molecular signature of DN prone to progress to HCC and suggest that oncosuppressor genes are determinants of the genetically transmitted resistance to hepatocarcinogenesis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24612" }, "primaryId" : "GEO:GSE24612", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24612" } ] }, "title" : "Expression data from synovium, bone marrow and nucleus pulposus", "dateAssigned" : "2010-10-11T00:00:00.000-05:00", "summary" : "Microarray analyses of rats were performed to investigate the closeness of the gene profiles between the nucleus pulposus cells and the synovial or bone marrow mesenchymal stem cells. To investigate interaction between synovial mesenchymal stem cells and nucleus pulposus cells, human synovial mesenchymal stem cells and rat nucleus pulposus cells were co-cultured, and species specific microarray were performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21054867" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24666" }, "primaryId" : "GEO:GSE24666", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24666" } ] }, "title" : "Basic helix-loop-helix transcription factor Tcf21 is downstream target of male sex-determining gene SRY", "dateAssigned" : "2010-10-12T00:00:00.000-05:00", "summary" : "The cascade of molecular events involved in mammalian sex determination has been shown to involve the SRY gene, but specific downstream events have eluded researchers for decades. The current study identifies one of the first direct downstream targets of the male sex-determining factor SRY as the basic-helix-loop-helix (bHLH) transcription factor TCF21. SRY was found to directly associate with the Tcf21 promoter SRY/SOX9 response element both in vitro and in vivo during male sex determination. TCF21 was found to promote an in vitro sex reversal of embryonic ovarian cells to promote precursor Sertoli cell differentiation. Therefore, SRY acts directly on the Tcf21 promoter to, in part, initiate a cascade of events associated with Sertoli cell differentiation and embryonic testis development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21637323" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24668" }, "primaryId" : "GEO:GSE24668", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24668" } ] }, "title" : "Hierarchical regulation in a KRAS-dependent transcriptional network revealed by a reverse-engineering approach", "dateAssigned" : "2010-10-13T00:00:00.000-05:00", "summary" : "Mutations in RAS proteins occur in 30% of human tumours and have a high relevance in tumor progression. Despite the importance of the underlying genetic network that governs the effects of oncogenic RAS, it is still poorly understood. We developed and applied a reverse-engineering approach in order to reconstruct the network structure of the signaling and gene-regulatory network downstream of RAS from perturbation experiments. We performed microarray, RT-PCR and Western Blot analysis to detect mRNA and protein levels of cytoplasmatic and nuclear targets downstream of RAS after systematic perturbation of the signaling pathways and knock-down of selected transcription factors in KRAS-transformed ovarian surface epithelium cell lines. The reconstructed model shows that the investigated components are connected through a complex network. The transcription factors decomposed into two hierarchically arranged groups. While knock-down of all investigated transcription factors showed a partial reversion of the malignant phenotype, different growth assays show that these two groups of transcription factors control different functions in the malignant anchorage-independent growth and cell cycle regulation of the ROSE cells. Furthermore, the model showed strong regulatory interplay of inhibitory and activating interactions between the RAS-dependent trancriptional network and cytoplasmatic signaling components.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24672" }, "primaryId" : "GEO:GSE24672", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24672" } ] }, "title" : "Estrogen regulated genes in rat testes and their relationship to recovery of spermatogenesis after irradiation", "dateAssigned" : "2010-10-13T00:00:00.000-05:00", "summary" : "Despite numerous observations of effects of estrogens on spermatogenesis, identification of estrogen-regulated genes in the testis is limited. We previously showed in rats, in which irradiation had completely blocked spermatogonial differentiation, that testosterone (T) suppression with GnRH-antagonist and antiandrogen stimulated spermatogenic recovery and addition of estradiol (E2) to this regimen accelerated this recovery. We report here the global changes in testicular cell gene expression induced by the E2 treatment. By minimizing the changes in other hormones and also having concurrent data on the regulation of the genes by those hormones, we were able to dissect the effects of estrogen on gene expression, independent of gonadotropin or T changes. Expression of 20 genes, largely in somatic cells, was up- or down-regulated between 2- and 5-fold by E2. There were also early germ cell genes whose expression increased but this was a result of a small increase in spermatogonial numbers. The striking enrichment of transcripts not corresponding to known genes among the E2-downregulated probes led to the identification of one as micro-RNA miR-34a. We propose that genes whose expression levels are altered in one direction by irradiation and in the opposite direction by both T suppression and E2 treatment are candidates for controlling the block in differentiation. Several genes, including insulin-like 3 (Insl3), satisfied those criteria. If they are indeed involved in the inhibition of spermatogonial differentiation, they may be candidate targets for clinical treatments to enhance recovery of spermatogenesis following gonadotoxic exposures, such as those resulting from cancer therapy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21653891" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24687" }, "primaryId" : "GEO:GSE24687", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24687" } ] }, "title" : "C-peptide regulates early transcription in rat proximal tubular cells", "dateAssigned" : "2010-10-13T00:00:00.000-05:00", "summary" : "C-peptide exerts beneficial effects on glomerular hyperfiltration in type I diabetic patients. As C-peptide localizes to the nucleus, we investigated the transcriptional activities of C-peptide in proximal tubular cells isolated from diabetic rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21618400" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24780" }, "primaryId" : "GEO:GSE24780", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24780" } ] }, "title" : "Peritoneal and testicular macrophage mrna expression after exposure to UPEC CFT073", "dateAssigned" : "2010-10-18T00:00:00.000-05:00", "summary" : "Ascending bacterial infections of the male genitourinary tract by Escherichia coli are an important cause of male infertility. Thus understanding mechanisms by which immunocompetent cells such as testicular macrophages (TM) respond to infection and how bacterial pathogens manipulate defense pathways is of great relevance. Following infection with uropathogenic E. coli (UPEC) whole genome expression profiling revealed induction of the calcium-dependent nuclear factor of activated T cells (NFAT) signaling pathway in TM as well as in peritoneal macrophages (PM) that were used in comparison. UPEC-dependent NFAT activation was confirmed in cultured TM and in TM using an in vivo infection model. Elevated expression of NFATC2-regulated anti-inflammatory cytokines was found in TM (IL-4, IL-13) and PM (IL-3, IL-4, IL-13). NFATC2 is activated by a rapid influx of calcium caused by the UPEC pore forming toxin alpha-hemolysin. Mutant analysis identified alpha-hemolysin as the main virulent factor responsible for UPEC-dependant suppression of IL-6 and TNF-a cytokine release from PM. Alpha-hemolysin caused differential activation of MAP kinase and AP-1 signaling pathways in TM and PM leading to differential expression profiles of key pro-inflammatory cytokines in PM (IL-1a, IL-1b and IL-6 downregulated) and TM (IL-1b and IL-6 upregulated). In contrast to PM, treatment with lipopolysaccharide did not result in activation of the NFkB pathway in TM as shown by lack of degradation of IkBa and lack of pro-inflammatory cytokine secretion (IL-6, TNF-a). In conclusion, these results propose a mechanism how TM can defend against microbes, while at the same time they are able to maintain the immune privileged status of the testis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22164293" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24790" }, "primaryId" : "GEO:GSE24790", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24790" } ] }, "title" : "Neonatal beta cells lack the specialized metabolic phenotype of mature beta cells", "dateAssigned" : "2010-10-19T00:00:00.000-05:00", "summary" : "Gene expression profile of neonatal (1 day old) and young adult (6 weeks old) Sprague-Dawley rat islets were evaluated and compared.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21240476" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24801" }, "primaryId" : "GEO:GSE24801", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24801" } ] }, "title" : "Cultured OEC versus cultured SC and versus native OEC", "dateAssigned" : "2010-10-19T00:00:00.000-05:00", "summary" : "This microarray study aimed at identifying the differences in the global gene expression growth program of adult cultured olfactory ensheathing cells (cOEC) (from the olfactory bulb) versus adult cultured Schwann cells (SC) (from the sciatic nerve) and versus adult OEC directly dissected from the olfactory nerve layer (nOEC). The aim of the comparison between cOEC and SC is to define intrinsic molecular differences that distinguish cOEC from SC (both cell types support neuronal regeneration). The aim of the comparison between cOEC and nOEC is to determine the transcriptional responses that are induced in OEC during culturing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18615567" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24821" }, "primaryId" : "GEO:GSE24821", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24821" } ] }, "title" : "Retinoid X receptor gamma signaling accelerates CNS remyelination", "dateAssigned" : "2010-10-20T00:00:00.000-05:00", "summary" : "The molecular basis of CNS myelin regeneration (remyelination) is poorly understood. Here we generate a comprehensive transcriptional profile of the separate stages of spontaneous remyelination following focal demyelination in the rat CNS. White matter tracts in the rat caudal cerebellar peduncles were focally demyelinated using 0.1% ethidium bromide, the lesions were isolated using laser capture microdissection at 5, 14 and 28 days postlesion, followed by RNA extraction and Illumina beadarray analysis of differentially expressed transcripts. We found transcripts encoding retinoid acid receptor RXR-gamma is highly differentially expressed during remyelination, and that oligodendrocyte lineage cells express RXR-gamma in rat tissues undergoing remyelination and in active and remyelinated MS lesions. RXR-gamma knockdown by RNA interference or RXR-specific antagonists severely inhibit oligodendrocyte differentiation in culture. In RXR-gamma deficient mice, adult oligodendrocyte precursor cells efficiently repopulate lesions following demyelination, but display delayed differentiation into mature oligodendrocytes. Administration of the RXR agonist 9-cis-retinoic acid to demyelinated cerebellar slice cultures and to aged rats following demyelination results in more remyelinated axons. RXR-gamma is therefore a positive regulator of endogenous oligodendrocyte precursor cell differentiation and remyelination, and may be a pharmacological target for CNS regenerative therapy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21131950" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24877" }, "primaryId" : "GEO:GSE24877", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24877" } ] }, "title" : "Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs NA16)", "dateAssigned" : "2010-10-21T00:00:00.000-05:00", "summary" : "Keywords: Expression profiling of a adhesion deprived transformed cell line", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21122158" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24878" }, "primaryId" : "GEO:GSE24878", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24878" } ] }, "title" : "Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs COLONY)", "dateAssigned" : "2010-10-21T00:00:00.000-05:00", "summary" : "Keywords: Expression profiling of a adhesion deprived transformed cell line", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21122158" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24879" }, "primaryId" : "GEO:GSE24879", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24879" } ] }, "title" : "Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs. Tumor)", "dateAssigned" : "2010-10-21T00:00:00.000-05:00", "summary" : "Keywords: Expression profiling of a adhesion deprived transformed cell line", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21122158" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24954" }, "primaryId" : "GEO:GSE24954", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24954" } ] }, "title" : "miRNA profile of Neonatal Rat Cardiomyocytes treated with 0.5% or 1.5% Oxygen for 48 h versus Normoxia", "dateAssigned" : "2010-10-27T00:00:00.000-05:00", "summary" : "The Purpose of this study is to screen for microRNAs regulated by hypoxia in neonatal rat cardiomyocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21841015" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24982" }, "primaryId" : "GEO:GSE24982", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE24982" } ] }, "title" : "mRNA expression profiling in the spinal nerve ligation model of neuropathic pain in rats", "dateAssigned" : "2010-10-28T00:00:00.000-05:00", "summary" : "Expression profiling of L4 and L5 Dorsal Root Ganglion (DRG) in the spinal nerve ligation model of neuropathic pain. The goal of the study was to identify genes involved in neuropathic pain", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21423802" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25032" }, "primaryId" : "GEO:GSE25032", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25032" } ] }, "title" : "Identification of Neuronal RNA Targets of TDP-43-Containing Ribonucleoprotein Complexes", "dateAssigned" : "2010-10-29T00:00:00.000-05:00", "summary" : "We identify the RNA targets of TAR DNA-binding protein 43 (TDP-43) from cortical neurons by RNA immunoprecipitation followed by deep sequencing (RIP-seq). We identify 4352 highly enriched RNA targets of TDP-43. We determined that the canonical TDP-43 binding site (TG)n was 55.1-fold enriched in our TDP-43 library. Moreover, our analysis shows there is often an adenine in the middle of the motif, (TG)nTA(TG)m. TDP-43 RNA targets are particularly enriched for Gene Ontology terms related to RNA metabolism, neuronal development, and synaptic function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21051541" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25039" }, "primaryId" : "GEO:GSE25039", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25039" } ] }, "title" : "Transcriptional response to serum stimulation of Rat1 fibroblasts in the presence or absence of the Myc interfering molecule termed Omomyc.", "dateAssigned" : "2010-10-29T00:00:00.000-05:00", "summary" : "We found that Omomyc differently affects Myc induced gene repression and activation, channelling the Myc interactome activity to repression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25043" }, "primaryId" : "GEO:GSE25043", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25043" } ] }, "title" : "microarray analysis of rat terminal end buds at neonatal diethlstilbestrol administration rats", "dateAssigned" : "2010-11-01T00:00:00.000-05:00", "summary" : "Diethlstilbestrol (DES) is a synthetic estrogen prescribed to several millions of pregnant women worldwide. The risk for breast cancer after age 40 in women prenatally exposed to DES has been reported, however, the precise mechanism of susceptibilities to breast cancer remains to be resolved. To understand the mechanism of effect of intrauterine exposure to DES on human mammary glands at peripubertal stage, we investigated the global gene expression profile of terminal end buds (TEBs), the target of carcinogen, in rat mammary glamds at postnatal days (PND) 35 and 49, equivalent to peripubertal stage in human, exposed to low or high dose of DES at neonatal period. In all group, the number of TEBs was gradually increased and peaked at PND35 and decreased at PND49. At PND 35 and 49, low dose of DES-treated group showed highest number of TEBs. At PND35, ß- and ¿-casein mRNA expression inreased 8.19-fold and 26.05-fold, respectively, and the most significant network revealed by IPA analyses showed relevance of NF-¿B in low dose of DES-treated group. The present findings suggested that deregulation of mammary gland differentiation and development-related genes group may contribute to the increase of number of TEBs at critical period of carcinogen susceptibilities.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25144" }, "primaryId" : "GEO:GSE25144", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25144" } ] }, "title" : "Comparison of effects of Iodine-deficiency and perchlorate on thyroid", "dateAssigned" : "2010-11-04T00:00:00.000-05:00", "summary" : "Perchlorate, which is a ubiquitous and persistent ion, competitively interferes with iodide accumulation in the thyroid, causing iodine deficiency, which may result in reduced thyroid hormone synthesis and secretion. Human studies suggest that perchlorate presents very little risk in healthy individuals; however, the precautionary principle demands that the sensitive populations of iodine deficient adults and mothers require extra consideration. In an attempt to determine if the effects on gene expression were similar, we compared the thyroidal effects of perchlorate (10 mg/kg) treatment for 14 days in drinking water with those caused by 8 weeks of Iodine-deficiency in rats. The thyroids were collected (N=3 each group) and total mRNA was analyzed using the Affymetrix Rat Genome 230 2.0 GeneChip®. Changes in gene expression were compared with appropriate control groups. We compared the 2-fold gene changes due to I-deficiency with changes due to perchlorate treatment. 189 transcripts were changed by the Iodine-deficient diet and 722 transcripts were changed by the perchlorate treatment. 34% of the transcripts changed by the I-deficient diet were also changed by perchlorate and generally in the same direction. three specific transporter genes, AQP1, NIS, & SLC22A3 were changed by both treatments, indicating that the membrane specific changes were similar. Iodine-deficiency primarily caused changes in retinol and calcium signaling pathways and perchlorate primarily caused changes related to the accumulation of extracellular matrix proteins. This study provides evidence that perchlorate, at least at this dose level, changes more genes and changes different genes compared to iodine deficiency.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25152" }, "primaryId" : "GEO:GSE25152", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25152" } ] }, "title" : "Tracheal occlusion conditioning in conscious rats modulates gene expression profile of medial thalamus", "dateAssigned" : "2010-11-04T00:00:00.000-05:00", "summary" : "The thalamus may be the critical brain area involved in sensory gating and the relay of respiratory mechanical information to the cerebral cortex for the conscious awareness of breathing. We hypothesized that respiratory mechanical stimuli in the form of tracheal occlusions would modulate the gene expression profile of the thalamus. Specifically, it was reasoned that conditioning to the respiratory loading would induce a state change in the medial thalamus consistent with a change in sensory gating and the activation of molecular pathways associated with learning and memory. In addition, respiratory loading is stressful and thus should elicit changes in gene expressions related to stress, anxiety, and depression. Rats were instrumented with inflatable tracheal cuffs. Following surgical recovery, they underwent ten days (5 days/week) of transient tracheal occlusion conditioning. On day 10, the animals were sacrificed and the brains removed. The medial thalamus was dissected and microarray analysis of gene expression performed. Tracheal obstruction conditioning modulated a total of 661 genes (p < 0.05, log2 fold change = 0.58), 250 genes were down-regulated and 411 up-regulated. There was a significant down-regulation of GAD1, GAD2 and HTR1A, HTR2A genes. CCK, PRKCG, mGluR4, and KCJN9 genes were significantly up-regulated. Some of these genes have been associated with anxiety and depression, while others have been shown to play a role in switching between tonic and burst firing modes in the thalamus and thus may be involved in gating of the respiratory stimuli. Furthermore, gene ontology and pathway analysis showed a significant modulation of learning and memory pathways. These results support the hypothesis that the medial thalamus is involved in the respiratory sensory neural pathway due to the state change of its gene expression profile following repeated tracheal occlusions.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25153" }, "primaryId" : "GEO:GSE25153", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25153" } ] }, "title" : "Tracheal Occlusion Modulates the Gene Expression Profile of the Medial Thalamus in Anesthetized Rats", "dateAssigned" : "2010-11-04T00:00:00.000-05:00", "summary" : "Conscious awareness of breathing requires the activation of higher brain centers. The sensation of breathing is believed to be a neural gating process. The thalamus provides the brain structure that could be responsible for the gating of respiratory sensory information to the cortex. It was reasoned that if the thalamus is the neural gate, then tracheal obstructions will modulate the gene expression profile of the thalamus. Anesthetized rats were instrumented with an inflatable cuff sutured around the trachea. The cuff was inflated to obstruct 2-4 breaths, then deflated for a minimum of 15 breaths. The obstructions were repeated for 10 min followed by immediate brain removal, and the medial thalamus was dissected and prepared for microarray analysis. Gene expression profiles were measured using Agilent Technology Oligo Microarrays. Following the occlusion protocol, 588 genes were found to be altered (p < 0.05, log2 fold change = 0.4), with 327 down-regulated and 261 genes up-regulated. A significant up-regulation of the serotonin HTR2A receptor and significant down-regulation of the dopamine DRD1 receptor genes were found. A pathway analysis was performed targeting serotonin and dopamine receptor pathways. The mitogen activated protein kinase 1 (MAPK1) gene was significantly down-regulated. MAPK1 is an inhibitory regulator of the serotonin HTR2A receptor and facilitatory regulator for the dopamine DRD1 receptor. Down-regulation of MAPK1 may be related to the 2-fold up-regulation of HTR2A and 2-fold down-regulation of DRD1 suggesting an interaction in the medial thalamus serotonin-dopamine pathway elicited by airway obstruction. These results demonstrate an immediate change in gene expression in thalamic arousal-fear-anxiety-motivation related serotonin and dopamine receptors in response to airway obstruction. The results support the hypothesis that the thalamus is a component in the respiratory mechanosensory neural pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21527662" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25196" }, "primaryId" : "GEO:GSE25196", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25196" } ] }, "title" : "Fetal Rat Testis mRNA Expression after 50 mg/kg Dibutyl Phthalate Exposure", "dateAssigned" : "2010-11-08T00:00:00.000-06:00", "summary" : "High dose level dibutyl phthalate (DBP) exposure of fetal rat testes in vivo inhibits testosterone production (i.e. endocrine disruption). Here, fetal testis mRNA levels were profiled following exposure to a DBP dose level that did not significantly reduce testosterone levels. The goal was to identify the constellation of gene expression changes that do not correlate with endocrine disruption.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21266533" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25556" }, "primaryId" : "GEO:GSE25556", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25556" } ] }, "title" : "Global miRNA transcriptomic profiling of permanent focal ischemia in an in vivo rat model", "dateAssigned" : "2010-11-23T00:00:00.000-06:00", "summary" : "Focal ischemia is triggered by the sudden significant reduction of blood supply to the brain, as a result of either the rupture or occlusion by thrombus/embolism of a blood vessel in the brain. Permanent focal ischemia occurred when blood supply to a specific part of the brain is impeded without reperfusion. Despite major steps achieved in the elucidation of the patho-physiology of cerebral ischemia, the available therapeutic avenues for acute ischemic stroke remain scarce. Cell cycle re-activation has been revealed as a novel signaling pathway during permanent focal ischemia. As such, non-specific aurora kinase inhibitor ZM447439, has been injected intracranial-ventricularly 30min post-ischemia induction to determine its efficacy in reduction of neuronal damage in terms of infarct volume.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25574" }, "primaryId" : "GEO:GSE25574", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25574" } ] }, "title" : "Hypothalamic transcriptome plasticity in two rodent species reveals divergent differential gene expression but conserved pathways", "dateAssigned" : "2010-11-23T00:00:00.000-06:00", "summary" : "We have addressed the question of how different rodent species cope with the life-threatening homeostatic challenge of dehydration at the level of transcriptome modulation in the supraoptic nucleus (SON), a specialised hypothalamic neurosecretory apparatus responsible for the production of the antidiuretic peptide hormone arginine vasopressin (AVP). AVP maintains water balance by promoting water conservation at the level of the kidney. Dehydration evokes a massive increase in the regulated release of AVP from SON axon terminals located in the posterior pituitary, and this is accompanied by a plethora of changes in the morphology, electrophysiological properties, biosynthetic and secretory activity of this structure. Microarray analysis was used to generate a definitive catalogue of the genes expressed in the mouse SON, and to describe how the gene expression profile changes in response to dehydration. Comparison of the genes differentially expressed in the mouse SON as a consequence of dehydration with those of the rat has revealed many similarities, pointing to common processes underlying the function-related plasticity in this nucleus. In addition we have identified many genes that are differentially expressed in a species-specific manner. However, in many cases, we have found that the hyperosmotic cue can induce species-specific alterations in the expression of different genes in the same pathway. The same functional end can be served by different means, via differential modulation, in different species, of different molecules in the same pathway. We suggest that pathways, rather than specific genes, should be the focus of integrative physiological studies based on transcriptome data.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21070396" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25612" }, "primaryId" : "GEO:GSE25612", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25612" } ] }, "title" : "Circadian regulation in rat Lung", "dateAssigned" : "2010-11-24T00:00:00.000-06:00", "summary" : "Circadian rhythms are oscillations with a periodicity of 24 hours that are controlled by an endogenous clock and are observed in virtually all aspects of mammalian function from expression of genes to complex physiological processes. The master clock is present in the suprachiasmatic nucleus (SCN) in the anterior part of the hypothalamus and controls peripheral clocks present in other parts of the body . Although much is known about the mechanism of the central clock in the SCN, the regulation of clocks present in peripheral tissues is still unclear. This study is designed to examine fluctuations in gene expression in lungs within the 24 hour circadian cycle in normal animals. The objectives of this study is to identify and analyze circadian oscillation in gene expression in lungs, and to identify the role of circadian regulation in coordinating the functioning of this dynamic organ.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21436464" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25629" }, "primaryId" : "GEO:GSE25629", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25629" } ] }, "title" : "Inhibitory Actions of Anti-Müllerian Hormone (AMH) on Ovarian Primordial Follicle Assembly", "dateAssigned" : "2010-11-28T00:00:00.000-06:00", "summary" : "We used microarrays to determine genes expressed differentially between control and AMH (Anti-Müllerian Hormone) treated P0 ovary", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21637711" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25670" }, "primaryId" : "GEO:GSE25670", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25670" } ] }, "title" : "p38 regulated genes in rat myelinating glia", "dateAssigned" : "2010-11-29T00:00:00.000-06:00", "summary" : "The drug concentration used for all experiments was 5 micromolar; controls were treated with vehicle (DMSO)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26714323" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25750" }, "primaryId" : "GEO:GSE25750", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25750" } ] }, "title" : "SAGE profile of rat hippocampus mRNA from Wistar rats", "dateAssigned" : "2010-12-01T00:00:00.000-06:00", "summary" : "SAGE profile of rat hippocampus mRNA from Wistar rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:11530848" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25752" }, "primaryId" : "GEO:GSE25752", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25752" } ] }, "title" : "hHGF Overexpression in Myoblast Sheets Enhances Their Angiogenic Potential in Rat Chronic Heart Failure", "dateAssigned" : "2010-12-01T00:00:00.000-06:00", "summary" : "Ischemia, fibrosis, and remodeling lead to heart failure after severe myocardial infarction (MI). Myoblast sheet transplantation is a promising therapy to enhance cardiac function and induce therapeutic angiogenesis via a paracrine mechanism in this detrimental disease. We hypothesized that in a rat model of MI-induced chronic heart failure this therapy could further be improved by overexpression of the antiapoptotic, antifibrotic, and proangiogenic hepatocyte growth factor (HGF) in the myoblast sheets. We studied the ability of wild type (L6-WT) and human HGF-expressing (L6-HGF) L6 myoblast sheet-derived paracrine factors to stimulate cardiomyocyte, endothelial cell, or smooth muscle cell migration in culture. Further, we studied the autocrine effect of hHGF-expression on myoblast gene expression using microarray analysis. We induced MI in Wistar rats by left anterior descending coronary artery (LAD) ligation and allowed heart failure to develop for four weeks. Thereafter, we administered L6-WT (n=15) or L6-HGF (n=16) myoblast sheet therapy. Control rats (n=13) underwent LAD ligation and rethoracotomy without therapy and five rats underwent sham-operation in both surgeries. We evaluated cardiac function with echocardiography at 2 and 4 weeks after therapy administration. We analyzed cardiac angiogenesis and left ventricular architecture from histological sections 4 weeks after therapy. Paracrine mediators from L6-HGF myoblast sheets effectively induced migration of cardiac endothelial and smooth muscle cells but not cardiomyocytes. Microarray data revealed that hHGF-expression modulated myoblast gene expression. In vivo, L6-HGF sheet therapy effectively stimulated angiogenesis in the infarcted and non-infarcted areas. Both L6-WT and L6-HGF therapies enhanced cardiac function and inhibited remodeling in a similar fashion. In conclusion, L6-HGF therapy effectively induced angiogenesis in the chronically failing heart. Cardiac function, however, was not further enhanced by hHGF-expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21541335" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25764" }, "primaryId" : "GEO:GSE25764", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25764" } ] }, "title" : "Multiorgan effects of IUGR caused by maternal protein depletion in rats (Placenta, Kidney, Heart, Lung, Liver)", "dateAssigned" : "2010-12-01T00:00:00.000-06:00", "summary" : "The protocol of growth restriction (length, duration) has been extensively described in Buffat et al (Journal of Pathology 2007a and Endocrinology, 2007b)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21731679" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25860" }, "primaryId" : "GEO:GSE25860", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25860" } ] }, "title" : "High-frequency stimulation of the ventrolateral thalamus regulates gene expression in hippocampus, motor cortex and caudate-putamen", "dateAssigned" : "2010-12-06T00:00:00.000-06:00", "summary" : "Transcriptional profiling of rat hippocampus comparing rats subjected to chronic (1 hour daily during 14 days) vetrolateral thalamus stimulation (DBS group) with sham operated rats (with electrode placement but without stimulation) and with naive rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21458429" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25863" }, "primaryId" : "GEO:GSE25863", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25863" } ] }, "title" : "Solexa sequencing of small RNAs in Sprague-Dawley (SD) rat [dorsal root ganglia]", "dateAssigned" : "2010-12-06T00:00:00.000-06:00", "summary" : "We applied Solexa sequencing technology to identify rat microRNA genes in dorsal root ganglia (DRGs) following sciatic nerve resection. Using Solexa sequencing, computational analysis and Q-PCR verification, 114 novel miRNAs in rats were discovered and identified, of which 52 novel miRNAs were first reported in rat DRGs and 62 novel miRNAs were produced at days 1, 4, 7 and 14 after sciatic nerve resection. These data provide an important resource relating to the role and regulation of miRNAs for future studies relating to peripheral nerve injury and regeneration.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25912" }, "primaryId" : "GEO:GSE25912", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25912" } ] }, "title" : "Classification of diet modified gene signatures at the colon cancer initiation and progression stages", "dateAssigned" : "2010-12-08T00:00:00.000-06:00", "summary" : "keywords: diet analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25929" }, "primaryId" : "GEO:GSE25929", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25929" } ] }, "title" : "Sex-biased suppression of chemically induced neural carcinogenesis in congenic BDIX-BDIV-Mss4a rats", "dateAssigned" : "2010-12-08T00:00:00.000-06:00", "summary" : "Gender specific expression profiling of congenic BDIX-BDIV-Mss4a rats vs. BDIX and BDIV parental strains using trigeminal nerve tissue", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21427360" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25980" }, "primaryId" : "GEO:GSE25980", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE25980" } ] }, "title" : "In vitro and in vivo analysis of hypoxic gene expression in rat gliomas", "dateAssigned" : "2010-12-09T00:00:00.000-06:00", "summary" : "We have employed the hypoxia marker EF5 coupled with laser capture microdissection to isolate RNA from viable hypoxic and normoxic regions of 9L experimental gliomas.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21266355" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26066" }, "primaryId" : "GEO:GSE26066", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26066" } ] }, "title" : "Expression analysis of astrocytes isolated from the rat forebrain", "dateAssigned" : "2010-12-14T00:00:00.000-06:00", "summary" : "Comparison of expression data of rat forebrain astrocytes from P1, P7 acutely isolated by immunopanning or cultured with astrocytes prepared by McCarthy and de Vellis' (1980) method. Elucidating the genes induced by serum in immunopannedrat astrocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21903074" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26108" }, "primaryId" : "GEO:GSE26108", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26108" } ] }, "title" : "Gene expression in colon tissue of rats fed digestion resistant carbohydrates", "dateAssigned" : "2010-12-16T00:00:00.000-06:00", "summary" : "Conventionally raised and germ-free newly weaned male Sprague-Dawley rats were fed a basal diet or a diet supplemented with digestion resistant carbohydrates in the form of inulin, resistant starch or konjac flour. Gene expression in colon tissue was measured to characterise interaction between food, microbes and host.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23700349" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26138" }, "primaryId" : "GEO:GSE26138", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26138" } ] }, "title" : "Expression data from rat regenerating livers after autonomic nervous system is disrupted", "dateAssigned" : "2010-12-17T00:00:00.000-06:00", "summary" : "We used microarrays to further highlight the regulatory role of autonomic nervous system in liver regeneration at gene transcription level.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21264506" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26167" }, "primaryId" : "GEO:GSE26167", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26167" } ] }, "title" : "MicroRNA 144 impairs insulin signaling by inhibiting the expression of insulin receptor substrate 1 in Type 2 Diabetes mellitus", "dateAssigned" : "2010-12-18T00:00:00.000-06:00", "summary" : "Dysregulation in expression of microRNAs (miRNAs) in various tissues has been linked to a wide spectrum of diseases, including Type 2 Diabetes mellitus (T2D). In this study, we compared the expression profiles of miRNAs in blood samples from Impaired Fasting Glucose (IFG) and T2D male patients with tissues from T2D rat models. Healthy adult males with no past history of T2D (n=158) and with desirable cholesterol and blood pressure profiles were enrolled in this study. They were then classified according to fasting glucose levels to have T2D, IFG or as healthy controls (CTL), for comparison of miRNA expression profiles. Employing miRNA microarray, we identified ‘signature miRNAs’ in peripheral blood samples that distinguished IFG and T2D. Eight selected miRNAs were further validated using stem-loop real-time RT-PCR. miR-144 expression was found to be dysregulated in Type 2 Diabetes, wherein its expression was significantly higher than in healthy controls. Insulin receptor substrate 1 (IRS1) has been predicted to be a potential target of miR-144. Consistent with this observation, IRS1 mRNA and protein levels, verified by quantitative real-time PCR and western blotting respectively, were found to be down-regulated. Using luciferase assay, we further demonstrated that miR-144 directly targets IRS1 and showed its effects on protein expression via immunocytochemistry. From this cross-sectional study in humans, we have identified signature miRNAs which could explain the pathogenesis of T2D. Whether miRNAs like miR-144 could be potential therapeutic targets for management of T2D will need to be explored by further mechanistic and functional studies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21829658" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26174" }, "primaryId" : "GEO:GSE26174", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26174" } ] }, "title" : "Gene Expression Profiling of the Retina after Transcorneal Electrical Stimulation in Wildtype Brown Norway Rats", "dateAssigned" : "2010-12-20T00:00:00.000-06:00", "summary" : "Conclusion: Our results demonstrate that TES applied to the retina of wildtype BN rats induce a variety of transcriptome level changes and may help to understand the mechanisms underlying TES. In addition TES has no negative effect on structure and function of wildtype BN retina 24hrs after application. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21873684" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26316" }, "primaryId" : "GEO:GSE26316", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26316" } ] }, "title" : "Expression data from normal rat and steroid induced necrosis of femoral head rat", "dateAssigned" : "2010-12-27T00:00:00.000-06:00", "summary" : "We used microarrays to compare the gene expression profile of SINFH rats with that of normal rats and identified gene expression changes between SINFH rats and normal rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26350" }, "primaryId" : "GEO:GSE26350", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26350" } ] }, "title" : "Signaling to Transcription Networks in the Neuronal Retrograde Injury Response", "dateAssigned" : "2010-12-29T00:00:00.000-06:00", "summary" : "Retrograde signaling from axon to soma activates intrinsic regeneration mechanisms in lesioned peripheral sensory neurons; however, the links between axonal injury signaling and the cell body response are not well understood. Here, we used phosphoproteomics and microarrays to implicate ~900 phosphoproteins in retrograde injury signaling in rat sciatic nerve axons in vivo and ~4500 transcripts in the in vivo response to injury in the dorsal root ganglia. Computational analyses of these data sets identified ~400 redundant axonal signaling networks connected to 39 transcription factors implicated in the sensory neuron response to axonal injury. Experimental perturbation of individual overrepresented signaling hub proteins, including Abl, AKT, p38, and protein kinase C, affected neurite outgrowth in sensory neurons. Paradoxically, however, combined perturbation of Abl together with other hub proteins had a reduced effect relative to perturbation of individual proteins. Our data indicate that nerve injury responses are controlled by multiple regulatory components, and suggest that network redundancies provide robustness to the injury response", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20628157" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26354" }, "primaryId" : "GEO:GSE26354", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26354" } ] }, "title" : "Positive emotion-specific changes in gene expression profile in brain and peripheral tissues of the tickled rats", "dateAssigned" : "2010-12-29T00:00:00.000-06:00", "summary" : "Keywords: Stress response", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26363" }, "primaryId" : "GEO:GSE26363", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26363" } ] }, "title" : "Hepatic gene expression profile in hydrogen water administrated SD rat", "dateAssigned" : "2010-12-30T00:00:00.000-06:00", "summary" : "The effects of the administration of molecular hydrogen-saturated drinking water (hydrogen water) on hepatic gene expression were investigated in rats. Using DNA microarrays, 548 upregulated and 695 downregulated genes were detected in the liver after a 4-week administration of hydrogen water. Gene Ontology analysis revealed that genes for oxidoreduction-related proteins, including hydroxymethylglutaryl CoA reductase, were significantly enriched in the upregulated genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21512236" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26528" }, "primaryId" : "GEO:GSE26528", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26528" } ] }, "title" : "NGF and proNGF activate functionally distinct mRNAs in PC12 cells: an early gene expression profiling", "dateAssigned" : "2011-01-10T00:00:00.000-06:00", "summary" : "The biological activities of NGF and of its precursor proNGF are quite distinct, due to different receptor binding profiles, but nothing is known about how proNGF regulates gene expression. We performed experiments to address this question, by verifying whether a proNGF specific transcriptional signature, distinct from that of NGF, could be identified. To this aim, we studied gene expression regulation by proNGF and NGF in PC12 cells incubated for 1 and 4 hours with recombinant NGF and proNGF, in its wild-type or in a furin-cleavage resistant form. mRNA expression profiles were analyzed by whole genome microarrays at these early time points, in order to identify specific profiles of NGF and proNGF.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21677785" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26532" }, "primaryId" : "GEO:GSE26532", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26532" } ] }, "title" : "Neuron-released a-synuclein is an endogenous ligand of TLR2 for paracrine activation of microglia", "dateAssigned" : "2011-01-10T00:00:00.000-06:00", "summary" : "Abnormal accumulation of aggregated proteins and sustained microglial activation are important contributors of neurodegenerative process in neurological diseases. Recent studies have shown that aggregation-prone proteins, such as a-synuclein, the protein implicated in Parkinson’s disease (PD), are released from neuronal cells and thus present in the extracellular fluid, pointing to the possible paracrine effects of these proteins on microglial immune responses. However, the mechanism underlying the disease-associated microglial activation and the role of neuronal proteins in this process remain unknown. Here, we show that extracellular a-synuclein released from neuronal cells is an endogenous ligand of toll-like receptor 2 (TLR2) and activates microglia, which in turn induces neurodegeneration. Interaction between neuron-released a-synuclein and TLR2 and subsequent activation of the TLR2 signaling were demonstrated comprehensively by using computational modeling of signaling network and by the experimental validation in TLR2-deficient microglia both in vitro and in vivo. In contrast to the neuron-released a-synuclein, recombinant a-synuclein proteins, including monomer, oligomer, fibril, or nitrated forms, were not able to interact or activate TLR2, suggesting that neuronal cells have a mechanism of enriching specific forms of a-synuclein capable of activating TLR2 during the process of releasing this protein. Taken together, the results suggest that both neuron-released extracellular a-synuclein and TLR2 might be novel therapeutic targets for modifying neuroinflammation in PD and related neurodegenerative diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24743837" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26542" }, "primaryId" : "GEO:GSE26542", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26542" } ] }, "title" : "Upregulation of pro-apoptotic microRNA mir-125a following massive small bowel resection in rats", "dateAssigned" : "2011-01-11T00:00:00.000-06:00", "summary" : "Upregulation of mir-125a suppresses the pro-survival protein Mcl1, producing the increase in apoptosis known to accompany the proliferative changes characteristic of intestinal adaptation. Our data highlight a potential role for microRNAs as mediators of the adaptive process and may facilitate the development of new therapeutic options for short bowel syndrome.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22418008" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26660" }, "primaryId" : "GEO:GSE26660", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26660" } ] }, "title" : "The transcriptome of the medullary area postrema: The thirsty rat, the hungry rat and the hypertensive rat", "dateAssigned" : "2011-01-18T00:00:00.000-06:00", "summary" : "The area postrema (AP) is a sensory circumventricular organ characterised by extensive fenestrated vasculature and neurons which are capable of detecting circulating signals of osmotic, cardiovascular, immune and metabolic status. The AP can communicate these messages via efferent projections to brainstem and hypothalamic structures that are able to orchestrate an appropriate response. We have used microarrays to profile the transcriptome of the AP in the Sprague Dawley (SD) and Wistar Kyoto (WKY) rat and present here a comprehensive catalogue of gene expression, focussing specifically on the population of ion channels, receptors and G protein-coupled receptors (GPCRs) expressed in this sensory tissue; of the GPCRs expressed in the rat AP we identified ~36% that are orphans having no established ligand. We have also looked at the ways in which the AP transcriptome responds to the physiological stressors of 72-hours dehydration (DSD) and 48-hours fasting (FSD) and have performed microarrays under these conditions. Comparison between the DSD and SD or between FSD and SD revealed only a modest number of AP genes that are regulated by these homeostatic challenges. The expression levels of a much larger number of genes are altered in the spontaneously hypertensive rat (SHR) AP compared to the normotensive WKY controls however. Finally, analysis of these ‘hypertension-related’ elements revealed genes that are involved in both the regulation of blood pressure and immune function and as such are excellent targets for further study.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21317217" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26703" }, "primaryId" : "GEO:GSE26703", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26703" } ] }, "title" : "Determining the Program of Leydig Cell Development", "dateAssigned" : "2011-01-19T00:00:00.000-06:00", "summary" : "In the present study, microarray analysis was performed on RNA isolated from purified SLCs, PLCs, ILCs, ALCs and bone stem cells, using Affymetrix Rat Genome RAE230 2.0 arrays which monitor ~30,000 transcripts from over ~28,000 well-substantiated genes. The focus is on the differences and similarities between SLCs and bone stem cells, and between SLCs and PLCs, ILCs and ALCs", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21832170" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26716" }, "primaryId" : "GEO:GSE26716", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26716" } ] }, "title" : "Analysis of gene expression in QKI knockdown CG-4 cells", "dateAssigned" : "2011-01-19T00:00:00.000-06:00", "summary" : "We have used Affymetrix exon arrays to assess changes in gene expression in response to QKI knockdown on an exon level in rat CG-4 oligodendrocyte precursor cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21253564" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26730" }, "primaryId" : "GEO:GSE26730", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26730" } ] }, "title" : "A role for nuclear factor interleukin-3 (NFIL3), a critical transcriptional repressor, in down-regulation of periovulatory gene expression", "dateAssigned" : "2011-01-19T00:00:00.000-06:00", "summary" : "The LH surge triggers dramatic transcriptional changes in genes associated with ovulation and luteinization. The present study investigated the spatiotemporal expression of nuclear factor interleukin-3 (NFIL3), a transcriptional regulator of the bZIP transcription factor superfamily, and its potential role in the ovary during the periovulatory period. NFIL3, also known as E4-binding protein 4 or NFIL3/E4BP4, was originally identified as a transcriptional repressor based on its DNA-binding activity at the promoter of the gene encoding the adenovirus E4 protein. Immature female rats were injected with PMSG, treated with hCG, and ovaries or granulosa cells were collected at various times after hCG. Nfil3 mRNA was highly induced both in intact ovaries and granulosa cells after hCG treatment. In situ hybridization demonstrated that Nfil3 mRNA was highly induced in theca-interstitial cells at 4-8 h after hCG, localized to granulosa cells at 12 h, and decreased at 24 h. Over-expression of NFIL3 in granulosa cells inhibited the induction of prostaglandin-endoperoxide synthase 2 (Ptgs2), progesterone receptor (Pgr), epiregulin (Ereg), and amphiregulin (Areg) and down regulated levels of prostaglandin E2. The inhibitory effect on Ptgs2 induction was reversed by NFIL3 siRNA treatment. In theca-interstitial cells the expression of hydroxyprostaglandin dehydrogenase 15-(NAD) (Hpgd) was also inhibited by NFIL3 over-expression. Data from luciferase assays demonstrated that NFIL3 over-expression decreased the induction of the Ptgs2 and Areg promoter activity. EMSA and ChIP analyses indicated that NFIL3 binds to the promoter region containing the DNA binding sites of CREB and C/EBP?. In summary, hCG induction of NFIL3 expression may modulate the process of ovulation and theca-interstitial and granulosa cell differentiation by regulating expression of PTGS2, PGR, AREG, EREG, and HPGD, potentially through interactions with CREB and C/EBP? on their target gene promoters.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21212137" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26737" }, "primaryId" : "GEO:GSE26737", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26737" } ] }, "title" : "Epigenetic Transgenerational Alterations to Stress Response in Brain Gene Networks and Behaviour", "dateAssigned" : "2011-01-19T00:00:00.000-06:00", "summary" : "We used microarrays to determine genes expressed differentially in rats' 4 brain areas - basolateral amygdala (BLA), primary and secondary motor cortex (Crtx), CA1 of the hippocampus (CA1), and CA3 of the hippocampus (CA3) - due to Vinclozolin treatments of their grand-grandmothers and/or to stress in adolescence age.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22615374" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26753" }, "primaryId" : "GEO:GSE26753", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26753" } ] }, "title" : "Solexa sequencing of small RNAs in Sprague-Dawley (SD) rat [proximal sciatic nerve]", "dateAssigned" : "2011-01-20T00:00:00.000-06:00", "summary" : "Keywords: Small RNA sequencing", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26871" }, "primaryId" : "GEO:GSE26871", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26871" } ] }, "title" : "Genome wide profiling of PAX8 binding stes in PCCL3 rat cells", "dateAssigned" : "2011-01-26T00:00:00.000-06:00", "summary" : "Analysis of PAX8 binding sites by chromatin immunoprecipitation coupled with ultra-high-throughput sequencing (ChIP-seq) in PCCL3 rat cells. Results provide insight into the contribution of this regulatory factor to transcription genome-wide.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22531031" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26933" }, "primaryId" : "GEO:GSE26933", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26933" } ] }, "title" : "Effects of polyglutamine expansion and subcellular localization of C-terminal fragment of Cav2.1 in PC12 rat pheochromocytoma cells", "dateAssigned" : "2011-01-28T00:00:00.000-06:00", "summary" : "Polyglutamine(polyQ) expansion of a1A voltage-dependent calcium channel (Cav2.1) is the causative mutation of spinocerebellar ataxia type 6 (SCA6). The C-terminal fragment (CTF) of Cav2.1 makes aggregates in the cytoplasm of SCA6 Purkinje cells and may relate to the pathogenesis. In order to identify genes associated with polyQ expansion and subcellular localization of CTF, we analyzed gene expression profiles of PC12 rat pheochromocytoma cells using Tet-off system.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23505410" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26936" }, "primaryId" : "GEO:GSE26936", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26936" } ] }, "title" : "Expression data from rat urinary bladder and non-glandular stomach tissue samples", "dateAssigned" : "2011-01-28T00:00:00.000-06:00", "summary" : "Seven novel and potent Raf small molecule kinase inhibitors were evaluated in 7-day oral repeat-dose rat toxicity studies. All compounds tested induced hyperplasia in multiple tissues. Microarrays were used to investigate transciptional changes associated by treatment with a single compound to gain insight into the cellular changes that may contribute to the tissue hyperplasia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21677315" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26937" }, "primaryId" : "GEO:GSE26937", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE26937" } ] }, "title" : "PAX8 transcriptional profiling in rat PCCL3 cells", "dateAssigned" : "2011-01-28T00:00:00.000-06:00", "summary" : "PAX8 transcriptional profiling of rat PCCL3 cells comparing wild type cells with PAX8 silenced cells and scramble treated with PAX8 silenced cells", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22531031" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27009" }, "primaryId" : "GEO:GSE27009", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27009" } ] }, "title" : "microRNA expression in CagA-expressing cells", "dateAssigned" : "2011-02-02T00:00:00.000-06:00", "summary" : "Comprehensive analysis of microRNA expression were performed with 238 rat genes of microRNA between CagA-expressing and -non-expressing cells. CagA expression was controlled by tetracycline-off system in RGM1 cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22936674" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27015" }, "primaryId" : "GEO:GSE27015", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27015" } ] }, "title" : "Rat model of MTLE: Animals with epilepsy vs animals without epilepsy (Agilent)", "dateAssigned" : "2011-02-02T00:00:00.000-06:00", "summary" : "Neither the molecular basis of the pathologic tendency of neuronal circuits to generate spontaneous seizures (epileptogenicity) nor anti-epileptogenic mechanisms that maintain a seizure-free state are well understood. Here, we performed transcriptomic analysis in the intrahippocampal kainate model of temporal lobe epilepsy in rats using both Agilent and Codelink microarray platforms to characterize the epileptic processes. The experimental design allowed subtraction of the confounding effects of the lesion, identification of expression changes associated with epileptogenicity, and genes upregulated by seizures with potential homeostatic anti-epileptogenic effects. Using differential expression analysis, we identified several hundred expression changes in chronic epilepsy, including candidate genes associated with epileptogenicity such as Bdnf and Kcnj13. To analyze these data from a systems perspective, we applied weighted gene co-expression network analysis (WGCNA) to identify groups of co-expressed genes (modules) and their central (hub) genes. One such module contained genes upregulated in the epileptogenic region, including multiple epileptogenicity candidate genes, and was found to be involved the protection of glial cells against oxidative stress, implicating glial oxidative stress in epileptogenicity. Another distinct module corresponded to the effects of chronic seizures and represented changes in neuronal synaptic vesicle trafficking. We found that the network structure and connectivity of one hub gene, Sv2a, showed significant changes between normal and epileptogenic tissue, becoming more highly connected in epileptic brain. Since Sv2a is a target of the antiepileptic levetiracetam, this module may be important in controlling seizure activity. Bioinformatic analysis of this module also revealed a potential mechanism for the observed transcriptional changes via generation of longer alternatively polyadenlyated transcripts through the upregulation of the RNA binding protein HuD. In summary, combining conventional statistical methods and network analysis allowed us to interpret the differentially regulated genes from a systems perspective, yielding new insight into several biological pathways underlying homeostatic anti-epileptogenic effects and epileptogenicity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21695113" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27023" }, "primaryId" : "GEO:GSE27023", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27023" } ] }, "title" : "Blood gene expression profile of control and crystalline silica exposed rats", "dateAssigned" : "2011-02-02T00:00:00.000-06:00", "summary" : "The present research aimed to investigate peripheral blood gene expression profiling as a minimally invasive surrogate approach to study silica-induced pulmonary toxicity. Rats were exposed to crystalline silica by inhalation (15 mg/m3, 6 hours/day, 5 days). Pulmonary damage and blood gene expression profiles were determined at various latency periods (0 - 16 weeks). Silica exposure resulted in pulmonary toxicity and this was evidenced by histological changes in the lungs and elevation of LDH activity, and total protein and albumin contents in the bronchoalveolar lavage fluid (BALF) of the rats. Microarray analysis of global gene expression profiles in the blood of the rats identified genes that were differentially expressed in response to silica exposure and toxicity. The number of significantly differentially expressed genes in the blood of silica exposed rats correlated with the severity of silica-induced pulmonary toxicity. Genes involved in biological functions such as inflammatory response, cancer, pulmonary damage, oxidative stress, energy metabolism, fibrosis, etc, were found differentially expressed in the blood of the silica exposed rats compared with the controls. Induction of pulmonary inflammation in the silica exposed rats, as suggested by differential expression of inflammatory response genes in the blood, was supported by significant increases in the number of macrophages and infiltrating neutrophils as well as the activity of pro-inflammatory chemokines – MCP1 and MIP2, observed in the BALF of the silica exposed rats. A silica-responsive blood gene expression signature developed using the gene expression data predicted with significant accuracy the exposure of rats to lower concentrations (1 and 2 mg/m3) of silica. Taken together our findings suggest the potential application of peripheral blood gene expression profiling as a minimally invasive and efficient surrogate approach to detect and study silica-induced pulmonary toxicity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21602193" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27042" }, "primaryId" : "GEO:GSE27042", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27042" } ] }, "title" : "Investigating RDX neurotoxicity in rat brain using gene expression analysis and transcriptional network modeling", "dateAssigned" : "2011-02-03T00:00:00.000-06:00", "summary" : "ABSTRACT: The central nervous system is remarkably plastic in its ability to recover from trauma. We examined recovery from hexahydro-1,3,5-trinitrotriazine (RDX) induced seizures in rat through changes in transcriptional networks. Transcriptional networks from time series experiments provide a good basis for organizing and studying the dynamic behavior of biological processes. The goal of this work was to identify networks affected by chemical exposure and track changes in these networks as animals recover. We examined brain microarray data from rats exposed to 0, 1.2, 12, 24, and 47 mg RDX/kg body weight at different time points after exposure (24hr, 48hr, 7d, 14d, 28d and 90d). RESULTS A credible transcriptional network was constructed from the gene expression microarray data, which predicts the role of some key genes such as heat shock proteins, neuropeptide Y, thyrotropin-releasing hormones, growth factors, and ion channels in neurotransmission and neuroprotective mechanisms. Examination of the dynamic changes in expression within this network over time provided insight into CNS protective mechanisms from traumas.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27065" }, "primaryId" : "GEO:GSE27065", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27065" } ] }, "title" : "Differential gene expression from microarray analysis distinguishes woven and lamellar bone formation in the rat ulna following mechanical loading", "dateAssigned" : "2011-02-04T00:00:00.000-06:00", "summary" : "The objective of our study was to use a microarray to distinguish the molecular responses between woven and lamellar bone formation induced through mechanical loading. The micorarray identified numerous genes and pathways that were differentially regulated for woven, but not lamellar bone formation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22216249" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27166" }, "primaryId" : "GEO:GSE27166", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27166" } ] }, "title" : "Rat model of MTLE: Animals with epilepsy vs animals without epilepsy (codelink)", "dateAssigned" : "2011-02-08T00:00:00.000-06:00", "summary" : "Neither the molecular basis of the pathologic tendency of neuronal circuits to generate spontaneous seizures (epileptogenicity) nor anti-epileptogenic mechanisms that maintain a seizure-free state are well understood. Here, we performed transcriptomic analysis in the intrahippocampal kainate model of temporal lobe epilepsy in rats using both Agilent and Codelink microarray platforms to characterize the epileptic processes. The experimental design allowed subtraction of the confounding effects of the lesion, identification of expression changes associated with epileptogenicity, and genes upregulated by seizures with potential homeostatic anti-epileptogenic effects. Using differential expression analysis, we identified several hundred expression changes in chronic epilepsy, including candidate genes associated with epileptogenicity such as Bdnf and Kcnj13. To analyze these data from a systems perspective, we applied weighted gene co-expression network analysis (WGCNA) to identify groups of co-expressed genes (modules) and their central (hub) genes. One such module contained genes upregulated in the epileptogenic region, including multiple epileptogenicity candidate genes, and was found to be involved the protection of glial cells against oxidative stress, implicating glial oxidative stress in epileptogenicity. Another distinct module corresponded to the effects of chronic seizures and represented changes in neuronal synaptic vesicle trafficking. We found that the network structure and connectivity of one hub gene, Sv2a, showed significant changes between normal and epileptogenic tissue, becoming more highly connected in epileptic brain. Since Sv2a is a target of the antiepileptic levetiracetam, this module may be important in controlling seizure activity. Bioinformatic analysis of this module also revealed a potential mechanism for the observed transcriptional changes via generation of longer alternatively polyadenlyated transcripts through the upregulation of the RNA binding protein HuD. In summary, combining conventional statistical methods and network analysis allowed us to interpret the differentially regulated genes from a systems perspective, yielding new insight into several biological pathways underlying homeostatic anti-epileptogenic effects and epileptogenicity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21695113" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27179" }, "primaryId" : "GEO:GSE27179", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27179" } ] }, "title" : "Chronic exposure to ambient particulate matter alters cardiac gene expression patterns and markers of oxidative stress in rats", "dateAssigned" : "2011-02-09T00:00:00.000-06:00", "summary" : "Exposure to ambient particulate matter (PM) significantly increases cardiovascular morbidity and mortality in the general population. We hypothesized that some components of PM can affect the gene expression patterns in the hearts of rats exposed for 3 months to filtered air (FA), coarse (CP; 2.5 < dp < 10 µm), fine (FP; dp = 2.5 µm) or ultrafine (UFP; dp = 0.18 µm) components of PM. The median diameters of CP, FP, and UFP were 3 µm, 0.7 µm and 0.07 µm, respectively. Exposures (n = 8 per group) were performed using a particle concentrator system in Riverside, California, an area with high ambient levels of photochemically derived gaseous and particulate pollutants. At the end of the exposure, hearts were subjected to gene expression profiling by using Illumina RatRef-12 bead chips and levels of malonaldehyde (MDA), a biomarker of oxidative stress, were measured. Applying fold ratio >1.5 (for both up- and downregulated genes), we found three genes in the CP and nine genes in the UFP groups with significantly changed expression, compared with FA. No significant changes in gene expression patterns were observed in the FP group. In the UFP group, thioredoxin-interacting protein (Txnip), a negative regulator of an antioxidant enzyme thioredoxin, and cytochrome P450 (Cyp2e1), an enzyme involved in the metabolism of foreign substances, demonstrated significant up-regulation (fold ratios 1.79 and 1.57, respectively, with false discovery rate, FDR < 0.05). In the CP group, there was also a trend towards increased Txnip expression (fold ratio 1.43, FDR > 0.05) and significant increase in the Cyp2e1 expression (fold ratio 1.79, FDR < 0.05). Changes in the Txnip and Cyp2e1 expression showed statistically significant positive correlation to each other (p < 0.0009) and were confirmed by real-time PCR. In addition, Txnip and Cyp2e1 expression demonstrated statistically significant moderate correlation with the levels of MDA in the heart. Up-regulation of both Cyp2e1 and Txnip are observed in hearts of patients with certain cardiac diseases. Therefore, chronic exposure to CP and UFP directly affects expression of disease-relevant genes in the myocardium.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27212" }, "primaryId" : "GEO:GSE27212", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27212" } ] }, "title" : "Gene expression in spinal cord neurons grown on polyornithine or on carbon nanotube (CNT)-based substrates", "dateAssigned" : "2011-02-10T00:00:00.000-06:00", "summary" : "In this context, we used microarrays to show whether cultured dissociated spinal neurons show a difference in gene expression when grown in control conditions (polyornithine-covered substrates) or on CNT-based substrates.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23951361" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27266" }, "primaryId" : "GEO:GSE27266", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27266" } ] }, "title" : "Fish oil/pectin temporally alters gene expression profiles in exfoliated rat colonocytes throughout oncogenesis", "dateAssigned" : "2011-02-12T00:00:00.000-06:00", "summary" : "KEYWORDS: Fish oil/pectin, pectin, exfoliated colonocytes, gene expression, apoptosis, colon cancer, chemoprevention", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21508209" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27274" }, "primaryId" : "GEO:GSE27274", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27274" } ] }, "title" : "Fibrinogen is upregulated following kidney damage and protects it against ischemia-reperfusion injury", "dateAssigned" : "2011-02-13T00:00:00.000-06:00", "summary" : "characterization of fibrinogen expression in the kidney, excretion in the urine following kidney damage and evaluating the therapeutic potential of fibrinogen in acute kidney injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24158981" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27368" }, "primaryId" : "GEO:GSE27368", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27368" } ] }, "title" : "Profiling of copy-number variation between BN and M520 rats", "dateAssigned" : "2011-02-16T00:00:00.000-06:00", "summary" : "We used Nimblegen HD aCGH to detect copy-number variants between genomes of BN and M520 rats", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27393" }, "primaryId" : "GEO:GSE27393", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27393" } ] }, "title" : "Gene expression in lungs from male HIV transgenic rats", "dateAssigned" : "2011-02-17T00:00:00.000-06:00", "summary" : "HIV Tg rats exhibit pulmonary hypertension and pulmonary artery remodeling. In an effort to begin to understand cell signaling pathways which are altered in lungs from HIV transgenic rats, we used microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21685241" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27449" }, "primaryId" : "GEO:GSE27449", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27449" } ] }, "title" : "Changes of mRNA expressin in rat kidney inner medulla in response to dDAVP stimulation/ withdrawal", "dateAssigned" : "2011-02-22T00:00:00.000-06:00", "summary" : "The E3 ubiquitin -protein ligases (E3s) plays a role as regulators of protein trafficking and degradation. We aimed to identify E3s in rat kidney which are associated with dDAVP-induced urine concentration.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21734099" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27465" }, "primaryId" : "GEO:GSE27465", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27465" } ] }, "title" : "Fish oil alters tamoxifen-modulated expression of genes related to differentiation, proliferation, metastasis, and immune response in rat mammary tumors", "dateAssigned" : "2011-02-23T00:00:00.000-06:00", "summary" : "Herein, we evidence that tamoxifen treatment modifies gene expression of mammary tumors depending upon the type of dietary fat fed to the animals. Rats initiated with MNU and treated with tam were fed a diet rich in corn oil (CO) or fish oil (FO). After 8 weeks, tumors of the same histological type (cribriform) were collected and comprehensive analysis of messenger RNA expression was performed. The mRNA expression of genes such as SerpinB10, Wisp2 and Apod in tumors from FO-treated rats is indicative of highly differentiated tumors. Decreased expression of H19 and Igf2 mRNA in tam-treated groups, and Thrsp and Wnt5b mRNA in FOtam group may be related to tumor growth impairment and lower metastatic capacity. Increased Irf7, RT1-CE3, RT1-CE16 transcript levels in FO-treated animals suggests an improved immune response against tumors (Th1 pattern) whereas decreased mRNA of Fcer1a, Hdc, Ms4a2, Slp1, Mcpt1 and Mcpt2 may indicate a shift of the immune response towards Th2 pattern.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23061905" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27576" }, "primaryId" : "GEO:GSE27576", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27576" } ] }, "title" : "Profile of small RNA transcriptome during cortical development in the Rat", "dateAssigned" : "2011-02-28T00:00:00.000-06:00", "summary" : "Small non-coding RNAs play important roles in regulating gene expression during development and disease. However, a comprehensive analysis of small RNAs in developing brain is largely lacking. By using next-generation sequencing technique, we carried out a systematic analysis of small RNA transcriptome of rat neocortex from early developmental stage till adult. Our results revealed an extraordinary degree of stage-specific profiling of miRNA, and other classes of small RNAs including snoRNA, rasRNA, scRNA and unexpectedly piRNA, which was considered to be solely expressed in germline tissues. Developmentally regulated miRNA editing was also observed. This study further showed the effectiveness of the high through-put sequencing in genome-wide analysis of small RNAs. The dataset described here will greatly contribute to our understanding of the divergence, variation, and function of small RNAs and may be a valuable resource in clarifying new regulatory mechanisms of cortical development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22691069" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27580" }, "primaryId" : "GEO:GSE27580", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27580" } ] }, "title" : "An interspecies analysis reveals sequence determinants of the bivalent chromatin state", "dateAssigned" : "2011-03-01T00:00:00.000-06:00", "summary" : "The sequence determinants of chromatin bivalency remain unclear. We analysed sequence determinants of chromatin bivalency genome-wide in several mammalian species and performed a series of transgenic experiments in mouse ES cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22056776" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27620" }, "primaryId" : "GEO:GSE27620", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27620" } ] }, "title" : "CHD5, A Brain-Specific Chromatin Remodeling Enzyme, Regulates Expression Of Neuronal Genes.", "dateAssigned" : "2011-03-01T00:00:00.000-06:00", "summary" : "CHD5 is frequently deleted in neuroblastoma, and appears to be a tumor suppressor gene; however, little is known about the role of CHD5. We found CHD5 mRNA was restricted to brain; by contrast most other remodeling ATPases were broadly expressed. CHD5 protein isolated from mouse brain was associated with HDAC2, p66, MTA3 and RbAp46 in a megadalton complex. CHD5 protein was detected in several rat brain regions and appeared to be enriched in neurons. CHD5 protein was predominantly nuclear in primary rat neurons and brain sections. Microarray analysis revealed genes that were upregulated and downregulated when CHD5 was depleted from primary neurons. CHD5 depletion altered expression of neuronal genes, transcription factors, and brain-specific subunits of the SWI/SNF remodeling enzyme. Aging and Alzheimers gene sets were strongly affected by CHD5 depletion from primary neurons. Chromatin immunoprecipitation revealed CHD5 bound to these genes, suggesting the regulation was direct. Together, these results indicate that CHD5 is found in a NuRD-like multi-protein complex. CHD5 is restricted to the brain, unlike the closely related family members CHD3 and CHD4. CHD5 regulates expression of neuronal genes, cell cycle genes and remodeling genes. CHD5 is linked to regulation of aging and Alzheimer’s genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21931736" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27625" }, "primaryId" : "GEO:GSE27625", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27625" } ] }, "title" : "Hepatic gene expression changes in aging and R-a-lipoic acid supplementation: Necroinflammatory phenotype, lipid synthesis regulation and circadian rhythms.", "dateAssigned" : "2011-03-02T00:00:00.000-06:00", "summary" : "To determine the effects of age and lipoic acid supplementation on hepatic gene expression, we fed young (3 months) and old (24 months) male Fischer 344 rats a diet with or without 0.2% (w/w) R-a-lipoic acid (LA) for two weeks. Total RNA isolated from liver tissue was analyzed by Affymetrix microarray to examine changes in transcriptional profile. Results showed an increase in pro-inflammatory gene expression in the aging liver, with increased immune cell function and tissue remodeling genes, representing 45% of the age-related transcriptome changes. Increased inflammation was corroborated by increases in soluble ICAM1 levels with age. There were also observed age-related increases in transcription of genes related to lipid and cholesterol synthesis including Acetyl CoA Carboxylase (Acacb) and Fatty acid Synthase (Fasn). Supplementation of old animals with LA did not reverse this necro-inflammatory phenotype, yet limited age-associated hepatic dyslipidemia. Dietary LA further affected a small but concerted number of hepatic genes regardless of age. These included declines in lipid and bile synthesis genes. Decline in lipid synthesis genes was further corroborated by a decrease in Fasn and Acc protein levels. Intriguingly, LA also altered the expression of genes governing circadian rhythm, most notably Bmal1, Npas2, and Per2, which changed in a coordinated manner with respect to their rhythmic transcription. Thus, advanced age is associated with a necro-inflammatory phenotype and increased lipid synthesis, while chronic LA supplementation influences hepatic genes associated with energy metabolism and circadian rhythm regardless of age.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22049228" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27638" }, "primaryId" : "GEO:GSE27638", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27638" } ] }, "title" : "Gene expression profile of hepatocellular carcinoma in low-dose, repeated diethylnitrosamine (DEN)-treated rat treated with erlotinib", "dateAssigned" : "2011-03-02T00:00:00.000-06:00", "summary" : "Hepatocellular carcinoma (HCC) is the sixth most common solid tumor worldwide and the third leading cause of cancer-related death. Given the lack of successful treatment options, chemoprevention in high-risk patients has been proposed as an alternative strategy. Mounting evidence supports a role for epidermal growth factor (EGF) during chronic liver disease and hepatocellular transformation. We address the hypothesis that blocking the EGF-EGF receptor (EGFR) pathway may be an effective strategy for inhibiting fibrogenesis and hepatocarcinogenesis. A rat model of diethylnitrosamine (DEN)-induced cirrhosis was used to examine the effects of erlotinib on underlying chronic liver disease and HCC formation. The DEN-induced rat model closely resembles disease progression in humans both pathologically and molecularly. Erlotinib significantly prevented the development of HCC tumor nodules in a dose-dependent fashion. Further, erlotinib inhibited the activation of hepatic stellate cells and prevented fibrogenesis. Erlotinib also reduced hepatotoxicity and improved liver function. Finally, a gene expression signature predictive of poor survival in human cirrhosis patients was reversed in response to erlotinib. Our data demonstrate for the first time that EGFR inhibition prevents liver fibrogenesis. Further, our results suggest that erlotinib is a potentially effective HCC chemoprevention strategy through inhibition of cirrhosis progression which can be monitored at the molecular level.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24677197" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27725" }, "primaryId" : "GEO:GSE27725", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27725" } ] }, "title" : "Genome-wide analysis of perinatal effect of nitric oxide (NO) donor molsidomine on the kidneys of Fawn-Hooded Hypertensive (FHH) rats at different ages", "dateAssigned" : "2011-03-07T00:00:00.000-06:00", "summary" : "Microarray was performed on kidneys in molsidomine-treated FHH rats in order to gain understanding why perinatal treatment with molsidomine in FHH was beneficial in FHH offspring (e.g. lower blood pressure and less renal damage)", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27926" }, "primaryId" : "GEO:GSE27926", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27926" } ] }, "title" : "Expression data from F344N rats in long and short photoperiods", "dateAssigned" : "2011-03-14T00:00:00.000-05:00", "summary" : "At each time point 4 rats were used in each photoperiod giving 24 rats in total.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21731713" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27956" }, "primaryId" : "GEO:GSE27956", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27956" } ] }, "title" : "Insulin biosynthesis in neuronal progenitors derived from adult hippocampus and the olfactory bulb", "dateAssigned" : "2011-03-14T00:00:00.000-05:00", "summary" : "In this study, we demonstrate that insulin is produced not only in the mammalian pancreas but also in adult neuronal cells derived from hippocampus and olfactory bulb. Paracrine Wnt3 plays an essential role in promoting the active expression of insulin in both hippocampus and olfactory bulb-derived neural stem cells. Our analysis indicates that the balance between Wnt3, which triggers the expression of insulin via NeuroD1 transcription factor, and IGFBP-4, which inhibits the original Wnt3 action, is regulated depending on the diabetic status. We also show that adult neural progenitors derived from diabetic animals retain the ability to give rise to insulin-producing cells and that grafting neuronal progenitors into the pancreas of diabetic animals reduces glucose levels. This study provides an example of a simple and direct use of adult stem cells from one organ to another, without introducing additional inductive genes. In this study, we demonstrate that insulin is produced not only in the mammalian pancreas but also in adult neuronal cells derived from hippocampus and olfactory bulb. Paracrine Wnt3 plays an essential role in promoting the active expression of insulin in both hippocampus and olfactory bulb-derived neural stem cells. Our analysis indicates that the balance between Wnt3, which triggers the expression of insulin via NeuroD1 transcription factor, and IGFBP-4, which inhibits the original Wnt3 action, is regulated depending on the diabetic status. We also show that adult neural progenitors derived from diabetic animals retain the ability to give rise to insulin-producing cells and that grafting neuronal progenitors into the pancreas of diabetic animals reduces glucose levels. This study provides an example of a simple and direct use of adult stem cells from one organ to another, without introducing additional inductive genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21984534" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27978" }, "primaryId" : "GEO:GSE27978", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE27978" } ] }, "title" : "IL-6-mediated activation of STAT3a prevents trauma/hemorrhagic shock-induced liver inflammation", "dateAssigned" : "2011-03-16T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global gene expression in response to T/HS and the effect of IL-6 on this model with and without pharmacologic blockade of Stat3-mediated IL-6 and identified distinct members of the inflammasome de-regulated during T/HS that normalized with IL-6 administration during resuscitation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28058" }, "primaryId" : "GEO:GSE28058", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28058" } ] }, "title" : "Expression data from livers of high fat fed rats treated with ACC inhibitor PF-04923503", "dateAssigned" : "2011-03-21T00:00:00.000-05:00", "summary" : "Fundamental alterations in lipid metabolism including increased rates of de novo lipogenesis (DNL), reduced fatty acid oxidation (FAOX) and ectopic lipid accumulation in skeletal muscle and liver are characteristic of type 2 diabetes mellitus (T2DM) and have been hypothesized to directly contribute to the molecular pathogenesis of the disease. Acetyl-CoA carboxylase (ACC) catalyzes the formation of malonyl-CoA, the rate limiting substrate for DML and key regulator of FAOX. ACC inhibitors have the potential to pharmacologically rebalance these metabolic alterations. In the present study, PF-04923503, a potent dual ACC1/ACC2 inhibitor with properties optimized for in vivo studies, suppressed levels of malonyl-CoA in primary hepatocytes, rat skeletal muscle ex vivo, as well as rat liver and skeletal muscle in vivo. This impact on malonyl-CoA was directly correlated (r2>0.9) with reduced hepatic DNL and inversely correlated with incresed rates of FAOX (r2>0.9). The pharmacological eccfect of PF-04923503 persisted with chronic treatment. High-fat fed rats treated with PF-04923503 for six weeks showed dose-dependent reductions in skeletal muscle and liver lipid accumulation. These changes correlated directly with markers for improved insulin sensitization. However, liver gene expression indicates that pharmacological inhibition results in compensation by up-regualtion of genes involved with DNL. These results suggest that pharmacological inhibition of ACC may have utility to help rebalance metabolic abnormalities in T2DM and improve insulin sensitivity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28150" }, "primaryId" : "GEO:GSE28150", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28150" } ] }, "title" : "Transcriptional responses of sympathetic neurons during BMP-induced primary dendritogenesis", "dateAssigned" : "2011-03-24T00:00:00.000-05:00", "summary" : "The objective of this study was to identify genes that are differentially regulated in cultured sympathetic neurons during BMP-induced dendritic growth and to determine the temporal expression patterns of these genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21765909" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28202" }, "primaryId" : "GEO:GSE28202", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28202" } ] }, "title" : "A molecular and phenotypic integrative approach to identify a no effect dose level for anti-androgen induced testicular toxicity", "dateAssigned" : "2011-03-28T00:00:00.000-05:00", "summary" : "With the advent of high information content technologies, especially microarrays, it is pertinent to determine the impact of molecular data on the NOAELs. Consequently, we conducted an integrative study to identify a no transcriptomic effect dose using microarray analyses coupled with qPCR and determined how this correlated with the NOAEL. We assessed the testicular effects of the antiandrogen, flutamide (FM), in a rat 28-day toxicity study using doses of 0.2-30 mg/kg/day. Concerning molecular data, we observed differential gene expression starting from 1 mg/kg/day and a deregulation of more than 1500 genes at 30 mg/kg/day. Dose-related changes were identified for the major pathways associated with the testicular lesion (eg fatty acid metabolism), that were confirmed by qPCR. These data, along with standard measurements supported the no effect dose of 0.2 mg/kg/day.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21525395" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28404" }, "primaryId" : "GEO:GSE28404", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28404" } ] }, "title" : "Genome-wide MicroRNA Downregulation as a Negative Feedback Mechanism in the Early Phases of Liver Regeneration", "dateAssigned" : "2011-04-05T00:00:00.000-05:00", "summary" : "Liver is one of the few organs that have the capacity to regenerate in response to injury. We carried out genome-wide miRNA microarray studies during liver regeneration in rats after 70% partial hepatectomy (PH) at early and mid-time points to more thoroughly understand their role. At 3, 12 and 18 hrs post-PH ~ 40% of the miRNAs tested were up-regulated. Conversely, at 24 hrs post-PH, ~ 70% of miRNAs were down-regulated. Further, we established that the genome-wide down-regulation of miRNA expression at 24 hrs was also correlated with decreased expression of genes such as Rnasen, Dgcr8, Dicer, Tarbp2 and Prkra that are associated with miRNA biogenesis. To determine if a potential negative feedback loop between miRNAs and their regulatory genes existed, 11 candidate miRNAs which were predicted to target the above genes were examined and found to be up-regulated at 3 hrs post-PH. Using reporter and functional assays, we determined that expression of these miRNA-processing genes could be regulated by a subset of miRNAs and some miRNAs could target multiple miRNA biogenesis genes simultaneously. We also demonstrated that over-expression of these miRNAs inhibited cell proliferation and modulated the cell cycle in both Huh-7 human hepatoma cells and primary rat hepatocytes. From these observations, we postulated that selective up-regulation of miRNAs in the early-phase after PH was involved in the priming and commitment to liver regeneration, while the subsequent genome-wide down-regulation of miRNAs was required for efficient recovery of liver cell mass. Conclusion: Our data suggest that miRNA changes are regulated by negative feedback loops between miRNAs and their regulatory genes that may play an important role in the steady-state regulation of liver regeneration.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21574170" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28435" }, "primaryId" : "GEO:GSE28435", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28435" } ] }, "title" : "Transcriptomic Analysis of Rat Brain Following Exposure to the Organophosphonate Anticholinesterase Sarin", "dateAssigned" : "2011-04-06T00:00:00.000-05:00", "summary" : "Organophosphorus nerve agents irreversibly inhibit acetylcholinesterase, causing a toxic buildup of acetylcholine at muscarinic and nicotinic receptors. Current medical countermeasures to nerve agent intoxication increase survival if administered within a short period of time following exposure but may not fully prevent neurological damage. Therefore, there is a need to discover drug treatments that are effective when administered after the onset of seizures and secondary responses that lead to brain injury. Methods To determine potential therapeutic targets for such treatments, we analyzed gene expression changes in the rat piriform cortex following sarin (O-isopropyl methylphosphonofluoridate) exposure. Male Sprague-Dawley rats were challenged with 1.0 x LD50 sarin and subsequently treated with atropine sulfate, 2-pyridine aldoxime methylchloride (2-PAM), and the anticonvulsant diazepam. Control animals received an equivalent volume of vehicle and drug treatments. The piriform cortex, a brain region particularly sensitive to neural damage from sarin-induced seizures, was extracted at 0.25, 1, 3, 6, and 24 h after seizure onset, and total RNA was processed for microarray analysis. Principal component analysis identified sarin-induced seizure occurrence and time point following seizure onset as major sources of variability within the dataset. Based on these variables, the dataset was filtered and analysis of variance was used to determine genes significantly changed in seizing animals at each time point. The calculated p-value and geometric fold change for each probeset identifier were subsequently used for gene ontology analysis to identify canonical pathways, biological functions, and networks of genes significantly affected by sarin-induced seizure over the 24-h time course. Results A multitude of biological functions and pathways were identified as being significantly altered following sarin-induced seizure. Inflammatory response and signaling pathways associated with inflammation were among the most significantly altered across the five time points examined. Conclusions This analysis of gene expression changes in the rat brain following sarin-induced seizure and the molecular pathways involved in sarin-induced neurodegeneration will allow a better identification of potential therapeutic targets for the development of effective neuroprotectants to treat nerve agent exposure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28441" }, "primaryId" : "GEO:GSE28441", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28441" } ] }, "title" : "Transcriptional profiling of fetal hypothalamic TRH neurons", "dateAssigned" : "2011-04-07T00:00:00.000-05:00", "summary" : "To our knowledge, this is the first report identifying transcripts with a potentially important role during the development of a specific hypothalamic neuronal phenotype. This genome-scale study forms a rational foundation for identifying genes that might participate in the development and function of hypothalamic TRH neurons.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21569245" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28471" }, "primaryId" : "GEO:GSE28471", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28471" } ] }, "title" : "miR-29c Targets Tropomyosin-1a and Is Down-regulated in Rat Remnant Kidneys and IgA Nephropathy Patients with Interstitial Fibrosis", "dateAssigned" : "2011-04-08T00:00:00.000-05:00", "summary" : "MicroRNAs (miRNAs) are small regulatory RNA molecules that modulate the activity of specific mRNA targets and play important roles in a wide range of physiologic and pathologic processes. We hypothesized that miRNAs might be involved in the progression of CKD. In our previous studies we found chronic renal damages developed progressively in rats with 5/6 nephrectomy. L-mimosine(L-Mim) intervention from wk 5 to wk 12 improved renal function and resulted in additional accumulation of HIF-1 a and -2 a at wk 12. In the current study we found miR-29c was up-regulated in the L-Mim treated group compared with the control using Agilent miRNA microarrays. Of the microRNAs and proteins that exhibited reciprocal changes in expression following the L-Mim treatment, miR-29c and tropomyosin 1a (TPM1), which is involved in stress fiber function, met the sequence criteria for microRNA-target interaction, were later confirmed by 3'-untranslated region reporter analysis. TGFß1 treatment (3 ng/ml, 24 hours) decreased miR-29c expression and up-regulated protein expression of TPM1 in human renal epithelial cells. Overexpression of miR-29c significantly attenuated TGF-ß1 induced increase in TPM1 in vitro. Moreover, intrarenal expression of miR-29c was decreased in IgAN patients with moderate to severe tubulointerstital fibrosis (TIF), compared with IgAN patients without TIF, and intrarenal protein expression of TMP1 was significantly increased in IgAN patients with TIF. The results suggest that intrarenal expression of miR-29c was down-regulated while its predicted target, TPM1 was up-regulated in the progression of CKD. Short term stabilizing of HIF up-regulates miR-29c and attenuates CKD in the remnant kidney model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23467423" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28474" }, "primaryId" : "GEO:GSE28474", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28474" } ] }, "title" : "Comparison between syngeneic kidney transplant and a model of allogeneic kidney transplant tolerance induced by anti-classII regimen in the rat", "dateAssigned" : "2011-04-08T00:00:00.000-05:00", "summary" : "The goal is to identify new molecules implicated in tolerance, to determine the implication of these molecules in immune responses to transplantation by gene expression comparison of 27,088 individual rat genes between tolerated kidney allotransplant and syngeneic kidney transplant.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22262763" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28482" }, "primaryId" : "GEO:GSE28482", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28482" } ] }, "title" : "Effects of 20 months Dietary Methionine Restriction on Hepatic Gene Expression in Fischer 344 Rats", "dateAssigned" : "2011-04-08T00:00:00.000-05:00", "summary" : "Dietary methionine restriction (MR) has been shown to increase lifespan and decrease adiposity in rodents. This study was designed to examine the transcriptional effects of MR in metabolically relevant tissues. This experiment contains data from the liver.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28545" }, "primaryId" : "GEO:GSE28545", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28545" } ] }, "title" : "Comparison between blood myeloid-derived suppressor cells (MDSCs) extracted from syngeneic kidney transplanted recipient and tolerant kidney allografted recipient induced by anti-CD28 antibody", "dateAssigned" : "2011-04-12T00:00:00.000-05:00", "summary" : "The goal is to identify molecules involved in the accumulation of blood MDSCs in tolerant kidney allografted recipients when compared to syngeneic grafted recipients.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22450806" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28599" }, "primaryId" : "GEO:GSE28599", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28599" } ] }, "title" : "Effects of 20 months Dietary Methionine Restriction on Gene Expression in inguinal white adipose tissue of Fischer 344 Rats", "dateAssigned" : "2011-04-13T00:00:00.000-05:00", "summary" : "Dietary methionine restriction (MR) has been shown to increase lifespan and decrease adiposity in rodents. This study was designed to examine the transcriptional effects of MR in metabolically relevant tissues. This experiment contains data from the inguinal white adipose tissue (IWAT).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23801581" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28717" }, "primaryId" : "GEO:GSE28717", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28717" } ] }, "title" : "Gene expression profiles of rat tissues surrounding Vcap xenograft tumors with chemical or physical denervation.", "dateAssigned" : "2011-04-19T00:00:00.000-05:00", "summary" : "We propose that nerves play a trophic function for epithelium, not only during development, but also in adult homeostasis. Hence, nerves are likely key in cancer progression. Furthermore nerves are a functional regulator of prostate cancer genesis and progression to malignancy. A further understanding of the role of nerves in prostate cancer progression and a dissection of specific mechanisms would aid in identifying potential therapeutic targets that are centered on cancer-nerve interactions. To address this in detail, we have examined the effects of nerve function in the VCaP prostate cancer xenograft model and have elucidated differential gene expression profiles in this model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29131367" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28723" }, "primaryId" : "GEO:GSE28723", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28723" } ] }, "title" : "Effect of Nocturnal Hemodialysis (NHD) on Cardiomyocyte Gene Expression", "dateAssigned" : "2011-04-19T00:00:00.000-05:00", "summary" : "Frequent hemodialysis is associated with improvement in myocardial mechanics and cardiac gene expression profile", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22647434" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28782" }, "primaryId" : "GEO:GSE28782", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28782" } ] }, "title" : "Chromatin occupancy of TCF7L2 in hepatocytes", "dateAssigned" : "2011-04-21T00:00:00.000-05:00", "summary" : "TCF7L2 is one of the strongest type 2 diabetes (T2DM) candidate genes to emerge from GWAS studies, but the mechanisms by which it regulates the pathways which are important in the pathogenesis of type 2 diabetes are unknown. Previous in vitro and in vivo studies have focused on the link between TCF7L2 and insulin secretion as an explanation for the association between TCF7L2 and T2DM. However, TCF7L2 and the Wnt/ß-catenin pathway are important for metabolic zonation in the liver. This raises the interesting possibility that TCF7L2 may influence glucose homeostasis by regulating hepatic glucose production (HGP). To examine this question, we utilized the H4IIE cell as a model of HGP. Inhibition of HGP in H4IIE cells from lactate and pyruvate was highly sensitive to physiological concentrations of insulin and metformin. Silencing of TCF7L2 protein expression induced a 5-fold increase in basal HGP (P<0.0001), and this was accompanied by marked increase in the expression of several key gluconeogenic genes. FBPase, PEPCK and G6Pase mRNA were up-regulated 2.5-fold (P<0.0001), 1.4-fold (P<0.01) and 2.3-fold (P<0.0001), respectively, compared to scramble siRNA. Compared to their respective baseline values, insulin and metformin suppressed HGP equally in the scramble and TCF7L2 siRNA cells, but HGP remained elevated in TCF7L2 silenced cells due to the increased baseline HGP. Using chromatin immunoprecipitation sequencing (ChIP-Seq), we investigated the direct transcriptional targets of TCF7L2 in hepatocytes. A total of 2119 ChIP peaks were detected, of which 36% were located inside gene boundaries and, overall, a total of 65% of all binding events were within 50 Kb of a gene. De novo motif analysis revealed remarkable conservation of the long and short TCF7L2 consensus binding sites in the rat hepatocytes. Pathway analysis showed that the top two disease categories over-represented in our dataset were “non-insulin dependent diabetes” (155 genes; P = 1.63 x 10-10) and “diabetes mellitus” (245 genes; P = 7.4 x 10-12). Inspection of genes in these categories revealed that TCF7L2 directly binds to multiple genes important in the regulation of glucose metabolism in the liver, including PEPCK, FBP1, IRS1, IRS2, AKT2 ADIPOR1, PDK4 and CPT1A. Our findings suggest a novel mechanism for the regulation of HGP by TCF7L2, and provide a possible explanation for the association of TCF7L2 polymorphisms with the incidence of T2DM. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21901280" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28804" }, "primaryId" : "GEO:GSE28804", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28804" } ] }, "title" : "Synergism of Iraqi Sand/Cigarette Smoke Co-Exposure in Rats", "dateAssigned" : "2011-04-22T00:00:00.000-05:00", "summary" : "Synergism of Iraqi Sand/Cigarette Smoke Co-Exposure in Rats. 24 samples are used.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28831" }, "primaryId" : "GEO:GSE28831", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28831" } ] }, "title" : "Changes in gene expression in the retina of diabetic Long Evans rats after one, four, and twelve weeks of diabetes", "dateAssigned" : "2011-04-25T00:00:00.000-05:00", "summary" : "Purpose. Patients with diabetic retinopathy may experience severe vision loss due to macular edema and neovascularization secondary to vascular abnormalities. However, before these abnormalities become apparent, there are functional deficits in contrast sensitivity, color perception, and dark adaptation. The goals of this study are to evaluate early changes (up to 3 months) in retinal gene expression, selected visual cycle proteins, and optokinetic tracking (OKT) in streptozotocin (STZ)-induced diabetic rats.Methods. Retinal gene expression in diabetic Long Evans rats was measured by whole genome microarray 7 days, 4 weeks, and three months after onset of hyperglycemia. Select gene and protein changes were probed by PCR and immunohistochemistry respectively, and OKT thresholds were measured using a virtual optokinetics system. Results. Microarray analysis showed that the most consistently affected molecular and cellular functions were cell-to-cell signaling and interaction, cell death, cellular growth and proliferation, molecular transport, and cellular movement. Further analysis revealed reduced expression of several genes encoding visual cycle proteins including lecithin:retinol acyltransferase (LRAT), retinal pigment epithelium (RPE)-specific protein 65kDa (RPE65) and RPE retinal G protein coupled receptor (RGR). Immunohistochemistry revealed a decrease in RPE65 in the RPE layer of diabetic rats. These molecular changes occurred simultaneously with a decrease in OKT thresholds by 4 weeks of diabetes. Conclusions. The data presented here are further evidence that inner retinal cells are affected by hyperglycemia prior to vasculopathy suggesting that glial and neuronal dysfunction may underlie some of the early visual deficits in diabetics.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21862641" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28886" }, "primaryId" : "GEO:GSE28886", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28886" } ] }, "title" : "Modulation of gene expression by complement protein C1q in amyloid-beta injured neurons", "dateAssigned" : "2011-04-27T00:00:00.000-05:00", "summary" : "Complement protein C1q is induced after injury in the brain and during Alzheimer's disease and has been shown to protect against amyloid-beta induced neuronal death. In this study, we used microarray approach to identify the pathways modulated by C1q that are associated with neuroprotection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23150673" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28958" }, "primaryId" : "GEO:GSE28958", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28958" } ] }, "title" : "Expression data from monoiodoacetate-induced arthritis in a rat model", "dateAssigned" : "2011-04-29T00:00:00.000-05:00", "summary" : "We used microarrays to determine temporal regulation of genes during the progression of monoiodoacetate-induced arthritis in the knees of rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28997" }, "primaryId" : "GEO:GSE28997", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE28997" } ] }, "title" : "Function-based discovery of significant transcriptional temporal patterns in insulin-stimulated muscle cells", "dateAssigned" : "2011-05-01T00:00:00.000-05:00", "summary" : "Conclusion: In response to insulin, 326 genes were selected as differentially expressed in response to in vitro insulin treatment in skeletal muscle myotubes. Approximately 20% of the genes that were differentially expressed were identified as belonging to the insulin signaling pathway. 12 different clusters of gene expression profiles are identified which shows patterns that includes a slow and gradual decrease in gene expression, a gradual increase in gene expression reaching a peak at about 5 hours and then reaching a plateau or an initial decrease and other different variable patterns of increase in gene expression over time. As far as we know, this is the first systematic study in the literature monitoring transcriptional response to insulin in endothelial cells, in a time series microarray experiment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22396763" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29004" }, "primaryId" : "GEO:GSE29004", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29004" } ] }, "title" : "Gene expression response to acrylamide in rat pups", "dateAssigned" : "2011-05-02T00:00:00.000-05:00", "summary" : "Acrylamide is a type-2 alkene monomer with established human neurotoxic effects. While the primary source of human exposure to acrylamide is occupational, other exposure sources include food, drinking water, and smoking. In this study, neurobehavioral assays coupled with transcriptional profiling analysis were conducted to assess both behavioral and gene expression effects induced by acrylamide neurotoxicity in rats when administered during early postnatal life. Acrylamide administration in rat pups induced significant characteristic neurotoxic symptoms including increased heel splay, decrease in grip strength, and decrease in locomotor activity. Transcriptome analysis with the Affymetrix Rat Genome 230 2.0 array indicated that acrylamide treatment caused a significant alteration in the expression of genes involved in muscle contraction, pain regulation, and dopaminergic neuronal pathways. First, in agreement with the observed behavioral effects, expression of the Mylpf gene involved in muscle contraction was downregulated in the spinal cord in response to acrylamide. Second, in sciatic nerves, acrylamide repressed the expression of the opioid receptor gene Oprk1 that is known to play a role in neuropathic pain regulation. Finally, in the cerebellum, acrylamide treatment caused a decrease in the expression of the nuclear receptor gene Nr4a2 that is required for development of dopaminergic neurons. Thus, our work examining the effect of acrylamide at the whole-genome level on a developmental mammalian model has identified novel genes previously not implicated in acrylamide neurotoxicity that can be further developed into biomarkers for assessing the risk of acrylamide exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22197712" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29095" }, "primaryId" : "GEO:GSE29095", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29095" } ] }, "title" : "Transcriptional Profiles Induced by the Aryl Hydrocarbon Receptor Agonists 2,3,7,8-Tetrachlorodibenzo-p-dioxin, 2,3,7,8-Tetrachlorodibenzofuran and 2,3,4,7,8-Pentachlorodibenzofuran in Primary Rat Hepatocytes", "dateAssigned" : "2011-05-05T00:00:00.000-05:00", "summary" : "Transcriptional profiling of primary rat hepatocytes exposed to high and low doses of three compounds, as well as untreated cells. All samples were co-hybridized with DMSO controls.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21724226" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29110" }, "primaryId" : "GEO:GSE29110", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29110" } ] }, "title" : "Fibrogenic and redox-related but not proinflammatory genes are upregulated in lewis rat model of chronic silicosis", "dateAssigned" : "2011-05-06T00:00:00.000-05:00", "summary" : "Silicosis, a fibrotic granulomatous lung disease, may occur through accidental high-dose or occupational inhalation of silica, leading to acute/accelerated and chronic silicosis, respectively. While chronic silicosis has a long asymptomatic latency, lung inflammation and apoptosis are hallmarks of acute silicosis. In animal models, histiocytic granulomas develop within days after high-dose intratracheal silica instillation. However, following chronic inhalation of occupationally relevant doses of silica, discrete granulomas resembling human silicosis arise months after the final exposure without significant lung inflammation/apoptosis. To identify molecular events associated with chronic silicosis, lung RNAs from controls or chronically silica-exposed rats were analyzed by Affymetrix at 28 wk after silica exposures. Results suggested a significant upregulation of 144 genes and downregulation of seven genes. The upregulated genes included complement cascade, chemokines/chemokine receptors, G-protein signaling components, metalloproteases, and genes associated with oxidative stress. To examine the kinetics of gene expression relevant to silicosis, qPCR, ELISA, Luminex-bead assays, Western blotting, and/or zymography were performed on lung tissues from 4 d, 28 wk, and intermediate times after chronic silica exposure and compared with 14 d acute silicosis samples. Results indicated that genes regulating fibrosis (secreted phosphoprotein-1, CCL2, and CCL7), redox enzymes (superoxide dismutase-2 and arginase-1), and the enzymatic activities of matrix metalloproteinases 2 and 9 were upregulated in acute and chronic silicosis; however, proinflammatory cytokines were strongly upregulated only in acute silicosis. Thus, inflammatory cytokines are associated with acute but not chronic silicosis; however, genes regulating fibrosis, oxidative stress, and metalloproteases may contribute to both acute and chronic silicosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21830856" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29114" }, "primaryId" : "GEO:GSE29114", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29114" } ] }, "title" : "MAPC culture condition supports the derivation of cells with nascent hypoblast features from bone marrow and blastocysts", "dateAssigned" : "2011-05-06T00:00:00.000-05:00", "summary" : "Rat Extraembryonic Endoderm Precursor (XEN-P) cells resemble the nascent hypoblast of the blastocyst. Here we show that rat Multipotent Adult Progenitor Cell (rMAPC) lines derived from bone marrow (BM) exhibit salient nascent hypoblast characteristics. We could not identify cells with hypoblast features in rat BM, but they appeared after prolonged in vitro culture under rMAPC conditions. However, rMAPC culture conditions supported the very rapid isolation of new lines with nascent hypoblast features from rat blastocysts that were more homogenous than XEN-P cells isolated on feeders. The gene expression profile, growth factor requirement, Oct4 promoter methylation, and in vitro/vivo differentiation potential of cells isolated using rMAPC culture conditions from BM or blastocysts or XEN-P cells were highly similar. We conclude that the three cell populations have characteristics of hypoblast stem cells (HypoSC) and that rMAPC culture conditions support the isolation of XEN-P/HypoSC from the blastocyst and induction of HypoSC from BM.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29170" }, "primaryId" : "GEO:GSE29170", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29170" } ] }, "title" : "Androgen regulation of genes in rat forebrain, prostate, ovary, and skin", "dateAssigned" : "2011-05-10T00:00:00.000-05:00", "summary" : "The goal of this study was to identify androgen regulated genes in the forebrain, prostate, ovary, and skin. The results of this study will be used to make comparisons between androgen regulation of gene expression in different androgen-receptor expressing tissues, and will contribute to our understanding of tissue-selective androgen activity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29247" }, "primaryId" : "GEO:GSE29247", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29247" } ] }, "title" : "Expression data from junctional zone of placenta in Brown Norway and Holtzman-Sprague Dawley rat strains at gestation day 18.5", "dateAssigned" : "2011-05-12T00:00:00.000-05:00", "summary" : "Placentation differs in the BN rat strain when compared to HSD and DSS rat strains. Intrauterine trophoblast invasion is shallow and the junctional zone is underdeveloped in the BN rat. These structural differences are striking but their quantification is not conducive to high throughput analyses. In the rat, the junctional zone can be readily dissected and is more homogenous than other components of the placentation site. HSD and BN rat gestation day 18.5 junctional zone gene expression profiles were determined using DNA microarray analysis to identity placenta-associate quantitate traits.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21652768" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29255" }, "primaryId" : "GEO:GSE29255", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29255" } ] }, "title" : "Transcriptional profiling from young, old, healthy, or injured rat iliac arteries.", "dateAssigned" : "2011-05-12T00:00:00.000-05:00", "summary" : "Transcriptional profiling from young, old, healthy, or injured rat iliac arteries.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22003410" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29287" }, "primaryId" : "GEO:GSE29287", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29287" } ] }, "title" : "MicroRNA profiling in subventricular zone after stroke: miR-124a regulates proliferation of neural progenitor cells through Notch signaling pathway", "dateAssigned" : "2011-05-13T00:00:00.000-05:00", "summary" : "Expression data of miRNAs from adult neural progenitor cells in subventricular zone after stroke.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29296" }, "primaryId" : "GEO:GSE29296", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29296" } ] }, "title" : "Multiple oxygen tension environments reveal diverse patterns of transcriptional regulation in primary astrocytes", "dateAssigned" : "2011-05-14T00:00:00.000-05:00", "summary" : "The central nervous system normally functions at O2 levels which would be regarded as hypoxic by most other tissues. However, most in vitro studies of neurons and astrocytes are conducted under hyperoxic conditions without consideration of O2-dependent cellular adaptation. We analyzed the reactivity of astrocytes to 1, 4 and 9% O2 tensions compared to the cell culture standard of 20% O2, to investigate their ability to sense and translate this O2 information to transcriptional activity. Variance of ambient O2 tension for rat astrocytes resulted in profound changes in ribosomal activity, cytoskeletal and energy-regulatory mechanisms and cytokine-related signaling. Clustering of transcriptional regulation patterns revealed four distinct response pattern groups that directionally pivoted around the 4% O2 tension, or demonstrated coherent ascending/decreasing gene expression patterns in response to diverse oxygen tensions. Immune response and cell cycle/cancer-related signaling pathway transcriptomic subsets were significantly activated with increasing hypoxia, whilst hemostatic and cardiovascular signaling mechanisms were attenuated with increasing hypoxia. Our data indicate that variant O2 tensions induce specific and physiologically-focused transcript regulation patterns that may underpin important physiological mechanisms that connect higher neurological activity to astrocytic function and ambient oxygen environments. These strongly defined patterns demonstrate a strong bias for physiological transcript programs to pivot around the 4% O2 tension, while uni-modal programs that do not, appear more related to pathological actions. The functional interaction of these transcriptional ‘programs’ may serve to regulate the dynamic vascular responsivity of the central nervous system during periods of stress or heightened activity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21738745" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29299" }, "primaryId" : "GEO:GSE29299", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29299" } ] }, "title" : "Differential gene expression of adult rat retinas exposed to light.", "dateAssigned" : "2011-05-14T00:00:00.000-05:00", "summary" : "We performed a microarray screening of adult rat retinas to identify genes that could show and up- or down-regulation due to exposure to light.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22039463" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29341" }, "primaryId" : "GEO:GSE29341", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29341" } ] }, "title" : "Gene expression profile changes upon knock-down of Pax8", "dateAssigned" : "2011-05-17T00:00:00.000-05:00", "summary" : "The results obtained suggest that Pax8 regulates numerous pathways, some of which involved in the regulation of cell cycle, thyroid cancer and apoptosis, thus confirming that Pax8 is a master regulatory gene.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21966443" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29412" }, "primaryId" : "GEO:GSE29412", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29412" } ] }, "title" : "To examine the influence of the early stress of maternal separation on the hippocampal transcriptome in young adulthood", "dateAssigned" : "2011-05-20T00:00:00.000-05:00", "summary" : "In this study, we examined the consequences of the early stress (ES) of maternal separation on hippocampal gene expression in young adulthood. Young adult (2 months old) ES animals exhibit hippocampal transcriptome changes with a significant regulation of genes associated with intracellular signaling, MAP kinase signaling, plasma membrane function, neurotransmitter and neuropeptide receptors and cytoskeletal components.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24025219" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29414" }, "primaryId" : "GEO:GSE29414", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29414" } ] }, "title" : "To examine the influence of the early stress of maternal separation on the hippocampal transcriptome in middle-aged life", "dateAssigned" : "2011-05-20T00:00:00.000-05:00", "summary" : "In this study, we examined the consequences of the early stress (ES) of maternal separation on hippocampal gene expression in middle-aged animals. Middle-aged (15 months old) ES animals exhibit hippocampal transcriptome changes with a significant regulation of genes associated with ion binding, transcriptional regulation, cellular projection, cellular stress responsive pathways, neuronal development and chromatin remodeling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24025219" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29445" }, "primaryId" : "GEO:GSE29445", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29445" } ] }, "title" : "Effect of telmisartan on prostate carcinogenesis in TRAP rats", "dateAssigned" : "2011-05-23T00:00:00.000-05:00", "summary" : "We investigate the direct effects of ARBs on prostate cancer growth and progression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22430461" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29457" }, "primaryId" : "GEO:GSE29457", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29457" } ] }, "title" : "Characterization of neuroendocrine tumors in heterozygous mutant MENX rats: a novel model of invasive medullary thyroid carcinoma [pituitary]", "dateAssigned" : "2011-05-23T00:00:00.000-05:00", "summary" : "As overwhelming evidence coming from transgenic mouse models but also from MEN4 patients seem to suggest that loss or inactivation of a single p27 allele plays an important role in neuroendocrine tumorigenesis, we decided to perform a detailed analysis of the phenotype of rats heterozygous for the MENX-associated germline Cdkn1b mutation. We here show that the reduction to a single functional p27 allele predisposes MENX heterozygous rats to the development of neuroendocrine malignancies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29142006" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29488" }, "primaryId" : "GEO:GSE29488", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29488" } ] }, "title" : "Patterns of gene Expression during the Spinal cord Injury/Regeneration", "dateAssigned" : "2011-05-23T00:00:00.000-05:00", "summary" : "In order to assess changes in gene expression involved in the regeneration process,microarrays were performed as a function of time after SCI for the various treatments.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29511" }, "primaryId" : "GEO:GSE29511", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29511" } ] }, "title" : "Induction of the neuronal major histocompatibility complex class I and paired immunoglobulin-like receptor B pathway in the hippocampus with aging and cognitive decline", "dateAssigned" : "2011-05-24T00:00:00.000-05:00", "summary" : "The aim of this study was to identify alterations in hippocampal synaptic mRNA expression with aging and cognitive decline. Transcriptional profiling and subsequent bioinformatic analysis was performed to identify the most highly regulated pathways of genes. Interestingly, the antigen processing and presentation pathway was identified as the most highly regulated pathway with aging.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29512" }, "primaryId" : "GEO:GSE29512", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29512" } ] }, "title" : "Circulating insulin-like growth factor (IGF)-1 Regulates Hippocampal IGF-1 Levels and Brain Gene Expression During Adolescence", "dateAssigned" : "2011-05-24T00:00:00.000-05:00", "summary" : "This study, using a growth hormone (GH)-deficient dwarf animal model and peripheral GH replacement, investigated the effects of circulating IGF-1 during adolescence on IGF-1 levels in the brain. Our results demonstrated that hippocampal IGF-1 protein concentrations during adolescence are highly regulated by circulating IGF-1, which were reduced by GH deficiency and restored by systematic GH replacement. In contrast, IGF-1 levels in the CSF were decreased by GH deficiency but not restored by GH replacement. Furthermore, analysis of gene expression using microarrays and RT-PCR indicated that circulating IGF-1 levels did not modify the transcription of IGF-1 or its receptor in the hippocampus but did regulate genes that are involved in microvascular structure and function, brain development, and synaptic plasticity, which potentially support brain structures involved in cognitive function during this important developmental period.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21750148" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29552" }, "primaryId" : "GEO:GSE29552", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29552" } ] }, "title" : "Developmental underpinnings of differences in rodent novelty-seeking and emotional reactivity", "dateAssigned" : "2011-05-26T00:00:00.000-05:00", "summary" : "Innate differences in human temperament strongly influence how individuals cope with stress and predispose for specific types of psychopathology. The present study examines the developing brain in an animal model of temperamental differences to understand how altered neurodevelopment may engender differences in emotional reactivity that are stable throughout the animal’s life. We utilize selectively-bred High Responder (bHR) and Low Responder (bLR) rats that exhibit dramatic emotional behavior differences, with bHRs exhibiting exaggerated novelty-exploration, aggression, impulsivity and drug self-administration, and bLRs showing marked behavioral inhibition, exaggerated anxiety- and depressive-like behavior. Using Affymetrix microarrays, we assessed bLR/bHR gene expression in the developing brain on postnatal days (P)7, 14, and 21, focusing on the hippocampus and nucleus accumbens, two regions related to emotionality and known to differ in adult bLR/bHR rats. We found dramatic bLR/bHR gene expression differences in the P7 and P14 hippocampus, with minimal differences in the nucleus accumbens. Some of the most profound differences involved genes critical for neurodevelopment and synaptogenesis. Stereological studies evaluated hippocampal structure in developing bHR/bLR pups, revealing enhanced hippocampal volume and cell proliferation in bLR animals. Finally, behavioral studies showed that the bHR/bLR behavioral phenotypes emerge very early in life, with exploratory differences apparent at P16 and anxiety differences present by P25. Together these data point to specific brain regions and critical periods when the bHR/bLR phenotypes begin to diverge, which may eventually allow us to test possible therapeutic interventions to normalize extreme phenotypes (e.g. the anxiety-prone nature of bLRs or drug addiction proclivity of bHRs).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21864320" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29574" }, "primaryId" : "GEO:GSE29574", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29574" } ] }, "title" : "Gene Expression Changes Associated with Respiratory Muscle Hypertrophy after Intermittent Transient Tracheal Occlusions", "dateAssigned" : "2011-05-26T00:00:00.000-05:00", "summary" : "The effect of intermittent transient tracheal occlusion (ITTO) on gene expression was compared in the diaphragm and parasternal intercostals. We hypothesized that genes responsible for protein metabolism, myogenic activation, neuromuscular transmission, and inflammatory modulation would be altered in animals exposed to this rodent model of respiratory load compensation rehabilitation. Eight adult male Sprague-Dawley rats underwent placement of a tracheal occluder cuff and were divided into ITTO (n=4) or SHAM (n=4) treatment groups. Animals received 10 days of their assigned treatments. The day following the last treatment session, the animals were euthanized and the diaphragm and parasternals extracted. Messenger RNA was profiled with microarray analysis (Amadid: 028279, Agilent Technologies, Palo Alto, CA). Results were further analyzed with immunofluorescent examination of cross-sectional area and with quantitative reverse transcriptase polymerase chain reaction on a subset of genes exhibiting differential expression. The cross-sectional area of type IIx/b fibers was larger in the muscles of ITTO-trained animals. Microarray analysis identified 650 genes in the diaphragm and 1,181 genes in the intercostals that were differentially expressed between the groups (p<.01). In both muscles, biological processes for cell adhesion and chemical stimulus for the detection of olfaction biological processes were over-expressed. Additionally, we found significant differential expression of the g-protein signaling pathway and protein-amino acid phosphorylation in the intercostals. The results provide insight into neuromuscular plasticity associated with respiratory load compensation rehabilitation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29666" }, "primaryId" : "GEO:GSE29666", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29666" } ] }, "title" : "Expression analysis of rat testis at early development stage", "dateAssigned" : "2011-06-01T00:00:00.000-05:00", "summary" : "Investigation of whole genome gene expression level changes in rat testes on the postnatal day 6, 8 and 10 to compare the differentially expressed genes between them.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29673" }, "primaryId" : "GEO:GSE29673", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29673" } ] }, "title" : "Toxicogenomic Study of Pentamethylchromanol (PMCol)", "dateAssigned" : "2011-06-01T00:00:00.000-05:00", "summary" : "The study demonstrated that chronic exposure to high doses of PMCol induces liver damage and dysfunction, probably due to both inhibition of synthesis and depletion of liver glutathione as well as modification of other drug metabolism pathways.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21920950" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29677" }, "primaryId" : "GEO:GSE29677", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29677" } ] }, "title" : "Effect of prenatal exposure to nicotine on kidney structure and gene expression in rats", "dateAssigned" : "2011-06-01T00:00:00.000-05:00", "summary" : "Here, we investigated whether prenatal exposure to nicotine alters kidney glomerular mass and genome-wide gene expression profiles in two genetically distant strains of rats, namely spontaneously hypertensive rats (SHR) and Brown Norway (BN) rats. Nicotine or saline were administered to BN and SHR dams via osmotic pumps throughout gestation. Kidneys from 9-week-old male offspring were studied.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29733" }, "primaryId" : "GEO:GSE29733", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29733" } ] }, "title" : "Comparison of the global gene expression of choroid plexus and meninges and associated vasculature under control conditions and after pronounced hyperthermia or amphetamine toxicity", "dateAssigned" : "2011-06-03T00:00:00.000-05:00", "summary" : "These tissue were harvested to complement and extend the studies that generated GSE23093. They served 3 purposes; 1) identify genes important to choroid plexus function and compare them with those important for meninges and associated vasculature (MAV) function, 2) determine genes in the choroid plexus and sensitivity hyperthermia and amphetamine toxicity, 3) identify the important gene expression changes related to the immune system in MAV, choroid plexus and trunk' blood", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29859" }, "primaryId" : "GEO:GSE29859", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29859" } ] }, "title" : "Expression data from hypervitaminosis A rat diaphyseal bone", "dateAssigned" : "2011-06-09T00:00:00.000-05:00", "summary" : "Vitamin A is the only known compound that produces spontaneous fractures in rats. In an effort to resolve the molecular mechanism behind this effect, we fed young rats high doses of vitamin A and performed a global transcriptional analysis of diaphyseal bone after one week, i.e. just before the first fractures appeared. Microarray gene expression analysis revealed that 68 transcripts were differentially expressed in hypervitaminotic cortical bone and 118 transcripts were found when the bone marrow was also included. 98% of the differentially expressed genes in the bone marrow sample were up-regulated. In contrast, hypervitaminotic cortical bone without marrow showed reduced expression of 37% of differentially expressed genes. Gene Ontology (GO) analysis revealed that only samples containing bone marrow were associated to a GO term, which principally represented extracellular matrix (ECM). This is consistent with the histological findings of increased endosteal bone formation. Four of the genes in this ECM cluster and four other genes, including Cyp26b1 which is known to be up-regulated by vitamin A, were selected and verified by real-time PCR. In addition, immunohistochemical staining of bone sections confirmed that the bone-specific molecule, osteoadherin (Omd) was up-regulated. Further analysis of the major gene expression changes revealed distinct differences between cortical bone and bone marrow, e.g. there appeared to be augmented Wnt signaling in the bone marrow but reduced Wnt signaling in cortical bone. Moreover, induced expression of hypoxia-associated genes was only found in samples containing bone marrow. Together, these results corroborate our previous observations of compartment-specific effects of vitamin A, with reduced periosteal but increased endosteal bone formation, and suggest important roles for Wnt signaling and hypoxia in the processes leading to spontaneous fractures.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22215263" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29885" }, "primaryId" : "GEO:GSE29885", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29885" } ] }, "title" : "Expression data from amoeboid and ramified microglia isolated from the corpus callosum of 5-day and 4-week old rat brain", "dateAssigned" : "2011-06-10T00:00:00.000-05:00", "summary" : "We used microarrays to identify the genes specific to amoeboid and ramified microglia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22697290" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29912" }, "primaryId" : "GEO:GSE29912", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29912" } ] }, "title" : "The effect of GW3965 and dexamethasone on gene expression of rat livers", "dateAssigned" : "2011-06-13T00:00:00.000-05:00", "summary" : "GLUCOCORTICOIDS are steroid hormones that strongly influence intermediary carbohydrate metabolism by increasing the transcription rate of glucose-6-phosphatase (G6Pase) a key enzyme of gluconeogenesis, and suppress the immune system which makes them one of the most important therapeutic agents in the treatment of allergic, autoimmune and inflammatory diseases. The biologic actions of circulating glucocorticoids are transmitted to the cells nucleus by the glucocorticoid receptor (GR). The nuclear liver X receptors (LXRs) bind to cholesterol metabolites, heterodimerize with the retinoid X receptor (RXR), and regulate the cholesterol turnover, the hepatic glucose metabolism by decreasing the expression of G6Pase, and repress a set of inflammatory genes in immune cells. The aim of this study is to evaluate the crosstalk between the GR- and LXR-mediated signaling systems. Transient transfection-based reporter assays and gene silencing methods using siRNAs for LXRs showed that overexpression/ligand (GW3965) activation of LXRs/RXRs repressed GR-stimulated transactivation of certain glucocorticoid response element (GRE)-driven promoters in a gene-specific fashion. Activation of LXRs by GW3965 attenuated dexamethasone-stimulated elevation of circulating glucose in rats and suppressed dexamethasone-induced mRNA expression of hepatic glucose-6-phosphatase (G6Pase) in rats, mice and human hepatoma HepG2 cells. In microarray transcriptomic analysis of rat liver, GW3965 differentially regulated glucocorticoid-induced transcriptional activity of about 15% of endogenous glucocorticoid-responsive genes. Mechanistically, and in vitro chromatin immunoprecipitation assay, we found that LXRa/RXRa bound GREs and inhibited GR binding to these DNA sequences in a gene-specific fashion. These novel results were further confirmed in in vivo binding assays, and in gel mobility shift assays, where recombinant LXRa/RXRa proteins were used to examine their interaction with classic or G6Pase GREs. We propose that administration of LXR agonists may be beneficial in glucocorticoid treatment- or stress-associated dysmetabolic states by directly attenuating the transcriptional activity of the GR on glucose and/or lipid metabolism.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22457708" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29963" }, "primaryId" : "GEO:GSE29963", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE29963" } ] }, "title" : "Expression data of pachytene spermatocytes and round spermatids from young and aged Brown Norway rats", "dateAssigned" : "2011-06-14T00:00:00.000-05:00", "summary" : "A full genome microarray was used to determine if distinct pathways of genes were altered in expression in germ cells (pachytene spermatocytes or round spermatids) with age.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21865553" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30081" }, "primaryId" : "GEO:GSE30081", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30081" } ] }, "title" : "Blueberry Diets during Early Development Only Is Sufficient to Prevent Senescence of Osteoblasts and Bone Loss in Adulthood", "dateAssigned" : "2011-06-19T00:00:00.000-05:00", "summary" : "Appropriate nutrition during early development is essential for optimal bone mass accretion; however, linkage between early nutrition, childhood bone mass and prevention of bone loss later in life has not been extensively studied. In this report, we have demonstrated several fundamental issues in the field. 1) A significant prevention of ovariectomy (OVX) -induced bone loss from adult rats can occur with only 14 days consumption of a blueberry-containing diet immediately prior to puberty. 2) The molecular mechanisms underlying these effects involve increased myosin production and preserved a shuttle for transcription factors such as Runx2 from cytoplasm to nucleolus which stimulates osteoblast differentiation and reduces mesenchymal stromal cell senescence. 3) The effects of blueberry diet on preserving fidelity of osteoblast differentiation also overcome reduced osteoblast differentiation and activity due to OVX-induced degradation of collagen matrix.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21912699" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30147" }, "primaryId" : "GEO:GSE30147", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30147" } ] }, "title" : "Expression data from rosiglitazone treated, rosiglitazone withdrawal and untreated control Zucker Diabetic Fatty rats.", "dateAssigned" : "2011-06-22T00:00:00.000-05:00", "summary" : "In this study we systematically investigated the gene expression profile and proliferative response of islets to insulin sensitization, insulin resistance, and islet failure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30165" }, "primaryId" : "GEO:GSE30165", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30165" } ] }, "title" : "Gene expression signatures following nerve injury in a rat model (0d-14d)", "dateAssigned" : "2011-06-22T00:00:00.000-05:00", "summary" : "We used microarrays to distinguish the gene expression differences among different time points after injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30178" }, "primaryId" : "GEO:GSE30178", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30178" } ] }, "title" : "Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (rat lungs)", "dateAssigned" : "2011-06-23T00:00:00.000-05:00", "summary" : "A proper understanding of the mechanisms underlying crystalline silica-induced pulmonary toxicity has implications in the management and potential prevention of the adverse health effects associated with silica exposure including silicosis, cancer and several auto-immune diseases. Human lung type II epithelial cells and rat lungs exposed to crystalline silica were employed as experimental models to determine global gene expression changes in order to understand the molecular mechanisms underlying silica-induced pulmonary toxicity. The differential gene expression profile induced by silica correlated with its toxicity in the A549 cells. The biological processes perturbed by silica exposure in the A549 cells and rat lungs, as identified by the bioinformatic analysis of the differentially expressed genes, demonstrated significant similarity. Functional categorization of the differentially expressed genes identified cancer, cellular movement, cellular growth and proliferation, cell death, inflammatory response, cell cycle, cellular development, and genetic disorder as top-ranking biological functions perturbed by silica exposure in the A549 cells and rat lungs. The involvement of oxidative stress and apoptosis in the silica-induced pulmonary toxicity was confirmed by ELISA and confocal microscopy analysis, respectively, of the silica-exposed A549 cells. Results of our study, in addition to confirming several previously identified molecular targets and mechanisms involved in silica toxicity, identified novel molecular targets and mechanisms potentially involved in silica-induced pulmonary toxicity. Further investigations, including those focused on the novel molecular targets and mechanisms identified in the current study, may result in a better management and, possibly, reduction and/or prevention of the potential adverse health effects associated with crystalline silica exposure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30198" }, "primaryId" : "GEO:GSE30198", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30198" } ] }, "title" : "Digital gene expression and global mapping of polyadenylation sites with PolyA-Seq", "dateAssigned" : "2011-06-24T00:00:00.000-05:00", "summary" : "We describe PolyA-Seq, a strand-specific method for high-throughput sequencing of the 3' ends of polyadenylated transcripts. PolyA-Seq is as accurate for digital gene expression as existing RNA sequencing approaches, and superior to microarrays. We used the approach to map polyadenylation (polyA) sites in 24 samples from normal tissues in human, rhesus, dog, mouse, and rat.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22454233" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30276" }, "primaryId" : "GEO:GSE30276", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30276" } ] }, "title" : "miRNA expression profiles from E18th rat embryonic striatal stem cells under conditioned environments", "dateAssigned" : "2011-06-28T00:00:00.000-05:00", "summary" : "To decipher the regulatory miRNAs involved in ESSC-derived neurogenesis, we have performed detailed miRNA profiling for ESSCs at passage 3 for groupD and group E derived ESSCs (based on their performance in vitro). Out data has explored cruicial mIRNAs involved in strital neurogenesis .", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30301" }, "primaryId" : "GEO:GSE30301", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30301" } ] }, "title" : "Skeletal Muscle Contraction Reduces Effects of Unloading on Bone Independently from the Central Nervous System: Studies Using Functional Electrical Stimulation after Spinal Cord Transection", "dateAssigned" : "2011-06-29T00:00:00.000-05:00", "summary" : "Spinal cord injury (SCI) causes severe bone loss and disrupts connections between higher centers in the central nervous system (CNS) and bone. Muscle contraction elicited by functional electrical stimulation (FES) partially protects against loss of bone but cellular and molecular events by which this occurs are unknown. Here, using a rat model, we characterized effects of 7 days of contraction-induced loading of tibia and fibula due to FES when begun 16 weeks after SCI. SCI reduced tibial and femoral BMD by 12-17% and promoted bone resorption, as indicated by increased serum CTX; SCI-related changes in CTX were reversed by FES. In cultures of bone marrow cell-derived cells, SCI increased the number of osteoclasts and mRNA levels of the several osteoclast differentiation markers; these changes were significantly reversed by FES. The number of osteoblasts was also reduced by SCI as was the ratio of OPG/RANKL mRNAs therein; the unfavorable change in OPG/RANKL ratio was partially reversed by FES. cDNA microarray analysis revealed that alterations in genes involved in signaling through Wnt, FSH/LH, PTH and calcineurin/NFAT pathways may be linked to the favorable action of FES on SCI-induced bone resorption. In particular, SCI increased levels of the Wnt inhibitors DKK1, sFRP2 and SOST in osteoblasts, These effects were completely or partially reversed by FES. Our results demonstrate an anti-bone resorptive activity of acute FES in bone loss after SCI and suggest potential underlying mechanisms, among them involving increased Wnt signaling to cause more favorable ratios of OPG and RANKL for the inhibition of osteoclastogenesis. The present study indicates that the effects of bone reloading on SCI- related bone remodeling occurred independently of the effects of higher CNS centers on bone.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23530032" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30308" }, "primaryId" : "GEO:GSE30308", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30308" } ] }, "title" : "Expression data from pregnant rat hearts", "dateAssigned" : "2011-06-29T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying hyperhomocysteinemia during pregnancy and identified distinct classes of differentially regulated genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26009634" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30322" }, "primaryId" : "GEO:GSE30322", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30322" } ] }, "title" : "Gene Expression Analyses of Subchondral Bone in Early Experimental Osteoarthritis by Microarray", "dateAssigned" : "2011-06-30T00:00:00.000-05:00", "summary" : "Osteoarthritis (OA) is a complex degenerative joint disease, which is not only a cartilage but also a bone disease. A better understanding of the early molecular mechanism changes of subchondral bone in vivo may contribute to elucidating the pathogenesis of OA. We used microarray technology to investigate the time-course molecular changes of subchondral bone just beneath damaged cartilage in early stage of experimental osteoarthritis, and found 2,234 differentially expressed (DE) genes at 1 week, 1,944 at 2 weeks and 1,517 at 4 weeks postsurgery.Further analysis of dysregulated genes indicated that subchondral bone remodeling occurred sequentially and in a time-dependent manner at the gene expression level. Some known dysregulated genes suspected roles in influencing bone development or bone remodeling, such as Alp, Igf1, Tgf ß1, Postn, Mmp3, Tnfsf11, Acp5, Bmp5, Aspn and Ihh, were confirmed by real-time PCR, and results indicated that our microarray data could accurately reflect gene expression patterns of early OA. Subsequently, to validate the results of our microarray analysis at protein level, immunohistochemistry staining was introduced to investigate the translational level of genes Mmp3 and Aspn in tissue sections, and results showed that the level of Mmp3 protein expression was totally matched the results of microarray and real-time PCR analysis. Nevertheless, the expression of Aspn protein was not observed differentially expressed at any time point.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22384228" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30365" }, "primaryId" : "GEO:GSE30365", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30365" } ] }, "title" : "Transcript Profiling of Arcuate Nucleus in Response to Electroacupuncture on Rats", "dateAssigned" : "2011-07-01T00:00:00.000-05:00", "summary" : "The electroacupuncture-induced analgesic effect has been used widely to alleviate diverse pains. However, significant individual variations in analgesic effect of EA for both experiments and clinics were reported. According to the sensitivity of the analgesic response to EA stimulation, the subjects could be categorized into high responders (HR) and non responders (NR). However, the molecular mechanism of individual variability in the analgesic response to acupuncture stimulation is still uncertain. This study aims to investigate the potential gene expression in arcuate nucleus induced by 2Hz/100Hz electroacupuncture in HR and NR rats. Rats were given 2Hz or 100Hz electroacupuncture for 30 min and using cDNA microarrays to compare different gene expression in arcuate nucleus.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22411682" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30469" }, "primaryId" : "GEO:GSE30469", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30469" } ] }, "title" : "comparison of mRNA expression among rat hepatoma cell lines with different metastatic ability", "dateAssigned" : "2011-07-07T00:00:00.000-05:00", "summary" : "To reduce cancer mortality, understanding of mechanisms of cancer metastasis is crucial. We have established 6 rat hepatocellular carcinoma (HCC) cell lines, which exhibit differing metastatic potential to the lung after inoculation into the tail veins of nude mice. Micorarray analysis of 4 kinds of HCC cells and rat normal liver tissue was performed to find a potent molecular target for prevention of cancer metastasis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22320152" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30526" }, "primaryId" : "GEO:GSE30526", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30526" } ] }, "title" : "COUP-TFII Controls Mouse Postnatal Pancreatic ß-Cell Mass through GLP-1 ß-Catenin", "dateAssigned" : "2011-07-08T00:00:00.000-05:00", "summary" : "Conclusions/significance: Our findings show that COUP-TFII is a novel component of the GLP-1 signaling cascade that increases b-cell number during the neonatal period. COUP-TFII is required for GLP-1 activation of the b-catenin-dependent pathwayand its expression is under the control of TCF7L2.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30532" }, "primaryId" : "GEO:GSE30532", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30532" } ] }, "title" : "Liver-protecting Effect of Maple Syrup", "dateAssigned" : "2011-07-08T00:00:00.000-05:00", "summary" : "Rats fed a 20%-maple syrup diet (maple syrup group) for 11 days showed significantly lower values of the hepatic function markers than those fed a 20%-sugar mix syrup diet (control) likewise. One reasons was suggested by DNA microarray analysis which revealed that the expression of genes for enzymes of ammonia production were down-regulated in the liver of maple syrup group.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30533" }, "primaryId" : "GEO:GSE30533", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30533" } ] }, "title" : "Influence of short-time feeding of rats with an iron-deficient diet on their hepatic gene expression profiles", "dateAssigned" : "2011-07-08T00:00:00.000-05:00", "summary" : "Iron deficiency-induced anemia is generally a representative nutritional problem in most populations. We reported that the anemia due to dietary iron deficiency causes a variety of changes in nutrient metabolism, even leading to apoptosis as a result of associated endoplasmic reticulum (ER) stress in the rat liver. On the other hand, it appears that non-anemic iron-deficiency causes no serious problem because no appreciable down-regulation of hemoglobin synthesis occurs. Biochemically, iron is essential for activation of cytochrome-related enzymes and its deficiency should yield some physiological problems. We performed a comprehensive transcriptome analysis to define the effects of non-anemic iron deficiency on hepatic gene expression. Four-week-old rats were fed a low-iron diet (ca. 3 ppm iron) for 2 days. These rats were compared with those fed a control diet (48 ppm iron) by pair feeding. On day 3, the rats were sacrificed under anesthesia, and their livers were dissected for DNA microarray analysis. Rats in the iron-deficient diet group, showed that their serum ferritin and iron levels decreased with an increase in the serum total iron binding capacity (TIBC) level, while the hemoglobin level was not changed. In the DNA microarray study, we identified 91 up-regulated and 186 down-regulated probe sets that characterized the iron-deficient diet group. In the up-regulated probe sets, genes involved in glucose and lipid metabolic processes were significantly enriched, whereas genes related to organic acid metabolic process, cellular ketone metabolic process, lipid metabolic process, oxidation reduction, response to drug, response to extracellular stimulus and gas transport were significantly enriched in the down-regulated probe sets. These results suggest that even the non-anemic iron-deficiency exerts various influences on nutrient metabolisms in the liver.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23755274" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30582" }, "primaryId" : "GEO:GSE30582", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30582" } ] }, "title" : "Real-time quantitative PCR analysis of rat embryonic stem cells (ESCs)", "dateAssigned" : "2011-07-12T00:00:00.000-05:00", "summary" : "Validation study of a focused microarray for evaluation of undifferentiated rat ESCs.Using a focused microarray, undifferentiated embryonic stem cells (ESCs) can be distinguished from differentiated ESCs and other cells derived from the early embryo since they have a unique gene expression pattern associated with pluripotency and lack of markers of differentiation. To date, however, such an array has not been developed for the rat species and differences in genomes of rat and human or rat and mouse preclude the use of ESC focused human or mouse microarrays for the rat. Here, we developed a focused microarray for screening rat ESCs and provide validation data that this array can distinguish undifferentiated rat ESCs from rat trophoblast stem cells (TS), rat extraembryonic endoderm cells (XEN), mouse embryonic fibroblast feeder cells (MEFs) and rat ESCs that have been differentiated in vitro. We used this tool to compare rat ESCs which have been expanded in a conventional rat ESC medium containing two inhibitors, e.g., GSK3 and MEK inhibitors, and leukemia inhibitory factor (LIF), and found expression of Cdx2, a gene associated with trophoblast determination. The rat ESC focused microarray described in this report has utility for rapid screening rat ESCs. This will enable optimization of culture conditions in the future.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30668" }, "primaryId" : "GEO:GSE30668", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30668" } ] }, "title" : "Life-long caloric restriction-associated remodeling of rat white adipose tissue", "dateAssigned" : "2011-07-14T00:00:00.000-05:00", "summary" : "This study explored the role of the growth hormone (GH) / insulin-like growth factor 1 (IGF-1) axis on the life-long caloric restriction (CR)-associated remodeling of white adipose tissue (WAT). Adipocyte size and gene expression profiles, using high-density oligonucleotide microarrays, were analyzed in WAT of six- to seven-month old wild Wistar rats fed ad libitum (AL) or subjected to a 30% caloric restriction (CR), and heterozygous transgenic dwarf rats bearing an anti-sense GH transgene fed ad libitum (Tg). While not significant in Tg rats, adipocyte size was significantly reduced in CR rats compared with AL rats. The microarray data based on the principal component analysis demonstrated that the gene expression profile of CR rats markedly differed from the AL rats, while Tg hardly differed, suggesting that CR-associated WAT remodeling was predominantly regulated in a GH/IGF-1-independent manner. The gene cluster with the largest change induced by CR included several genes involved in lipid biosynthesis and inflammation. Moreover, many of the genes transcriptionally regulated by sterol regulatory element binding proteins (SREBPs) were found in the cluster related to lipid biosynthesis. Real-time reverse transcription polymerase chain reaction analysis confirmed that the expression of SREBP-1 and its down-stream targets was particularly up-regulated in CR rats compared with SREBP-2 and its down-stream targets. Our findings suggest that SREBP-1 is a major transcription factor in CR-associated remodeling of WAT, and might be one of the key regulators of the anti-aging and pro-longevity effects of CR.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22645024" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30691" }, "primaryId" : "GEO:GSE30691", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30691" } ] }, "title" : "Multiple chronic pain states are associated with a common amino acid-changing allele in KCNS1", "dateAssigned" : "2011-07-14T00:00:00.000-05:00", "summary" : "Not all patients with nerve injury develop neuropathic pain. The extent of nerve damage and age at the time of injury are two of the few risk factors identified to date. In addition, preclinical studies show that neuropathic pain variance is heritable. To define such factors further, we performed a large-scale gene profiling experiment which plotted global expression changes in the rat dorsal root ganglion in three peripheral neuropathic pain models. This resulted in the discovery that the potassium channel alpha subunit KCNS1, involved in neuronal excitability, is constitutively expressed in sensory neurons and markedly downregulated following nerve injury. KCNS1 was then characterized by an unbiased network analysis as a putative pain gene, a result confirmed by single nucleotide polymorphism association studies in humans. A common amino acid changing allele, the 'valine risk allele', was significantly associated with higher pain scores in five of six independent patient cohorts assayed (total of 1359 subjects). Risk allele prevalence is high, with 18-22% of the population homozygous, and an additional 50% heterozygous. At lower levels of nerve damage (lumbar back pain with disc herniation) association with greater pain outcome in homozygote patients is P = 0.003, increasing to P = 0.0001 for higher levels of nerve injury (limb amputation). The combined P-value for pain association in all six cohorts tested is 1.14 E-08. The risk profile of this marker is additive: two copies confer the most, one intermediate and none the least risk. Relative degrees of enhanced risk vary between cohorts, but for patients with lumbar back pain, they range between 2- and 3-fold. Although work still remains to define the potential role of this protein in the pathogenic process, here we present the KCNS1 allele rs734784 as one of the first prognostic indicators of chronic pain risk. Screening for this allele could help define those individuals prone to a transition to persistent pain, and thus requiring therapeutic strategies or lifestyle changes that minimize nerve injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22171041" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30733" }, "primaryId" : "GEO:GSE30733", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30733" } ] }, "title" : "Transcriptomic analysis of the osmotic and reproductive remodelling of the female rat supraoptic nucleus", "dateAssigned" : "2011-07-18T00:00:00.000-05:00", "summary" : "The supraoptic nucleus (SON) of the hypothalamus is an important integrative brain structure that co-ordinates responses to perturbations in water balance and regulates maternal physiology through the release of the neuropeptide hormones vasopressin and oxytocin into the circulation. Both dehydration and lactation evoke a dramatic morphological remodelling of the SON, a process known as function-related plasticity. We hypothesise that some of the changes seen in SON remodelling are mediated by differential gene expression, and have thus used microarrays to document global changes in transcript abundance that accompany chronic dehydration in female rats, and in lactation. In situ hydridisation analysis has confirmed the differential expression of 3 of these genes, namely Tumour necrosis factor induced protein 6, Gonadotrophin inducible transcription factor 1 and Ornithine decarboxylase antizyme inhibitor 1. Comparison of differential gene expression patterns in male and female rats subjected to dehydration and in lactating rats has enabled the identification of common elements that are significantly enriched in gene classes with particular functions. Two of these are related to the requirement for increased protein synthesis and hormone delivery in the physiologically stimulated SON (translation initiation factor activity and endoplasmic reticulum-Golgi intermediate compartment respectively), whilst others are consistent with concept of SON morphological plasticity (collagen fibril organisation, extracellular matrix organization and biogenesis, extracellular structure organization and biogenesis and homophilic cell adhesion). We suggest that the genes co-ordinately regulated in the SON as a consequence of dehydration and lactation form a network that mediates the plastic processes operational in the physiologically activated SON.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21791562" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30770" }, "primaryId" : "GEO:GSE30770", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30770" } ] }, "title" : "Impaired endosomal recycling in proximal tubules is mechanistically linked to proteinuria", "dateAssigned" : "2011-07-19T00:00:00.000-05:00", "summary" : "Through substitution mapping studies, we previously identified that a <330kb region from a rat strain with no renal pathology (the Lewis rat), which when introgressed onto the genetic background of a rat with renal disease (the Dahl Salt-sensitive (S) rat), caused an increase rather than the expected decrease in proteinuria. The purpose of this study was to prioritize a candidate gene and further delineate the mechanism underlying the observed increased in proteinuria. A higher level of proteinuria independent of dietary salt was observed in the congenic rat at a very young age (50-52 day old). The critical congenic segment was further mapped to <42.5kb containing a single candidate gene, rififylin. Rififylin was expressed 1.59 fold higher in the congenic strain compared with S. Overexpression of rififylin is known to delay recycling of endosomes. Renal transcriptome analysis indicated that Atp1a1 one of the most highly differentially expressed genes. Atp1a1 was 5.33 fold higher in the congenic strain compared with S. The protein product of Atp1a1, the alpha subunit of Na+K+ATPase, was also significantly higher in the endosomes of proximal tubules from the congenic strain compared with S. To determine whether the higher amounts of this protein in the endosomes is due to a delay in recycling of endosomes caused by the overexpression of rififylin in the congenic strain, recycling of exogenously labeled-transferrin by single cell cultures of proximal tubules was monitored by confocal microscopy. Recycling of transferrin was significantly delayed in the congenic strain compared with S. These results suggest that impaired endosomal recycling in the proximal tubules from the congenic strain caused by the overexpression of rififylin is a novel molecular mechanism linked to the observed increase in proteinuria of the congenic strain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30797" }, "primaryId" : "GEO:GSE30797", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30797" } ] }, "title" : "Olfactory Enshealting Cells : p75 High vs p75 Low cells population", "dateAssigned" : "2011-07-19T00:00:00.000-05:00", "summary" : "Comparative gene expression profiling of olfactory enshealting cells : p75 High vs p75 Low cells population", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30823" }, "primaryId" : "GEO:GSE30823", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30823" } ] }, "title" : "H4IIE liver cell line ChIP-Chip with Egr1", "dateAssigned" : "2011-07-20T00:00:00.000-05:00", "summary" : "This experiment includes a custom ChIP-chip design incorporating many genes that are dynamically regulated by insulin signaling. The Egr1 antibody used was from Santa Cruz sc-189.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21712389" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30848" }, "primaryId" : "GEO:GSE30848", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30848" } ] }, "title" : "Muscle wasting and the temporal gene expresion pattern in a novel rat ICU model", "dateAssigned" : "2011-07-21T00:00:00.000-05:00", "summary" : "Acute quadriplegic myopathy (AQM) or critical illness myopathy (CIM) is frequently observed in intensive care unit (ICU) patients. In order to elucidate duration-dependent effects of the ICU intervention on molecular and functional networks that control the muscle wasting and weakness in AQM, gene expression profile was analyzed at time points varying from 6 hours to 14 days in a unique experimental rat model mimicking ICU conditions, i.e., post-synaptically paralyzed, mechanically ventilated and extensively monitored animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22165895" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30851" }, "primaryId" : "GEO:GSE30851", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30851" } ] }, "title" : "Expression data from the hearts of aged Norway Brown rats (18-22 months-old)", "dateAssigned" : "2011-07-21T00:00:00.000-05:00", "summary" : "Despite an abundance of evidence to the contrary from animal studies, large clinical trials on humans have shown that estrogen administered to post-menopausal women increases the risk of cardiovascular disease. However, timing may be everything, as estrogen is often administered immediately after ovariectomy (ovx) in animal studies, while estrogen administration in human studies occurred many years post-menopause. This study investigates the discrepancy by administering 17ß-estradiol (E2) in a slow-release capsule to Norway Brown rats both immediately following ovx and 9 weeks post-ovx (Late), and studying differences in gene expression between these 2 groups as compared to age-matched ovx and sham operated animals. Two different types of microarray were used to analyze the left ventricles from these groups: an Affymetrix array (2 samples/group, each sample contained total RNAs pooled from 3 rats) and an Inflammatory Cytokines and Receptors PCR array (N=4 /group). Key genes were analyzed by western blotting. Ovx without replacement led to an increase in caspase 3, caspase 9, calpain 2, MMP9, and TNFa. Caspase 6, STAT3, and CD11b increased in the Late group, while TIMP2, MMP14, and collagen I a1 were decreased. MADD and fibronectin were increased in both Ovx and Late. TNFa protein levels increased with Late replacement. Many of these changes were prevented by early E2 replacement. These findings suggest that increased TNFa may be involved in some of the deleterious effects of delayed E2 administration seen in human studies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21750230" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30862" }, "primaryId" : "GEO:GSE30862", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30862" } ] }, "title" : "Different effects of 17 beta estrodial and soy protein isolate on bone gene expression in the pre-pubertal female rats", "dateAssigned" : "2011-07-21T00:00:00.000-05:00", "summary" : "Beneficial effects of a soy diet on bone quality have been assumed to be due to the putative estrogenic actions of isoflavones. We studied the effects of soy protein isolate (SPI) on bone quality and compared these effects to 17ß-estradiol (E2) in pre-pubertal rats. Female rats were weaned to a control diet with or without E2 (0.1, 1, 10 µg/kg/d), or SPI-containing diet with or without E2 (10 µg/kg/d) for 14 days beginning on postnatal day 20. In long bones from SPI-fed rats, only cancellous bone mineral density (BMD) was increased (p<0.05), while cortical BMD was decreased accompanied by lower bone strength compared to control casein-fed rats (p<0.05). In sharp contrast, 10 µg/kg/d E2 not only increased trabecular BMD, but also cortical BMD compared to controls. Rats treated with the combination of SPI and E2 had an intermediate bone effect. SPI increased while E2 decreased bone turnover, and increased trabecular BMD by both E2 and SPI was associated with decreased serum sclerostin levels. Microarray analysis revealed 652 genes regulated by SPI diet, 491 genes regulated by E2, and 266 genes regulated in common by both SPI diet and E2 compared to rats fed casein. The expression of caveolin-1, a protein localized in cell membrane, was down-regulated (p<0.05) in rats fed SPI, but not by E2 compared to rats fed casein. Down-regulated caveolin-1 by SPI was associated with increased BMP2, Smad and Runx2 expression in bone and osteoblasts (p<0.05). These results suggest SPI consumption results in significant non-classical estrogenic stimulation of cancellous bone formation prior to puberty, but may have adverse effects on overall bone quality and strength at this developmental stage as a result of reduced cortical bone formation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30890" }, "primaryId" : "GEO:GSE30890", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30890" } ] }, "title" : "P15 Rat Sciatic Nerve ChIP-Chip with NuRD complex components", "dateAssigned" : "2011-07-22T00:00:00.000-05:00", "summary" : "This experiment includes two custom ChIP-chip design incorporating many genes that are dynamically regulated during myelination. The antibodies used in this platform were Chd3/4 (Santa Cruz sc-11378) Chd4 (gift from Paul Wade), Mta2 (Santa Cruz sc-9447), and Nab2 (Santa Cruz sc-22815).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22302795" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30935" }, "primaryId" : "GEO:GSE30935", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30935" } ] }, "title" : "The effect of mequindox on gene expression in rat liver tissue", "dateAssigned" : "2011-07-25T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying mequindox toxicity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22845897" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30964" }, "primaryId" : "GEO:GSE30964", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE30964" } ] }, "title" : "Genome-wide mRNA expression profiles of FACS-purified rat beta cells freshly isolated from control and 24h-fasted rats", "dateAssigned" : "2011-07-26T00:00:00.000-05:00", "summary" : "Short periods of fasting are thought to mediate the beta cells’ competence for insulin synthesis and secretion. We examined whether it influenced their typical mRNA expression. After 24h of fasting, a 1.5 fold change was detected in 1.5% of all assayed transcripts (p<0.05), with 95% of altered genes (430 of 452) being down-regulated (Fig.6A). Suppression was more marked for a panel of genes with beta cell-specific expression, of which 12% were 1.5-fold suppressed. Suppressed beta cell marker genes were statistically enriched in gene clusters of endoplasmic reticulum (ER), ER to Golgi transport, protein folding and secretory vesicle-mediated transport, i.e. the pathways of protein synthesis and transport. (See Martens G.A. et al. PLoS One 2011)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21912665" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31080" }, "primaryId" : "GEO:GSE31080", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31080" } ] }, "title" : "Effect of interleukin-1 and PDGF-DD on SMCs", "dateAssigned" : "2011-08-01T00:00:00.000-05:00", "summary" : "This experiment tests the hypothesis that interleukin-1 promotes SMC phenotypic modulation to a distinct inflammatory state relative to the growth factor PDGF-DD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22318995" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31081" }, "primaryId" : "GEO:GSE31081", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31081" } ] }, "title" : "Methamphetamine administration causes differential alterations in gene expression and dynamic patterns of histone acetylation/hypoacetylation in the rat nucleus accumbens", "dateAssigned" : "2011-08-01T00:00:00.000-05:00", "summary" : "Methamphetamine (METH) addiction is associated with a plethora of neuropsychiatric symptoms. In rodents, administration of the drug is accompanied by complex changes in gene expression in the dorsal striatum. Very little is known about the effects of the drug on gene expression and epigenetic modifications in the nucleus accumbens (NAc). The present study was conducted in order to investigate the effects of a single injection of METH on gene expression in that structure. We also queried whether changes in transcript levels were accompanied by alterations in histone acetylation as well as in the expression of the histone acetyltransferase (HAT), ATF2, and of the histone deacetylases (HDACs), HDAC1 and HDAC2. Microarray analyses revealed that METH caused significant time-dependent increases in the expression of several genes that had previously been implicated in the acute and longterm effects of psychostimulants in the brain. These include several immediate early genes (c-fos, Egrs, c-jun, and Nurr1) and corticotropin-releasing factor (Crf). There were also increases in the levels of neuromedin U, Tnf-alpha, and Kcnk18, among others. In contrast, the METH injection caused decreases in the expression of many genes including Npas4 and cholecystokin (Cck). Pathway analyses showed that differentially affected genes participate in behavioral performance, cell-to-cell signaling and interactions, and regulation of gene expression. Other differentially affected genes are known to be involved in cellular compromise and death pathways. PCR analyses were used to confirm the changes in the expression of c-fos, fosB, c-jun, junB, Crf, NmU, Cck, and Npas4 transcripts. Western blot analyses also identified METH-mediated decreases in the acetylation of histone H3 at lysine 9 (H3K9) and lysine 18 (H3K18) as well as in histone 4 at lysine 16 (H4K16). In contrast, the METH injection caused time-dependent increases in the acetylation of H4K8 and H4K12. The changes in histone acetylation were also accompanied by decreased expression of HDAC1 but increased expression of ATF2 and of HDAC2. These results suggest that METH-induced alterations in global gene expression might be due, in part, to diverse effects of METH-induced histone acetylation secondary to changes in HAT and HDAC expression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31117" }, "primaryId" : "GEO:GSE31117", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31117" } ] }, "title" : "Expression data from Ad-atrogin-1-GFP or Ad-GFP infected cardiomyocytes", "dateAssigned" : "2011-08-02T00:00:00.000-05:00", "summary" : "We used DNA microarrays to detail the global trends in gene expression underlying atrogin-1- overexpressed cardiomyocytes and identified distinct classes of up-regulated genes during this process. Our findings suggest that atrogin-1 plays a critical role in regulating cardiac dysfunction at transcriptional level and may provide novel insight into how atrogin-1 modulates the programming of cardiac muscle gene expression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31121" }, "primaryId" : "GEO:GSE31121", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31121" } ] }, "title" : "Novel targets of microRNA miR-142 in cardiac myocytes", "dateAssigned" : "2011-08-02T00:00:00.000-05:00", "summary" : "The nuclear acetyltransferase p300 is a dose-dependent and limiting regulator of cardiac hypertrophy. p300 regulates hypertrophy by controlling the expression of specific microRNAs.The objective of this study was to dissect the role of miR-142 during p300 regulated hypertophic growth in vitro and in vivo and to verify its targets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22367739" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31201" }, "primaryId" : "GEO:GSE31201", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31201" } ] }, "title" : "Inter-species array between human, rat and mouse", "dateAssigned" : "2011-08-04T00:00:00.000-05:00", "summary" : "We propose a new microarray method, called an inter-species array, that can measure gene expression levels of multiple species at once. As the array operates simply by changing the probes on an Agilent commercial customized array, and conventional facilities and protocols can be used, the method is cost-efficient. We generated an array for humans, rats and mice that covers 6683 genes. The number of genes is larger than that of previous arrays. We measured the expression of genes in astrocyte cells for humans and rats, and in cortex cells for rats and mice.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31247" }, "primaryId" : "GEO:GSE31247", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31247" } ] }, "title" : "Gene expression profile on the penile tissue of erectile dysfunction (ED) in cavernous nerve injury (CNI) RAT model", "dateAssigned" : "2011-08-08T00:00:00.000-05:00", "summary" : "We performed microarray experiment focused on theto understanding the gene signature alteration in the corporal cavernous tissue of the CNI-induced ED rat model.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31307" }, "primaryId" : "GEO:GSE31307", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31307" } ] }, "title" : "Discriminant for genotoxic and non-genotoxic carcinogens by differentially expressed gene profiling", "dateAssigned" : "2011-08-10T00:00:00.000-05:00", "summary" : "The need for an efficient carcinogenicity test prompted this study, in which we used a microarray-based genomics approach, with a short-term in vivo model, in combination with insights from statistical and mechanistic analyses. We performed additional experiments to support the significance of the microarray results. Carcinogens were evaluated based on differences in the mechanisms involved in the response to genotoxic (GTX) carcinogens and non-genotoxic (NGTX) carcinogens. Microarray data were analyzed for 2 time points after treatment with the following 6 carcinogens. The analysis was performed using t-tests to compare the fold changes, and we selected differentially expressed genes (DEGs) and evaluated the reasons for differential expression in terms of cellular pathways and processes. We mapped the DEG-related pathways to analyze cellular processes, and we were able to uncover significant mechanisms that involve critical cellular components, such as CDKN1A (p21) and BAX. In addition, a comparison of the data from two time points showed that the repeated administration model was more effective than a single administration for carcinogen research. The classification analysis of selected DEGs was performed by setting microarray data of 4 carcinogens as test sets; these test sets were evaluated as classifiers. Microarray results were further supported using the Comet and micronucleus assays. It was found that gene expression profiling using microarrays, followed by pathway analysis, was effective in increasing the understanding of the characteristics of different carcinogens, and the efficiency of these methods was exemplified by the short-term (3 day) nature of the animal experiments.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31314" }, "primaryId" : "GEO:GSE31314", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31314" } ] }, "title" : "Gene expression profile of preclinical arthritis and its modulation by antigen-induced tolerance", "dateAssigned" : "2011-08-10T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21914168" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31357" }, "primaryId" : "GEO:GSE31357", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31357" } ] }, "title" : "Common molecular signature of two neuroprotective agents", "dateAssigned" : "2011-08-12T00:00:00.000-05:00", "summary" : "The current lack of proven pharmacological treatment options for traumatic brain injury (TBI) patients reflects the poor translation of successful preclinical studies in clinical trials. This may be due to poor choice of therapeutic agents based on incomplete knowledge of critical elements of neuroprotection. Our goal is to expedite discovery and translation of therapeutic agents that can improve functional outcome by identifying the common molecular profile of neuroprotective drugs. Since damage to the hippocampus is associated with TBI-induced deficits in learning and memory, we analyzed of the hippocampal transcriptional profiles of TBI rats treated with two clinically used drugs metyrapone and carbenoxolone, which have been shown to improve cognitive deficits in previous studies. Despite their different structures, we found that MT and CB have similar effects on several known biological pathways. The neuroprotective effects of these drugs are associated with a distinctive molecular signature which is characterized not by changes in expression of any individual gene but by a common global effect on multiple cell signaling pathways. These data suggest that drug treatments that induce a coordinated attenuation of multiple injury-induced cell signaling networks, both deleterious and protective, have high translational potential.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23326402" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31399" }, "primaryId" : "GEO:GSE31399", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31399" } ] }, "title" : "Optimized amplification and single-cell analysis identify GnRH-mediated activation of Rap1b in primary rat gonadotropes.", "dateAssigned" : "2011-08-16T00:00:00.000-05:00", "summary" : "Identifying the early gene program induced by GnRH would help understand how GnRH-activated signaling pathways modulate gonadotrope secretory response. We previously analyzed GnRH-induced early genes in LbT2 cells, however these lack GnRH self-potentiation, a physiological attribute of gonadotropes. To minimize cellular heterogeneity, rat primary pituitary cultures were enriched for gonadotropes by 40-60% using a sedimentation gradient. Given the limited number of gonadotropes, RNA was amplified prior to microarray analysis. Thirty-three genes were up-regulated 40 minutes after GnRH stimulation. Real-time PCR confirmed regulation of several transcripts including fosB, c-fos, egr-2 and rap1b, a small GTPase and member of the Ras family. GnRH stimulated rap1b gene expression in gonadotropes, measured by a sensitive single cell assay. Immunocytochemistry revealed increased Rap1 protein in GnRH-stimulated gonadotropes. These data establish rap1b as a novel gene rapidly induced by GnRH and a candidate to modulate gonadotropin secretion in rat gonadotropes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22127306" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31411" }, "primaryId" : "GEO:GSE31411", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31411" } ] }, "title" : "Inter-strain Heterogeneity in Responses to TCDD", "dateAssigned" : "2011-08-16T00:00:00.000-05:00", "summary" : "We profiled hepatic transcriptional responses of 6 strains of rats with varying sensitivity to a dioxin, TCDD, at 19 hours following exposure. The resistant rats exhibited significantly reduced transcriptional responses in comparison to the sensitive strains. We hypothesize that genes which show differential changes between the resistant and sensitive rats may potentially explain sensitivity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22342509" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31430" }, "primaryId" : "GEO:GSE31430", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31430" } ] }, "title" : "Dietary zinc status reversibly alters both the feeding behaviors of the rats and gene expression patterns in diencephalon", "dateAssigned" : "2011-08-17T00:00:00.000-05:00", "summary" : "Nutritional status influences feeding behaviors, food preferences and taste sensations. For example, zinc-deficient rats have been reported to show reduced and cyclic food intake patterns with increased preferences for NaCl. Although some impairments of the central nervous and endocrine systems have been speculated to be involved in these phenomena, the effects of short-term zinc deficiency on the brain have not been well examined to date. In this study, we performed a comprehensive analysis of the gene expression patterns in the rat diencephalon, which is a portion of the brain that includes the hypothalamus and thalamus, after short-term zinc deficiency and also during zinc recovery. The rats showed reduced and cyclic food intake patterns with increased salt preferences after a 10-day dietary zinc deficiency. A comparative analysis of their diencephalons using cDNA microarrays revealed that approximately 1% of the genes expressed in the diencephalons showed significantly altered expression levels. On the other hand, a 6-day zinc supplementation following the deprivation allowed for the recovery to initial food intake behaviors and salt preferences. The expression levels of most of the genes that had been altered by exposure to zinc deficient conditions were also recovered. These results show that feeding behaviors, taste preferences and gene expression patterns in the diencephalon respond quickly to changing zinc levels. This suggests that the gene expression changes observed in the diencephalon and the accompanying functional changes may be related to the development of deviations in feeding behaviors and increased preferences for NaCl in zinc-deficient rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22488846" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31457" }, "primaryId" : "GEO:GSE31457", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31457" } ] }, "title" : "Gene expression in the adrenal glands of two spontaneously hypertensive rat strains at 3 and 6 weeks of age", "dateAssigned" : "2011-08-18T00:00:00.000-05:00", "summary" : "We examined gene expression profiles in the rat adrenal glands using genome-wide microarray technology, and determined gene expression profiles in 3 rat strains: normotensive WKY, spontaneously hypertensive rats (SHR), and stroke-prone SHR (SHRSP). To identify candidate genes involved in the genesis of hypertension in the SHR strains, we compared the gene expression levels at 3 and 6 weeks of age, isolated 407 genes showing a more than 4-fold increase or a less than 1/4-fold decrease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23525202" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31503" }, "primaryId" : "GEO:GSE31503", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31503" } ] }, "title" : "Exposure to Nickel, Chromium, or Cadmium Causes Distinct Changes in the Gene Expression Patterns of a Rat Liver Derived Cell Line", "dateAssigned" : "2011-08-18T00:00:00.000-05:00", "summary" : "We identified both common and unique biological responses to exposure to the three metals. Nickel, cadmium, chromium all induced oxidative stress with both similar and unique genes and pathways responding to this stress. Although all three metals are known to be genotoxic, evidence for DNA damage in our study only exists in response to chromium. Nickel induced a hypoxic response as well as inducing genes involved in chromatin structure, perhaps by replacing iron in key proteins. Cadmium distinctly perturbed genes related to endoplasmic reticulum stress and invoked the unfolded protein response leading to apoptosis. With these studies, we have completed the first gene expression comparative analysis of nickel, cadmium, and chromium in H4-II-E-C3 cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22110744" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31571" }, "primaryId" : "GEO:GSE31571", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31571" } ] }, "title" : "High resolution methylome map of rat reveals role of intragenic DNA methylation in identifying coding region and alternative splice site.", "dateAssigned" : "2011-08-22T00:00:00.000-05:00", "summary" : "We report the application of next generation sequencing technology for high-throughput profiling of cytosine methylation in adult rat liver tissue.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22355382" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31635" }, "primaryId" : "GEO:GSE31635", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31635" } ] }, "title" : "Isolation of a Novel Rat Neural Progenitor Clone that Expresses Dlx Family Transcription Factors and Gives Rise to Functional GABAergic Neurons in Culture", "dateAssigned" : "2011-08-24T00:00:00.000-05:00", "summary" : "The purpose was to compare differentiation patterns of several different immortalized rat neural progenitor clones to identify early stages in differentiation. The cell clones studies were: GE6 (GABAergic neuronal precursor), GE2 (non-neuronal precursor, CTX8 (multipotential precursor), L2.2 (interneuronal precursor), and L2.3 (multipotential precursor).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21913335" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31668" }, "primaryId" : "GEO:GSE31668", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31668" } ] }, "title" : "Inhibitory Role of Notch1 in Calcific Aortic Valve Disease", "dateAssigned" : "2011-08-25T00:00:00.000-05:00", "summary" : "We found significant downregulation of Sox9 along with several cartilage-specific genes that were direct targets of the transcription factor, Sox9. Loss of expression Sox9 has been published to be associated with aortic valve calcification. Utilizing an in vitro porcine aortic valve calcification model system, inhibition of Notch activity resulted in accelerated calcification while stimulation of Notch signaling attenuated the calcific process. Finally, the addition of Sox9 was able to prevent the calcification of porcine AVICs that occurs with Notch inhibition. In conclusion, loss of Notch signaling contributes to aortic valve calcification via a Sox9-dependent mechanism.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22110751" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31678" }, "primaryId" : "GEO:GSE31678", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31678" } ] }, "title" : "MAP Kinase Phosphatase-1 Modulates Regional Effects of Injurious Mechanical Ventilation in Rodent Lungs", "dateAssigned" : "2011-08-26T00:00:00.000-05:00", "summary" : "Regionally injurious ventilation is associated with discrete differential lung transcriptomic changes. Ventilating in the prone, compared with the supine position abrogates regional injury by depressing MKP-1.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31695" }, "primaryId" : "GEO:GSE31695", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31695" } ] }, "title" : "Comparison of Differences in Gene Expression in the Ventral Tegmental Area of 5 Pairs of Rat Lines Selectively Bred for High or Low Alcohol Consumption", "dateAssigned" : "2011-08-26T00:00:00.000-05:00", "summary" : "The objective of this study was to determine common innate differences in gene expression in the ventral tegmental area (VTA) among the selectively bred (a) alcohol-preferring (P) vs. alcohol-non-preferring (NP) rats: (b) high-alcohol-drinking (HAD) vs. low-alcohol-drinking (LAD) rats (both replicates); (c) ALKO alcohol (AA) vs. nonalcohol (ANA) rats; and (d) Sardinian alcohol-preferring (sP) vs. alcohol-nonpreferring (sNP) rats. There were between 350 and 1400 unique named genes that were significantly different between the individual line-pairs. Gene Ontology (GO) and Ingenuity Pathways analyses indicated significant categories and networks in common for up to 3 line-pairs, but not for all 5 line-pairs; there were few genes in common between any of the line-pairs in these categories and networks. The overall ANOVAs of the combined data for the 5 line-pairs indicated over 1300 significant differences in expression of named genes. Ingenuity analysis revealed (a) several significant networks with clusters of genes associated with App, Egfr, Ccnd1, Itga2b, Rxra and Vcl; and (b) changes in genes within networks associated with dopamine, the glutamate synapse, Nfkb signaling, IL pathways and integrin. There were 22 genes that were significantly different in the overall ANOVA and were significantly different (in the direction) in at least 3 line-pairs, e.g., Crebl2, Gsta4, Itga9 & Itg2. In conclusion, the findings suggest that (a) different innate mechanisms may be contributing to vulnerability to high alcohol drinking behavior among the selectively bred lines, and (b) small contributions in expression of multiple genes within certain transmitter systems and intracellular signaling pathways may contribute to the disparate alcohol drinking characteristics of the 5 line-pairs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22579914" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31705" }, "primaryId" : "GEO:GSE31705", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31705" } ] }, "title" : "Comparison of Differences in Gene Expression in the Nucleus Accumbens Shell of 5 Pairs of Rat Lines Selectively Bred for High or Low Alcohol Consumption", "dateAssigned" : "2011-08-29T00:00:00.000-05:00", "summary" : "The objective of this study was to determine common innate differences in gene expression in the nucleus accumbens shell among the selectively bred (a) alcohol-preferring (P) vs. alcohol-non-preferring (NP) rats: (b) high-alcohol-drinking (HAD) vs. low-alcohol-drinking (LAD) rats (both replicates); (c) ALKO alcohol (AA) vs. nonalcohol (ANA) rats; and (d) Sardinian alcohol-preferring (sP) vs. alcohol-nonpreferring (sNP) rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22579914" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31708" }, "primaryId" : "GEO:GSE31708", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31708" } ] }, "title" : "Comparison of Differences in Gene Expression in the Central Nucleus of the Amygdala (CeA) of 5 Pairs of Rat Lines Selectively Bred for High or Low Alcohol Consumption", "dateAssigned" : "2011-08-29T00:00:00.000-05:00", "summary" : "The objective of this study was to determine common innate differences in gene expression in the Central Nucleus of the Amygdala (CeA) among the selectively bred (a) alcohol-preferring (P) vs. alcohol-non-preferring (NP) rats: (b) high-alcohol-drinking (HAD) vs. low-alcohol-drinking (LAD) rats (both replicates); (c) ALKO alcohol (AA) vs. nonalcohol (ANA) rats; and (d) Sardinian alcohol-preferring (sP) vs. alcohol-nonpreferring (sNP) rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22579914" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31736" }, "primaryId" : "GEO:GSE31736", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31736" } ] }, "title" : "Gene expression in response to short and long term cAMP stimulation in the INS-1 insulinoma cell line", "dateAssigned" : "2011-08-30T00:00:00.000-05:00", "summary" : "We used rat microarray analysis to compare the genome-wide gene expression response to short-term (2 hours) and long-term (16 hours) stimulations of the cAMP agonist forskolin in INS-1 insulinoma cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21949366" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31973" }, "primaryId" : "GEO:GSE31973", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE31973" } ] }, "title" : "Effect of a High Phosphorus Diet on Renal Gene Expressions in Rat", "dateAssigned" : "2011-09-07T00:00:00.000-05:00", "summary" : "The mechanism by which phosphorus levels are maintained in the body was investigated by analyzing changes in gene expression in the rat kidney following administration of a high-phosphorus diet. Male Wistar rats were fed a high phosphorous (HP) diet containing 1.2% phosphorous, or 0.3% HP as a control, for 24 days. Phosphorous retention was not significantly increased in HP rats, but fractional excretion of phosphorus was significantly increased in the HP group compared to controls, with an excessive amount of the ingested phosphorus being passed through the body. DNA microarray analysis of kidney tissue from both groups revealed changes in gene expression profile induced by a HP diet. Among the genes that were upregulated, gene ontology (GO) terms related to ossification, collagen fibril organization, and inflammation and immune response were significantly enriched. In particular, there was significant upregulation of type IIb sodium-dependent phosphate transporter (NaPi-IIb) in the HP rat kidney compared to control rats. This upregulation was confirmed by in situ hybridization. Discreet signals for NaPi-IIb in both the cortex and medulla of the kidney were apparent in the HP group, while the corresponding signals were much weaker in the control group. Immunohistochemical analysis showed that NaPi-IIb localized to the basolateral side of kidney epithelial cells surrounding the urinary duct in HP rats but not in control animals. These data suggest that NaPi-IIb is upregulated in the kidney in response to the active excretion of phosphate in HP diet-fed rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22235299" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32050" }, "primaryId" : "GEO:GSE32050", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32050" } ] }, "title" : "5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging [5hmC Capture and Seq]", "dateAssigned" : "2011-09-12T00:00:00.000-05:00", "summary" : "DNA methylation dynamics influence brain function and are altered in neurological disorders. 5-hydroxymethylcytosine (5-hmC), a DNA base derived from 5-methylcytosine (5mC) accounts for ~40% of modified cytosine in brain, and has been implicated in DNA methylation-related plasticity. Here we map 5-hmC genome-wide across three ages in mouse hippocampus and cerebellum, allowing assessment of its stability and dynamic regulation during postnatal neurodevelopment through adulthood. We find developmentally programmed acquisition of 5-hmC in neuronal cells. Epigenomic localization of 5-hmC-regulated regions reveals stable and dynamically modified loci during neurodevelopment and aging. By profiling 5-hmC in human cerebellum we establish conserved genomic features of 5-hmC. Finally, we implicate 5-hmC in neurodevelopmental disease by finding that its levels are inversely correlated with methyl-CpG-binding protein 2 (Mecp2) dosage, a protein encoded by a gene in which mutations cause Rett Syndrome. These data point toward critical roles for 5-hmC-mediated epigenetic modification in neurodevelopment and diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22037496" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32122" }, "primaryId" : "GEO:GSE32122", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32122" } ] }, "title" : "MicroRNA expression profiling of NGF-treated PC12 cells revealed a critical role for miR-221 in neuronal differentiation", "dateAssigned" : "2011-09-14T00:00:00.000-05:00", "summary" : "MicroRNAs (miRNAs) are small non-coding RNAs that control protein expression through translational inhibition or mRNA degradation. MiRNAs have been implicated in diverse biological processes such as development, proliferation, apoptosis and differentiation. Upon treatment with nerve growth factor (NGF), rat pheochromocytoma PC12 cells elicit neurite outgrowth and differentiae into neuron-like cells. NGF plays a critical role not only in neuronal differentiation but also in protection against apoptosis. In an attempt to identify NGF-regulated miRNAs in PC12 cells, we performed miRNA microarray analysis using total RNAs harvested from cells treated with NGF. In response to NGF treatment, expression of 8 and 12 miRNAs were up- and down-regulated, respectively. Quantitative RT-PCR analysis confirmed increased expression of miR-221, miR-181a* and miR-326, and decreased expression of miR-143, miR-210 and miR-532-3p after NGF treatment, among which miR-221 was drastically up-regulated. Overexpression of miR-221 induced neurite outgrowth of PC12 cells in the absence of NGF treatment, and also enhanced neurite outgrowth caused by low-dose NGF. More importantly, knockdown of miR-221 by antagomir attenuated NGF-mediated neurite outgrowth. Finally, miR-221 decreased expression of Foxo3a and Apaf-1, both of which are involved in apoptosis in PC12 cells. Our results indicate that miR-221 plays a critical role for neuronal differentiation as well as protection against apoptosis in PC12 cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22465943" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32125" }, "primaryId" : "GEO:GSE32125", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32125" } ] }, "title" : "Mammary Gland Morphological and Gene Expression Changes Underlying Pregnancy Protection of Breast Cancer Tumorigenesis", "dateAssigned" : "2011-09-14T00:00:00.000-05:00", "summary" : "We used the rat microarray technology to observe total transcriptome changes after the pregnancy and exogenous reproductive hormone stimulation of the mammary gland.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22085904" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32147" }, "primaryId" : "GEO:GSE32147", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32147" } ] }, "title" : "Molecular insights into the progression of crystalline silica-induced pulmonary toxicity in rats", "dateAssigned" : "2011-09-15T00:00:00.000-05:00", "summary" : "Identification of molecular target(s) and mechanism(s) of silica-induced pulmonary toxicity is important for the intervention and/or prevention of diseases associated with occupational exposure to crystalline silica. Rats were exposed to crystalline silica by inhalation (15 mg/m3, 6 h/day, 5 days) and global gene expression profile was determined in the lungs by microarray analysis at 1, 2, 4, 8, and 16 weeks following termination of silica exposure. The number of significantly differentially expressed genes (>1.5 fold change and <0.01 FDR p value) detected in the lungs during the post-exposure time intervals analyzed exhibited a steady increase in parallel with the progression of silica-induced pulmonary toxicity noticed in the rats. Quantitative real-time PCR analysis of a representative set of 10 genes confirmed the microarray findings. The various biological functions, canonical pathways, and molecular networks affected by silica exposure, as identified by the bioinformatics analysis of the significantly differentially expressed genes, also exhibited a steady increase similar to the silica-induced pulmonary toxicity. Genes involved in oxidative stress, inflammation, respiratory diseases, cancer, and tissue remodeling and fibrosis were significantly differentially expressed in the rat lungs; however, unresolved lung inflammation was the single most significant biological response to pulmonary exposure to crystalline silica. Excessive mucus production, as implicated by significant overexpression of the pendrin coding gene, SLC26A4, was identified as a novel mechanism for silica-induced pulmonary toxicity. Collectively, the findings of our study provided insights into the molecular mechanisms underlying the progression of crystalline silica-induced pulmonary toxicity in the rat and these findings may be useful in future to develop strategies to prevent occupational silicosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22431001" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32156" }, "primaryId" : "GEO:GSE32156", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32156" } ] }, "title" : "Expression data from PBDE treated rats at PND22 and Week 13", "dateAssigned" : "2011-09-15T00:00:00.000-05:00", "summary" : "PBDE treatment induced 1,066 liver gene transcript changes in females and 1,200 transcriptional changes in males at PND 22 (false discovery rate (FDR) < 0.01), but only 263 liver transcriptional changes at 13 weeks in male rats (FDR <0.05). No significant differences in dose response were found between male and female pups.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22267650" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32296" }, "primaryId" : "GEO:GSE32296", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32296" } ] }, "title" : "Estrogenic modulation of inflammation-related genes in male rats following volume overload", "dateAssigned" : "2011-09-22T00:00:00.000-05:00", "summary" : "The purpose of this study was to determine whether estrogen had an effect on inflammation-related genes that contribute to this estrogen-mediated cardioprotection. Volume overload on the heart was induced by aortocaval fistula in 8 week old male Sprague Dawley rats and genes of interest in shams, fistula , and fistula +estrogen were identified using an inflammatory PCR array.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22274565" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32312" }, "primaryId" : "GEO:GSE32312", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32312" } ] }, "title" : "Gene Expression in Rats Fed a Western Diet", "dateAssigned" : "2011-09-22T00:00:00.000-05:00", "summary" : "Resistant starches (RS), fed as high amylose maize starch (HAMS) or butyrylated HAMS (HAMSB), oppose dietary protein-induced colonocyte DNA damage in rats. In this study, rats were fed diets high in fat (19%) and protein (20%) with different forms of digestible starch (low amylose maize starch (LAMS) or low amylose whole wheat (LAW)) or RS (HAMS, HAMSB, or a whole high amylose wheat (HAW) generated by RNA interference (RNAi)) for 11 wk. A control diet contained 7% fat, 13% protein and LAMS. The aim of this study was to detect changes in the expression of DNA damage and repair genes in response to the above dietary treatments.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32432" }, "primaryId" : "GEO:GSE32432", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32432" } ] }, "title" : "Expression data from in utero exposure to genistein, vinclozolin and the mixture of genistein and vinclozolin on the mammary gland", "dateAssigned" : "2011-09-27T00:00:00.000-05:00", "summary" : "We used microarrays to detail the program of gene expression underlying different classes of up-regulated genes during the peripubertal process after administration of endocrine disruptors during the fetal and neonatal development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23160963" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32437" }, "primaryId" : "GEO:GSE32437", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32437" } ] }, "title" : "Gene profiles during vestibular compensation in unilateral labyrinthectomized rats", "dateAssigned" : "2011-09-28T00:00:00.000-05:00", "summary" : "Changes in gene expression during the chronic phase of vestibular compensation following unilateral labyrinthectomy in rats", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32459" }, "primaryId" : "GEO:GSE32459", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32459" } ] }, "title" : "Dioxin effect on the pituitary and hypothalamic expression of genes in male fetal Wistar rats", "dateAssigned" : "2011-09-28T00:00:00.000-05:00", "summary" : "2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) causes the many forms of reproductive toxicity, such as defects in sexual behaviors, in pups of which mother is exposed to this substance at lower doses. However, the mechanism underlying these defects remains to be clarified in spite of many researches conducted so far. Our previous studies have revealed that maternal treatment with TCDD attenuates the production of pituitary gonadotropins [luteinizing hormone (LH) and follicle-stimulating hormone] in the late fetuses, leading to the impairment of sexual behavior in adulthood. To identify the target genes for a fetal reduction in gonadotropin ß-subunit, we performed DNA microarray analysis using the fetal pituitary and its regulatory organ, the hypothalamus. The result showed that TCDD induced histone deacetylases (HDACs), and altered the expression of genes including gonadotropin-releasing hormone and activin signaling in the fetal pituitary. Moreover, our data indicated that the increased deacetylation of histone due to HDAC induction plays a critical role for a dioxin-induced attenuation of LHß in the fetal pituitary. This study suggests a novel molecular mechanism explaining dioxin-produced reproductive toxicity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22493514" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32622" }, "primaryId" : "GEO:GSE32622", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32622" } ] }, "title" : "In utero allergen exposure reprograms primary developmental patterns of lung gene expression and influences respiratory phenotype in rat models of asthma susceptibility.", "dateAssigned" : "2011-10-05T00:00:00.000-05:00", "summary" : "Transcriptome of whole lung of rat from 3 genetic strains, 3 postnatal time points and 2 exposures (saline versus ovalbumin) in (mainly) 4 replicate measurements per condition.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22983352" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32705" }, "primaryId" : "GEO:GSE32705", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32705" } ] }, "title" : "Congenital hypothryrodism and male rat liver: control vs congenital hypothryoidism", "dateAssigned" : "2011-10-08T00:00:00.000-05:00", "summary" : "Thyroid hormones are required for normal growth and development in mammals. Congenital-neonatal hypothyroidism (CH) has a profound impact on physiology but its specific influence in liver is less understood. Here we studied how CH influences liver gene expression program in adulthood. Pregnant rats were given anti-thyroid drug methimazole (MMI) from GD12 until PND30 to induce CH in male offspring. Growth defects due to CH were evident as a reduction in body weight and tail length from the second week of life. Once the MMI treatment was discontinued, feed efficiency increased in CH and this was accompanied by significant catch-up growth. On PND80, significant reduction in body mass, tail length, and circulating IGF-I remained in CH rats. On the other hand, mRNA levels of known GH targeted genes were significantly up-regulated. Serum levels of thyroid hormones, cholesterol, and triglycerides showed no significant differences. In contrast, CH rats showed significant changes in expression for hepatic genes involved in lipid metabolism with an increased transcription of PPAR and reduced expression of genes involved in fatty acids and cholesterol uptake, cellular sterol efflux, triglycerides assembly, bile acid synthesis, and lipogenesis. These changes were associated with a decrease of intrahepatic lipids. Finally, CH rats responded to hypothyroidism onset in adulthood with a reduction of serum fatty acids and hepatic cholesteryl esters, and to T3 replacement with enhanced activation of lipogenic transcriptional program. In summary, we provided in vivo evidence that neonatal hypothyroidism causes long-lasting effects on hepatic transcriptional program and tissue sensitivity to hormone treatment. This highlights the critical role that a euthyroid state during development plays on normal liver physiology in adulthood.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22666351" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32869" }, "primaryId" : "GEO:GSE32869", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32869" } ] }, "title" : "Genome-wide time series analysis of gastrin induced gene expression in AR42J cells with and without protein synthesis", "dateAssigned" : "2011-10-11T00:00:00.000-05:00", "summary" : "Genome-wide gene expression time series experiments are an important approach to studying a cells response to a given stimulus, as they enable capturing of the dynamics of the response. Moreover, information about the dynamics of the system is an important prerequisite for inferences on interactions between its components. We have performed extensive microarray-based genome-wide gene expression analyses up to 14h of the response to gastrin in AR42J adenocarcinoma cells. The gastrin reponse was also investigated in presence of the protein translation inhibitor cycloheximide. The rat cell line AR42J derived from pancreatic duct has the feature of pluripotency of the precursor cells of the gut endoderm. Furthermore, AR42J cells express gastrin receptors endogenously and are therefore frequently used as a model system to study gastrin responses. The hormone gastrin is the central regulator of gastric acid secretion and in addition plays a prominent role in regulation of growth and differentiation of gastric and colonic mucosa. Hypergastrinaemia has been linked to development of neuroendocrine gastrointestinal tumours (NE-GI) and, in conjugation with additional factors such as inflammation, to development of gastric adenocarcinoma (GA)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21995960" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32890" }, "primaryId" : "GEO:GSE32890", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32890" } ] }, "title" : "Transcriptional signature of the developing rat testes and ovaries following embryonic exposure to 2,3,7,8-TCDD", "dateAssigned" : "2011-10-11T00:00:00.000-05:00", "summary" : "We determined global gene changes in immature ovaries and testes in response to an in utero exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure. Microarray analysis was performed using testes and ovaries of the dioxin-exposed dams’ offspring. One hundred and thirteen genes were differentially expressed in ovaries and 56 genes in testes of 14 and 5 days-old, respectively. Real-time PCR was used to validate and extend data using RNA extracted from 5 to 145-day old rat testes and 3 to 25-day old rat ovaries. A single gene of the classic dioxin battery, i.e., the repressor of the aryl hydrocarbon receptor (Ahrr) was found altered in testes. In contrast, several of them including Cyp1a1, Cyp1b1, Nqo1, and Ahrr were found up-regulated in ovary, pituitary (a different endocrine organ) and liver. In addition to Ahrr, we identified 6 genes targeted by dioxin in both gonads, including the chemokines Cxcl4, Ccl5. Ccl5 gene expression levels were also regulated in pituitary and liver, so as pituitary Cxcl4. Four genes targeted by TCDD in testis and meeting stringent criteria were further surveyed. It included 2 genes with no previous reported function in testis, Art2b, Gzmf, Hpgds and Fgf13. Fgf13 was down-regulated in testis, and pituitary but not in ovary or liver. Interestingly, Art2b and Gzmf were up-regulated in testis, liver and pituitary but not ovary. Finally, Hpgds was unique in that expressed in various tissues it was regulated by TCDD in the gonads but not in the other tissues studied.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32891" }, "primaryId" : "GEO:GSE32891", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32891" } ] }, "title" : "Discover preclinical biomarkers of hepatotoxicity: Acetaminophen and Carbon tetrachloride", "dateAssigned" : "2011-10-11T00:00:00.000-05:00", "summary" : "Preclinical biomarkers useful for identification of idiosyncratic drugs have not been identified. It is hypothesized that patterns of transcript expression for the hepatotoxicants, including classical and idiosyncratic hepatotoxicants, are similar and the patterns differ from those of non-hepatotoxicants. This experiment is part of the biomarkers study, and focus on two clasical hepatotoxicants: Acetaminophen and Carbon tetrachloride. We have employed whole genome microarray expression profiling to identify liver gene expression changes induced by hepatotoxicants. For the same animal, urinary microRNA profiling were analyzed. APAP and CCl4 both significantly increased the urinary levels of 44 and 28 miRNAs, respectively. In addition, 10 of the increased miRNAs were in common between APAP and CCl4. Computational analysis was used to predict target genes of the 10 shared hepatotoxicant-induced miRNAs. From the same animals, liver gene expression profiling was performed using whole genome microarrays. Eight putative target genes were found to be significantly altered in the liver of APAP and CCl4 treated animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22112502" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32990" }, "primaryId" : "GEO:GSE32990", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE32990" } ] }, "title" : "In vitro differentiation of rat multipotent adult porgenitor cells to smooth muscle like cells", "dateAssigned" : "2011-10-14T00:00:00.000-05:00", "summary" : "The aim of the study was to characterize the molecular mechanism involved in TGF-ß mediated smooth muscle formation in vitro. We employed rat bone marrow derived Oct4 expressing clones of multipotent adult progenitor cells (rMAPC). We subjected these cells to differentiation towards smooth muscle cell as previously reported using TGF-ß1. The differentiation process reuires 6 days with media change every 2 days followed by RNA harvest. RNA was isolated using commercially available kits (Qiagen RNA easy micro kit). RNA integrity and quality was assessed prior to labeling and hybridization. As a control RNA from rat aortic smooth muscle cells was commercially obtained.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23110084" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33005" }, "primaryId" : "GEO:GSE33005", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33005" } ] }, "title" : "Effects of corn oil gavage on gene expression profiles of thymus in Wistar Rats", "dateAssigned" : "2011-10-14T00:00:00.000-05:00", "summary" : "To investigate the effects of corn oil (CO), common drug vehicle, on the gene expression profiles in rat thymus with microarray technique. Female Wistar Rats were administered daily with normal saline (NS), CO 2, 5, 10 ml/kg for 14 days, respectively. Then, the thymus samples of rats were collected for microarray test and histopathology examination. The microarray data showed that 0, 40, 458 differentially expressed genes (DEGs) in 2, 5, 10 ml/kg CO group compared to NS group, respectively. The altered genes were associated with immune response, cellular response to organic cyclic substance, regulation of fatty acid beta-oxidation, et al. However, no obvious histopathologic change was observed in the three CO dosage groups. These data show that 10 ml/kg CO , that dosage has been determined as the vehicle in drug safety assessment , can cause obvious influence on gene expression in rat thymus. Our study suggest that the dosage of CO gavage as the vehicle for water-in-soluble agents in drug development should be no more than 5 ml/kg if agents’ molecular effects in thymus want to be assessed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22760963" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33019" }, "primaryId" : "GEO:GSE33019", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33019" } ] }, "title" : "Activated YAP1 stimulates cardiomyocyte proliferation", "dateAssigned" : "2011-10-17T00:00:00.000-05:00", "summary" : "After transduction, cells were cultured in serum free media and collected 48 hours later.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22308401" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33056" }, "primaryId" : "GEO:GSE33056", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33056" } ] }, "title" : "Expression data from polycystic kidney disease susceptible and resistant rat strains", "dateAssigned" : "2011-10-18T00:00:00.000-05:00", "summary" : "To facilitate the search for genetic modifiers that modulate ARPKD disease progression and severity, we sought to generate a congenic rat model that carries the PCK Pkhd1 mutation but is resistant to the development of ARPKD. We transferred the Pkhd1 mutation from the PCK rat onto the genetic background of the FHH (Fawn-Hooded Hypertensive) rat. This newly developed strain, called FHH.Pkhd1, showed significant amelioration of renal disease, and delayed onset of biliary abnormalities. To initiate the exploration for genes and pathways that modulate susceptibility to renal cystogenesis, we investigated transcriptional changes in kidneys from PCK, SD, FHH and FHH.Pkhd1 rats by microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22669842" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33137" }, "primaryId" : "GEO:GSE33137", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33137" } ] }, "title" : "Expression data from hippocampus and cortex of 6- and 12-week curcumin-treated 15-month-old rats", "dateAssigned" : "2011-10-21T00:00:00.000-05:00", "summary" : "We used microarrays to investigate the effects of short-term (6-week) and long-term (12-week) curcumin-supplemented diet on gene expression of hippocampus and cortex in aged rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33144" }, "primaryId" : "GEO:GSE33144", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33144" } ] }, "title" : "The role of dietary leucine and dairy protein on gastrocemius muscle gene expression", "dateAssigned" : "2011-10-21T00:00:00.000-05:00", "summary" : "The primary aims of this study were: (i) to compare the effects of diets with protein derived from casein, casein supplemented with leucine, and complete dairy on body composition and insulin sensitivity; and (ii) to determine if there is a synergistic effect of dietary Ca and protein source on body composition and insulin sensitivity. Secondarily, we used microarray analysis to examine the effect of casein, leucine, or complete dairy containing diets on the expression of gastrocnemius muscle genes related to lipid and glucose metabolism.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33166" }, "primaryId" : "GEO:GSE33166", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33166" } ] }, "title" : "Effect of Concentration and type of Dietary Fatty Acid on Development of Nonalcoholic Fatty Liver Disease", "dateAssigned" : "2011-10-24T00:00:00.000-05:00", "summary" : "The current study was designed to determine if dietary fatty acid concentration and composition affects the development and progression of nonalcoholic fatty liver disease. Male SD rats were overfed diets low (5%) or high (70%) fat diets via total enteral nutrition where the fat source was olive oil (monounsaturated), or corn oil (polyunsaturated). Overfeeding 5% corn oil produced little steatosis relative to feeding 5% olive oil. This was associated with lower fatty acid synthesis and reduced SREBP-c signaling in the 5% corn oil group. Overfeeding 70% fat diets increased steatosis and lead to increased liver necrosis in the 70% corn oil but not olive oil group. Increased injury after feeding polyunsaturated fat diets was linked to peroxidizability of hepatic free fatty acids and triglycerides and appearance of peroxidaized lipid products HETES and HODES previously linked to clinical nonalcoholic steatohepatitis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22991207" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33170" }, "primaryId" : "GEO:GSE33170", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33170" } ] }, "title" : "Comparison of gene expression profiles in rat sarcomas and masenchymal stem cells (MSCs)", "dateAssigned" : "2011-10-24T00:00:00.000-05:00", "summary" : "Several altered pathways have identified including down-regulation of Wnt, Cell adhesion, ECM interaction and up-regulation of Hedgehog, cell cycling pathways in rat sarcomas compared to MSCs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33175" }, "primaryId" : "GEO:GSE33175", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33175" } ] }, "title" : "Gene expression signatures following nerve injury in a rat model (0h-9h)", "dateAssigned" : "2011-10-24T00:00:00.000-05:00", "summary" : "We used microarrays to distinguish the gene expression differences among different time points after injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23028454" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33195" }, "primaryId" : "GEO:GSE33195", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33195" } ] }, "title" : "A Comparison between In Vivo and Whole Embryo Culture using Transcriptomics: Developmental Changes, Model Differences and Retinoic Acid Response", "dateAssigned" : "2011-10-25T00:00:00.000-05:00", "summary" : "Cultured embryos mimic the morphological developmental progression of embryos (in vivo) undergoing neurulation and early organogenesis. Using available genomics technologies, comparative molecular-based assessments between cultured embryos and in vivo models may further clarify commonalities and dissimilarities which contribute to differences between systems. Therefore, in this study, using a transcriptomic approach, we compared cultured whole rat embryos and embryos in vivo at comparable time points in development (gestational day (GD) 10 + 2-48h, GD 0 = copulatory plug) to assess for commonalities and differences in gene expression in relation to morphology. We reveal strong parallels in time-dependent expression of genes in terms of magnitude, directionality and functionality between whole embryo culture (WEC) and in vivo (rat). Genes changing in expression over time resemble previously hypothesized mechanisms underlying early development in mammalian systems. Furthermore, at the gene and functional level, we identify genes which differ in expression between models, including genes related to development, oxygen transport and metabolism. In summary, our results support the use of WEC for toxicological studies aimed at representing in vivo development during this time-window at the molecular level. Additionally, we indicate genes which differ in expression between models, providing possible insights for improvement of culture conditions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22262565" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33310" }, "primaryId" : "GEO:GSE33310", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33310" } ] }, "title" : "Rat primary chondrocyte: Control vs. IL-1beta treated", "dateAssigned" : "2011-10-28T00:00:00.000-05:00", "summary" : "microRNA expression profilings of chondrocytes comparing control untreated cells with cells treated with IL-1beta. Three timepoints included are 6h,12h and 24h. Many microRNAs change their expression patterns owing to IL-1beta stimulation. Some of them are chosen for further investigation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33311" }, "primaryId" : "GEO:GSE33311", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33311" } ] }, "title" : "Modification of genes expression in the somatolactotrope GH4C1 cell line in presence of the dominant negative mutant POU1F1(R271W)", "dateAssigned" : "2011-10-28T00:00:00.000-05:00", "summary" : "Gene expression microarray assays were used to detect genes that have their expression modified in somatolactotrope GH4C1 cells by the expression of a dominant negative form of POU1F1, POU1F1(R271W).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22638072" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33360" }, "primaryId" : "GEO:GSE33360", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33360" } ] }, "title" : "Discovery of novel microRNAs in rat kidney using microarray analyses", "dateAssigned" : "2011-11-01T00:00:00.000-05:00", "summary" : "MicroRNAs are small non-coding RNAs that regulate a variety of biological processes. In the last version of the miRBase database (Release 17), 720 mouse microRNAs are accompanied by only 408 rat microRNAs. Given the importance of rat as a model organism, we used next generation sequencing and microarray technologies to discover novel microRNAs in rat kidneys.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33423" }, "primaryId" : "GEO:GSE33423", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33423" } ] }, "title" : "Environmental Toxicants Induce Epigenetic Transgenerational Inheritance of Ovarian Disease [Affymetrix]", "dateAssigned" : "2011-11-02T00:00:00.000-05:00", "summary" : "We used transcriptome microarray analysis to determine genes expressed differentially between F3 control and F3 vinclozolin lineage rat ovary granulosa cell and see which genes might be connected to or cause observed ovary diseases", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22570695" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33497" }, "primaryId" : "GEO:GSE33497", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33497" } ] }, "title" : "The effects on transcriptome from absence of Spt4/Supt4h by RNA-seq", "dateAssigned" : "2011-11-04T00:00:00.000-05:00", "summary" : "We have done RNAseq analyses in yeast and in rat and mouse striatal neurons. The experiments in yeast examine globally the physiological effects of spt4 deletion on the transcriptome. The experiments in neurons examine the global effects of supt4 knockdown to a cellular level (i.e., 50% knockdown) that we have shown prevents toxicity of variant Htt protein by interfering with transcription of extended CAG repeats. The results of both sets of experiments indicate that absent spt4 function has limited effects on overall transcription. Moreover, the mammalian cell experiments indicate that supt4h knockdown to a cellular level that alters production of transcripts containing long CAG repeats has minimal effects on normal genes, supporting the notion that anti-supt4h measures may prove useful in combating trinucleotide repeat diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22341442" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33551" }, "primaryId" : "GEO:GSE33551", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33551" } ] }, "title" : "Effects of dietary obesity in fathers on gene expression of fat in the female offspring (mRNA data)", "dateAssigned" : "2011-11-08T00:00:00.000-06:00", "summary" : "The global prevalence of obesity is increasing across age and gender. The rising burden of obesity in young people contributes to the early emergence of type 2 diabetes. Having one parent obese is an independent risk factor for childhood obesity. While the detrimental impact of diet-induced maternal obesity on offspring is well established, the extent of the contribution of obese fathers is unclear, as is the role of non-genetic factors in the casual pathway. Here we show that paternal high fat diet exposure programmed ß-cell ‘dysfunction’ in their F1 female offspring. Chronic high fat diet consumption in Sprague Dawley fathers led to increased body weight, adiposity, impaired glucose tolerance and insulin sensitivity. Relative to controls, their female offspring had lower body weight at day-1, increased pubertal growth rate, impaired insulin secretion and glucose tolerance, in the absence of obesity or increased adiposity. Paternal high fat diet altered the expression of 211 pancreatic islet genes in adult female offspring (P < 0.001); genes belonged to 8 functional clusters, including calcium ion binding, primary metabolic processes and ATP binding, and organ/system development. Broader KEGG pathway analysis of 2014 genes differentially expressed at the P < 0.01 level further demonstrated involvement of insulin and calcium signaling, and MAPK pathways. This is the first reported study in mammals describing non-genetic, intergenerational transmission of metabolic sequelae of high fat diet from father to offspring. These findings support a role of fathers in metabolic programming of offspring and form a framework for further studies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24421403" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33559" }, "primaryId" : "GEO:GSE33559", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33559" } ] }, "title" : "Effects of dietary obesity in fathers on gene expression of fat in the female offspring (miRNA data)", "dateAssigned" : "2011-11-08T00:00:00.000-06:00", "summary" : "The global prevalence of obesity is increasing across age and gender. The rising burden of obesity in young people contributes to the early emergence of type 2 diabetes. Having one parent obese is an independent risk factor for childhood obesity. While the detrimental impact of diet-induced maternal obesity on offspring is well established, the extent of the contribution of obese fathers is unclear, as is the role of non-genetic factors in the casual pathway. Here we show that paternal high fat diet exposure programmed β-cell ‘dysfunction’ in their F1 female offspring. Chronic high fat diet consumption in Sprague Dawley fathers led to increased body weight, adiposity, impaired glucose tolerance and insulin sensitivity. Relative to controls, their female offspring had lower body weight at day-1, increased pubertal growth rate, impaired insulin secretion and glucose tolerance, in the absence of obesity or increased adiposity. Paternal high fat diet altered the expression of 211 pancreatic islet genes in adult female offspring (P < 0.001); genes belonged to 8 functional clusters, including calcium ion binding, primary metabolic processes and ATP binding, and organ/system development. Broader KEGG pathway analysis of 2014 genes differentially expressed at the P < 0.01 level further demonstrated involvement of insulin and calcium signaling, and MAPK pathways. This is the first reported study in mammals describing non-genetic, intergenerational transmission of metabolic sequelae of high fat diet from father to offspring. These findings support a role of fathers in metabolic programming of offspring and form a framework for further studies.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33563" }, "primaryId" : "GEO:GSE33563", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33563" } ] }, "title" : "Effects of dietary obesity in fathers on gene expression of islets in the female offspring (miRNA data)", "dateAssigned" : "2011-11-08T00:00:00.000-06:00", "summary" : "The global prevalence of obesity is increasing across age and gender. The rising burden of obesity in young people contributes to the early emergence of type 2 diabetes. Having one parent obese is an independent risk factor for childhood obesity. While the detrimental impact of diet-induced maternal obesity on offspring is well established, the extent of the contribution of obese fathers is unclear, as is the role of non-genetic factors in the casual pathway. Here we show that paternal high fat diet exposure programmed β-cell ‘dysfunction’ in their F1 female offspring. Chronic high fat diet consumption in Sprague Dawley fathers led to increased body weight, adiposity, impaired glucose tolerance and insulin sensitivity. Relative to controls, their female offspring had lower body weight at day-1, increased pubertal growth rate, impaired insulin secretion and glucose tolerance, in the absence of obesity or increased adiposity. Paternal high fat diet altered the expression of 211 pancreatic islet genes in adult female offspring (P < 0.001); genes belonged to 8 functional clusters, including calcium ion binding, primary metabolic processes and ATP binding, and organ/system development. Broader KEGG pathway analysis of 2014 genes differentially expressed at the P < 0.01 level further demonstrated involvement of insulin and calcium signaling, and MAPK pathways. This is the first reported study in mammals describing non-genetic, intergenerational transmission of metabolic sequelae of high fat diet from father to offspring. These findings support a role of fathers in metabolic programming of offspring and form a framework for further studies.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33597" }, "primaryId" : "GEO:GSE33597", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33597" } ] }, "title" : "CD36-DEFICIENT CONGENIC STRAINS SHOW IMPROVED GLUCOSE TOLERANCE AND DISTINCT SHIFTS IN METABOLIC AND TRANSCRIPTOMIC PROFILES", "dateAssigned" : "2011-11-09T00:00:00.000-06:00", "summary" : "Deficiency of fatty acid translocase Cd36 has been shown to play major role in pathogenesis of metabolic syndrome components in the spontaneously hypertensive rat (SHR). We have tested the hypothesis that effects of Cd36 mutation on features of metabolic syndrome are contextually-dependent on genomic background. We have derived two new congenic strains by introgression of limited chromosome 4 regions of SHR origin, both including defective Cd36 gene, into genetic background of highly inbred model of insulin resistance and dyslipidemia, polydactylous (PD) rat strain. We have subjected standard diet-fed adult males of PD and the 2 congenic PD.SHR4 strains to metabolic, morphometric and transcriptomic (Affymetrix Rat 1.0 ST Exon array) profiling. We observed significantly improved glucose tolerance and lower fasting insulin in PD.SHR4 congenics than in PD. One of the PD.SHR4 strains also showed lower triglyceride concentrations across major lipoprotein fractions combined with higher concentrations of LDL cholesterol compared to PD progenitor. The other PD.SHR4 strain had lower total and HDL cholesterol as well as lower LDL and HDL triacylglycerol content compared to PD. The hepatic transcriptome assessment revealed network of genes differentially expressed between PD and PD.SHR4 with significant enrichment by members of circadian rhythmicity pathway (Arntl (Bmal1), Clock, Nfil3, Per2 and Per3). In summary, the introduction of chromosome .4 region of SHR origin including defective Cd36 into PD genetic background resulted in disconnected shifts of metabolic profile along with distinct changes in hepatic transcriptome. The synthesis of the current results with those obtained in other Cd36-deficient strains indicate that the eventual metabolic effect of deleterious mutation such as that of SHR-derived Cd36 is not absolute, but rather a function of complex interactions between environment and genomic background, upon which it operates.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22473311" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33639" }, "primaryId" : "GEO:GSE33639", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33639" } ] }, "title" : "Global expression analysis identified a preferentially NGF-induced transcriptional program regulated by sustained MEK/ERK and AP-1 activation during PC12 differentiation.", "dateAssigned" : "2011-11-12T00:00:00.000-06:00", "summary" : "Neuronal differentiation of PC12 cells in response to NGF is a prototypical model in which signal duration determines a biological response. Sustained ERK activity induced by NGF, as compared to transient activity induced by EGF, is critical to the differentiation of these cells. To characterize the transcriptional program activated preferentially by NGF, we compared global gene expression profiles between cells treated with NGF and EGF for 2-4 hrs, when sustained ERK signaling in response to NGF is most distinct from the transient signal elicited by EGF. This analysis identified 69 genes that were preferentially upregulated in response to NGF.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22065583" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33703" }, "primaryId" : "GEO:GSE33703", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33703" } ] }, "title" : "Deep sequencing and proteomics analysis reveal globally dysregulated expression of microRNA and their target genes in rat kidneys treated by carcinogenic dose of Aristolochic Acid", "dateAssigned" : "2011-11-15T00:00:00.000-06:00", "summary" : "MicroRNAs (miRNAs) play an important role in carcinogenesis by regulating the protein translation from their targeted messenger RNAs (mRNA). Aristolochic Acid (AA) is a potent carcinogen that can induce kidney tumors in both human and experimental animals. Although the expression and roles of miRNAs have been extensively studied in cancer tissues or tissues treated by carcinogens, it is still unclear how the three levels of gene expression, including miRNA, mRNA and protein, are regulated and coordinated during the early stage of carcinogenesis. Here, we treated rats with 10 mg/kg AA or vehicle control for 12 weeks and the kidney tissues were quickly isolated and frozen immediately after the treatment. Eight kidney samples (4 for the treatment and 4 for the control) were used for analyzing miRNA and mRNA expressions with deep sequencing, and protein expressions with proteomics. MiRNA expressions were significantly changed by AA treatment. The treated samples were well separated from the control samples in both principal component analysis (PCA) and hierarchical clustering analysis (HCA). Quantitative measurements of six miRNAs using TaqMan real-time PCR were consistent with the deep sequencing results in terms of both direction and magnitude of gene expression change. Sixty-three miRNAs (adjusted p value < 0.05 and fold change > 1.5), 6,794 mRNAs (adjusted p value < 0.05 and fold change > 2.0), and 800 proteins (fold change > 2.0) were significantly altered by AA treatment. By combining the results of a computational target predicting algorithm, and the mRNA and protein expression data, 143 genes were found by the differentially expressed miRNAs (DEMs). The DEM-targeted genes are mainly related to cancer, cell growth, which reflects the carcinogenic processes in the AA-treated rat kidneys.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33725" }, "primaryId" : "GEO:GSE33725", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33725" } ] }, "title" : "Effect of erythropoietin on cerebral ischemia-induced changes in gene expression in rats", "dateAssigned" : "2011-11-16T00:00:00.000-06:00", "summary" : "Analysis of the gene expression profile in the cerebral cortex of rats 2h or 6h after middle cerebral artery occlusion with or without a single erythropoietin treatment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22645329" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33785" }, "primaryId" : "GEO:GSE33785", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33785" } ] }, "title" : "Gene expression in the chronic ethanol-treated rat liver during liver regeneration", "dateAssigned" : "2011-11-17T00:00:00.000-06:00", "summary" : "In this study, we analyzed the effects of chronic alcohol consumption on liver repair and regeneration after partial hepatectomy (PHx). Rats were fed a liquid diet containing 36% of total calories derived from ethanol for 5 weeks; corresponding pair-fed calorie-matched controls were fed diets in which ethanol calories were replaced either by carbohydrate or by fat. After 5 weeks, rats were subjected to 70% PHx and liver samples were collected at 1, 6 and 24h after the surgery. The excised liver samples at t=0 served as within-animal controls. We used Affymetrix Rat Gene 1.0 ST arrays to obtain global gene expression data from each liver sample (n=4 replicate rats, 72 arrays total).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27012785" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33830" }, "primaryId" : "GEO:GSE33830", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33830" } ] }, "title" : "Gene Bionetworks Involved in Epigenetic Transgenerational Inheritance of Environmentally Altered Sexual Selection: Role of Epigenetics in Evolutionary Biology", "dateAssigned" : "2011-11-20T00:00:00.000-06:00", "summary" : "We used Affymetrix Rat Gene 1.0 ST microarrays to determine genes expressed differentially in F3 Vinclozolin lineage male or female rats' 6 brain areas - amygdala (Amy), hippocampus (Hipp), olfactory bulb (OlfB), cingulate cortex (CngCtx), entorhinal cortex (EnCtx), and preoptic area-anterior hypothalamus (POAH) - due to Vinclozolin treatments of their grand-grandmothers (F0).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24885959" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33975" }, "primaryId" : "GEO:GSE33975", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE33975" } ] }, "title" : "Gene expression profiling reveals potential breast cancer prevention mechanisms associated with the rat Mcs5a allele (DGE)", "dateAssigned" : "2011-11-28T00:00:00.000-06:00", "summary" : "Using global gene expression profiling in T-cells from untreated Mcs5a resistant and susceptible congenic rats, we asked if signatures of potential risk-decreasing mechanisms could be identified.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34000" }, "primaryId" : "GEO:GSE34000", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34000" } ] }, "title" : "Expression data from the dorsal root ganglia during streptozotocin-induced painful diabetic neuropathy in rats", "dateAssigned" : "2011-11-29T00:00:00.000-06:00", "summary" : "We analyzed gene expression of the dorsal root ganglia together with measurement of mechanical allodynia in diabetic rats to try to capture the global fingerprint of changes in gene expression associated with FK1706 administration and also to elucidate the putative mechanisms of its neurotrophic activity in vivo.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22642793" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34003" }, "primaryId" : "GEO:GSE34003", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34003" } ] }, "title" : "Time course expression study in the rat superior olivary complex", "dateAssigned" : "2011-11-29T00:00:00.000-06:00", "summary" : "The superior olivary complex (SOC) is a prominent auditory brainstem center and represents one of the prime model systems to study the development of sensory circuits. We recently performed genome-wide microarray studies to analyze the SOC-related genetic program at postnatal day (P)4 and P25. Here, we extended this analysis by including two additional time points, P0 and P16. Data sets were validated by qRT-PCR. Statistical analysis were performed for the different developmental time points as well as with for differences between the SOC and our previously analyzed brain samples. This analysis revealed that after hearing-onset (P16 and P25), 918 oligos were up-regulated and 810 oligos down-regulated in the SOC compared to the two prehearing stages (P0 and P4). Of the up-regulated oligos, 530 were significantly higher expressed compared to the brain at P25. Concerning neurotransmission, SOC-related elevation was mainly observed for K+ channels, G-proteins, and myelination-related proteins, whereas Ca2+-related proteins showed a decreased expression. In the pre-hearing period, 47 oligos were up-regulated compared to the brain. Several of them were transcription factors, previously associated with other auditory structures, and might ensure coordinated development of peripheral and central auditory structures. Stage-specific comparison identified distinct genetic programs during development: Circuit formation/refinement at P4; myelination and circuit refinement/consolidation at P16; and neuroprotection at P25. Altogether, our study defines the genetic program of postnatal SOC development and provides strong functional candidates for various developmental processes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23893414" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34057" }, "primaryId" : "GEO:GSE34057", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34057" } ] }, "title" : "miRNA expression during liver regeneration in the chronic ethanol-fed rat", "dateAssigned" : "2011-11-30T00:00:00.000-06:00", "summary" : "miRNA expression was profiled before and during liver regeneration following 2/3 partial hepatectomy (PHx) in chronic ethanol-fed (EtOH) and pair-fed carbohydrate control (CHO) rats. Prior to PHx, EtOH animals were fed a liquid diet containing 36% of the calories from ethanol for 5 weeks. Left lateral and medial (LLM) lobes were removed at time of PHx and used as t = 0 biological controls. Remnant liver tissue (PHx) was harvested 1 h, 6 h, 12 h, and 24 h after PHx. RNA from 4 biological replicates was pooled for profiling miRNA expression on Agilent Rat miRNA Microarrays v1.0.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22823254" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34058" }, "primaryId" : "GEO:GSE34058", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34058" } ] }, "title" : "Maternal immune activation by LPS selectively alters specific gene expression profiles of interneuron migration and oxidative stress in the fetus without triggering a fetal immune response.", "dateAssigned" : "2011-11-30T00:00:00.000-06:00", "summary" : "Maternal immune activation is a risk factor for the development of schizophrenia and autism. Infections during pregnancy activate the mother's immune system and alter the fetal environment with sub-sequence effects of CNS function and behavior in the offspring, but the cellular and molecular links between infection-induced altered fetal development and risk for neuropsychiatric disorders are unknown. We investigated the immunological, molecular, and behavioral effects of MIA in the offspring of pregnant Sprague-Dawley rats given an intraperitoneal (0.25 mg/kg) injection of lipopolysaccharide (LPS) on embryonic day 15. LPS significantly elevated pro-inflammatory cytokines in maternal serum, amniotic fluid, and fetal brain at 4 h, and levels decreased but remained elevated at 24 h. Offspring born to LPS-dams exhibited reduced social and exploration behaviors as juveniles and young adults. Whole genome microarray analysis of the fetal brain at 4 h post maternal LPS was performed to elucidate possible molecular mechanisms by which MIA effects the fetal brain. We observed dysregulation of 3,285 genes in restricted functional categories, with increased mRNA expression of cellular stress and cell death genes and reduced expression of developmentally-regulated and brain-specific genes, specifically those that regulate neuronal migration of GABAergic interneurons.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22310921" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34076" }, "primaryId" : "GEO:GSE34076", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34076" } ] }, "title" : "Transcriptional profiling of apolipoprotein-O-overexpressing H9c2 cardiomyoblasts", "dateAssigned" : "2011-12-01T00:00:00.000-06:00", "summary" : "Mitochondrial dysfunction and excessive lipid accumulation in non-adipose tissues have been proposed widely as the roots for comorbidities generated by the growing epidemia of type 2 diabetes mellitus. Mouse models of lipotoxic cardiomyopathy have underlined this detrimental situation, but so far the proteins involved in diabetic patients’s induced mitochondrial dysfunction remain unknown. Apolipoprotein O (ApoO), originally found overexpressed in human diabetics hearts (Lamant et al. JBC 2006), is a candidate that was investigated here at the transcriptome level using H9c2 cardiomyoblasts after stable integration of an expression vector (pTT-ApoO) constitutively expressing ApoO.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34119" }, "primaryId" : "GEO:GSE34119", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34119" } ] }, "title" : "Aberrant microRNA expression in radiation-induced rat mammary cancer: the potential role of miR-194 overexpression in cancer cell proliferation.", "dateAssigned" : "2011-12-02T00:00:00.000-06:00", "summary" : "Aberrant expression of microRNAs (miRNAs) is frequently associated with a variety of cancers, including breast cancer. We and others have demonstrated that radiation-induced rat mammary cancer exhibits a characteristic gene expression profile and a random increase in aberrant DNA copy number; however, the role of aberrant miRNA expression is unclear. We performed a microarray analysis of frozen samples of eight mammary cancers induced by gamma-irradiation (2 Gy), eight spontaneous mammary cancers, and seven normal mammary samples. We found that a small set of miRNAs was characteristically overexpressed in radiation-induced cancer. Quantitative RT-PCR analysis confirmed that miR-135b, miR-192, miR-194, and miR-211 were significantly upregulated in radiation-induced mammary cancer compared with spontaneous cancer and normal mammary tissue. The expression of miR-192 and miR-194 also was upregulated in human breast cancer cell lines compared with non-cancer cells. Manipulation of the miR-194 expression level using a synthetic inhibiting RNA produced a small but significant suppression of cell proliferation and upregulation in the expression of several genes that are suggested to act as tumor suppressors in MCF-7 and T47D breast cancer cells. Thus, the induction of rat mammary cancer by radiation involves aberrant expression of miRNAs, which may favor cell proliferation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23273170" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34136" }, "primaryId" : "GEO:GSE34136", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34136" } ] }, "title" : "Influence of intrauterine low protein diet on ductal morphogenesis of the rat mammary gland.", "dateAssigned" : "2011-12-05T00:00:00.000-06:00", "summary" : "Following intrauterine low protein diet, the lumbar mammary gland of control and low protein rats were removed for further analysis via genarray on day 21 and day 28 postpartum.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24955840" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34139" }, "primaryId" : "GEO:GSE34139", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34139" } ] }, "title" : "Molecular pathology of the ARF induced by choline deficiency and of the protection afforded by fish oil", "dateAssigned" : "2011-12-05T00:00:00.000-06:00", "summary" : "Male weanling Wistar rats from the Animal Facility at the Center for Experimental and Applied Pathology were divided into 4 groups and fed the following diets: 1) choline-deficient diet with VO [corn and hydrogenated oils) as lipids (CDVO); 2) choline-supplemented diet with VO as lipids (CSVO); 3) choline-deficient diet with MO as lipid (CDMO); and 4) choline-supplemented diet with MO as lipid (CSMO). Authors have adhered to appropriate NIH Guide for the Care and Use of Laboratory Animals. It is known that female rats are more resistant than male rats to AKI. Animals were sacrificed after receiving the experimental diets for 6 days. The left kidney was fixed in formaldehyde-buffer and stained with hematoxiline-eosin for histopathological analysis. The right kidney was cryopreserved for microarray analysis. Cryopreserved kidney was wrapped with aluminum foil and broken with a hammer previously wrapped with tape paper on a counter covered in aluminum. The pieces of the kidney were located in a mortar with liquid nitrogen to keep cryopreservation and were pulverized with a pestle. Nitrogen was added as it evaporated. The tissue was broken up to be completely pulverized. Powder was placed with a spatula in a cryotube supported on a dry ice with a layer of aluminum above. Before proceeding with another sample and to avoid contamination, the mortar, the pestle and the spatula were washed with tap water, distilled water and then alcohol. The tape of the hammer, the aluminum on the counter and the latex gloves were also replaced by new ones. Total RNA was purified from 30 milligrams of frozen rat kidney pools, using RNeasy Mini Kit [Qiagen GmbH, Hilden, Germany) according to the manufacturer's instructions. The biological concentration, integrity and quality of the RNA obtained were performing using NanoDrop 2000c (Thermo Fisher Scientific, Delaware, USA) and RIN (RNA Integrity Number). Five hundred nanograms of total RNA were processed and hybridized to Affymetrix GeneChip Rat Gene 1.0 ST Array (Affymetrix Inc, Singapore, Singapore), according to Ambion WT Expression Kit instructions (Ambion Inc, Texas, USA). Total RNA obtained during the tissue extraction was processed to obtain a double strand cDNA. After that we performed a in-vitro transcripition to generate antisence cRNA (aRNA). This aRNA was used to generate a single-stranded DNA (ss-DNA) using random primers and the dUTP +dNTP mix. The resulting single-stranded DNA (ss-DNA) containing the unnatural uracilbase is then treated with Uracil DNA Glycosylase, which specifically removes the uracilresidue from the ss-DNA molecules. In the same reaction, the APE 1 enzyme then cleaves the phosphodiester backbone where the base is missing, leaving a 3’-hydroxyland a 5’-deoxyribose phosphate terminus. Before this prosses, shorts ss-DNA fragments were labeled by terminal deoxynucleotidyl transferase (TdT) that covalently linked the 3’-hydrosyl phosphate terminus whit Biotin Allonamide Triphosphate. The GeneChip® Rat Gene 1.0 ST Array enables whole-genome, gene-level expression studies for well-characterized genes. It is a single GeneChip®-brand array comprised of more than 722 254 unique 25-mer oligonucleotide features accounting for more than 27 342 gene-level probe sets. Results were scanned with GeneChip® Scanner 3000 7G (Affymetrix Inc, Tokyo, Japan), and normalized by RMA algorithm using Affymetrix Expression Console Software. In addition, call values were retrieved by MAS5 algorithm, and only genes with a “p” (present) call value were used in the analysis. Differentially expressed genes were identified using limma (www.bioconductor.org) and “p” adjusted values and absolute log fold change greater than 1.5 were used for gene selection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24129499" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34225" }, "primaryId" : "GEO:GSE34225", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34225" } ] }, "title" : "Effect of dDAVP on outer medullary gene expression in Brattleboro rats", "dateAssigned" : "2011-12-07T00:00:00.000-06:00", "summary" : "We used microarray analysis of AVP-regulated gene products in a rat model of central diabetes insipidus (DI) to generate a comprehensive database documenting these changes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27681558" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34250" }, "primaryId" : "GEO:GSE34250", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34250" } ] }, "title" : "Cross-Species Comparisons of Transcriptomic Alterations in Human and Rat Primary Hepatocytes Exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin: rat samples", "dateAssigned" : "2011-12-08T00:00:00.000-06:00", "summary" : "A toxicogenomics approach was used to qualitatively and quantitatively compare the gene expression changes in human and rat primary hepatocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Hepatocytes from five individual rats and five individual humans were exposed for 24 hours to 11 concentrations of TCDD ranging from 0.00001 nM to 100 nM and a vehicle control. Gene expression changes were analyzed using whole genome microarrays.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24046277" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34272" }, "primaryId" : "GEO:GSE34272", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34272" } ] }, "title" : "Whole transcriptome sequencing reveals dynamic RNA changes in the aging rat brain", "dateAssigned" : "2011-12-08T00:00:00.000-06:00", "summary" : "Using RNA-seq, 9 cerebral cortex RNA samples were sequenced from 6 month (n=3, 6 individuals pooled), 12 month (n=3, 6 individuals pooled) and 28 month (n=3, 6 individuals pooled) rats. Allowing brain aging in the cerebral cortex to be assessed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22555619" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34411" }, "primaryId" : "GEO:GSE34411", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34411" } ] }, "title" : "Cardiovascular gene expression", "dateAssigned" : "2011-12-13T00:00:00.000-06:00", "summary" : "Tissue engineering of blood vessels and heart valves aims to create high quality prostheses, with preservation of their growth potential. However, the current markers used to identify the necessary cell phenotypes might not take the developmental properties of such structures into account.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34424" }, "primaryId" : "GEO:GSE34424", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34424" } ] }, "title" : "The Influence of Sleep Deprivation on Hippocampal CA1 Gene Expression: Relation to Stress and Aging", "dateAssigned" : "2011-12-13T00:00:00.000-06:00", "summary" : "Sleep deprivation (SD) in young adults is associated with metabolic, stress and cognitive responses that are also characteristic of brain aging. Given that sleep architecture changes with age, including increased fragmentation and decreased slow wave activity, it seems reasonable to investigate potential molecular relationships between SD and aging in brain tissue. Here, we tested the hypothesis that young rats exposed to 24 or 72 hour SD would respond with stress and aging-like shifts in brain hippocampal CA1 gene expression. SD animals showed blood corticosterone and weight changes consistent with a stress response. Microarray results, validated by Western blot and comparison to prior SD studies, pointed to disruptions in neurotransmission, sleep pressure signaling, and macromolecular synthesis. In a separate experiment, animals exposed to 24 or 72 hour novel environment stress recapitulated nearly one third of the SD transcriptional profile, particularly upregulated apoptotic and immune signaling pathways. Compared to aging (based on three previously published independent hippocampal aging studies), SD transcriptional profiles agreed for neurogenesis and energy pathways. However, immune signaling, glial activity, macromolecular synthesis and neuronal function all showed an SD profile that was, at least in part, opposed by aging. We conclude that while stress and SD have discrete molecular signatures, they do show a subset of highly similar changes. However, the same could not be said of aging and SD, where a similar subset of genes is changed, but in partially divergent directions. Finally, this work identifies presynaptic vesicular release and intercellular adhesion molecular signatures as novel targets for future SD-countering therapeutics.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22792227" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34451" }, "primaryId" : "GEO:GSE34451", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34451" } ] }, "title" : "Altered gene expression profiles in the hippocampus and prefrontal cortex of type 2 diabetic rats", "dateAssigned" : "2011-12-14T00:00:00.000-06:00", "summary" : "There has been an incresing body of epidemiologic and biochemical evidence implying the role of cerebral insulin resistance in Alzheimer-type dementia. For a better understanding of the insulin effect on the central nervous system we performed microarray-based gene expression profiling in the hippocampus, striatum and prefrontal cortex of streptozotocin-induced and spontaneously diabetic Goto-Kakizaki rats as model animals for type 1 and type 2 diabetes, respectively. Following pathway analysis and validation of gene lists by RT-PCR, 30 genes from hippocampus, such as the inhibitory neuropeptide galanin, synuclein gamma and uncoupling protein 2, and 22 genes from the prefrontal cortex, e.g. galanin receptor 2, protein kinase gamma and epsilon, ABCA1, CD47 and the RET protooncogene, were found to exhibit altered expression levels in type 2 diabetic model animals in comparison to non-diabetic control animals. These gene lists proved to be partly overlapping and encompassed genes related to neurotransmission, lipidmetabolism, neuronal development, insulin secretion, oxidative damage and DNA repair. On the other hand, no significant alterations were found in the transcriptomes of the corpus sriatum in the same animals. Changes in the cerebral gene expression profiles seemed to be specific for the type 2 diabetic model, as no such alterations were found in streptozotocin-treated animals. According to our knowledge this is the first characterization of the whole-genome expression changes of specific brain regions in a diabetic model. Our findings shed light on the complex role of insulin signaling in fine-tuning brain functions, and provide further experimental evidence in support of the recently elaborated theory of type 3diabetes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22369239" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34565" }, "primaryId" : "GEO:GSE34565", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34565" } ] }, "title" : "Male-dominant activation of rat renal organic anion transporter 1 (Oat1) and 3 (Oat3) expression by transcription factor BCL6", "dateAssigned" : "2011-12-19T00:00:00.000-06:00", "summary" : "Organic anion transporters 1 (Oat1) and 3 (Oat3) play a critical role in transport of organic anions, including frequently prescribed drugs, across cell membranes in proximal tubules of kidneys. In rats, these transporters are known to be male-predominant and testosterone dependently expressed. The molecular mechanisms that are involved in the sex-dependent expression are unknown. Our aim was to identify genes that show a sex-dependent expression and could be involved in sex-dependent regulation of Oat1 and Oat3.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22530049" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34614" }, "primaryId" : "GEO:GSE34614", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34614" } ] }, "title" : "Comprehensive expression analyses of neural cell type-specific miRNAs identify new determinants of the specification and maintenance of neuronal phenotypes.", "dateAssigned" : "2011-12-21T00:00:00.000-06:00", "summary" : "We performed microarray profiling of miRNA expression across the four principal cell types of the central nervous system: neurons, astrocytes, oligodendrocytes and microglia, isolated from rat cortex. Our microarray results showed that the four cell types differ extensively in their miRNA expression. Over one third of the 351 miRNAs examined had higher than 5-fold differences in expression between two of the four cell types. As expected, cell types of common developmental origin differed least in their miRNA expression profiles (astrocytes and oligodendrocytes), while neurons and microglia showed more unique miRNA expression profiles. 63 miRNAs showed cell type specific enrichment (39 miRNAs) or depletion (24 miRNAs) when comparing the four cell types using criteria of a minimum 5-fold difference in expression in one cell type compared to the average expression in the other three and minimum 2-fold change compared to each of the other three types individually and a false positive rate (FDR) p value lower than 0.01. When comparing only neurons, astrocytes and oligodendrocytes 115 miRNAs were specifically enriched (89 miRNAs) or depleted (36 miRNAs) in one cell type.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23516279" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34641" }, "primaryId" : "GEO:GSE34641", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34641" } ] }, "title" : "Sperm mRNA transcripts are indicators of sub-chronic low dose testicular injury in the Fischer 344 rat ", "dateAssigned" : "2011-12-21T00:00:00.000-06:00", "summary" : "Current human reproductive risk assessment methods rely on semen and serum hormone analyses, which are not easily comparable to the histopathological endpoints and mating studies used in animal testing. Because of these limitations, there is a need to develop universal evaluations that reliably reflect male reproductive function. We hypothesized that toxicant-induced testicular injury can be detected in sperm using mRNA transcripts as indicators of insult. To test this, we exposed adult male Fischer 344 rats to low doses of model testicular toxicants and classically characterized the testicular injury while simultaneously evaluating sperm mRNA transcripts from the same animals. Overall, this study aimed to: 1) identify sperm transcripts altered after exposure to the model testicular toxicant, 2,5-hexanedione (HD) using microarrays; 2) expand on the HD-induced transcript changes in a comprehensive time course experiment using qRT-PCR arrays; and 3) test these injury indicators after exposure to another model testicular toxicant, carbendazim (CBZ). Microarray analysis of HD-treated adult Fischer 344 rats identified 128 altered sperm mRNA transcripts when compared to control using linear models of microarray analysis (q < 0.05). All transcript alterations disappeared after 3 months of post-exposure recovery. In the time course experiment, time-dependent alterations were observed for 12 candidate transcripts selected from the microarray data based upon fold change and biological relevance, and 8 of these transcripts remained significantly altered after the 3-month recovery period (p < 0.05). In the last experiment, 8 candidate transcripts changed after exposure to CBZ (p < 0.05). The two testicular toxicants produced distinct molecular signatures with only 4 overlapping transcripts between them, each occurring in opposite directions. Overall, these results suggest that sperm mRNA transcripts are indicators of low dose toxicant-induced testicular injury in the rat. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22952946" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34651" }, "primaryId" : "GEO:GSE34651", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34651" } ] }, "title" : "Mechanisms of Pancreatic Acinar Cell Neoplasia Associated with Gene Expression Changes caused by Dietary Exposure of Rats to Ammonium perfluorooctanoate, Wyeth 14,643 or Diethylhexyl phthalate", "dateAssigned" : "2011-12-22T00:00:00.000-06:00", "summary" : "To assess whether this putative mechanism(s) of carcinogenesis occurs in ‘target’ cells we have also performed transcriptional profiling in isolated pancreatic acinar cells obtained from animals exposed to these compounds in vivo.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34737" }, "primaryId" : "GEO:GSE34737", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34737" } ] }, "title" : "Comparative analysis of mRNA expression in untreated lymph node stroma cells and upon treatment with exosomes derived from ASMLwt, ASML cd44v knockdown cells.", "dateAssigned" : "2011-12-27T00:00:00.000-06:00", "summary" : "Comparison of total RNA isolated from ASML and ASML CD44v knockdown exosomes; and RNA from untreated B12 lymph node stroma cells vs. cells treated for 24h with ASML wt or ASML CD44v kd exosomes", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23479506" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34738" }, "primaryId" : "GEO:GSE34738", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34738" } ] }, "title" : "Characterization of exosomes from highly metastatic pancreatic adenocarcinoma line: ASML and a CD44v kd of ASML based on their miRNA content", "dateAssigned" : "2011-12-27T00:00:00.000-06:00", "summary" : "Comparing the miRNA profile of exosomes from ASML vs ASML CD44v kd pancreatic adenocarcinoma line revealed that the expression level of 33 from the 40 most abundant miRNA differed significantly between ASMLwt and ASML-CD44vkd exosomes", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23479506" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34772" }, "primaryId" : "GEO:GSE34772", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34772" } ] }, "title" : "Expression data from Ad-ß-catenin-GFP or Ad-GFP infected cardiomyocytes", "dateAssigned" : "2011-12-29T00:00:00.000-06:00", "summary" : "We used DNA microarrays to detail the global trends in gene expression underlying ß-catenin-overexpressed cardiomyocytes and identified distinct classes of up- or down-regulated genes during this process. Our findings suggest that ß-catenin plays a critical role in regulating cardiac dysfunction at transcriptional level and may provide novel insight into how ß-catenin modulates heart diseases.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34790" }, "primaryId" : "GEO:GSE34790", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34790" } ] }, "title" : "Differential Expression of microRNAs following activated protein C treatment in a rat model of septic shock", "dateAssigned" : "2011-12-30T00:00:00.000-06:00", "summary" : "Sepsis induces systemic stress by augmenting inflammatory and pro-coagulant responses resulting in microvascular dysfunction and end organ failure, events modulated by the Protein C pathway. MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional regulation of gene transcription yet their role in sepsis remains poorly defined. We hypothesized that aPC selectively alters the expression of specific miRNAs implicated in protection of hepatic function during septic shock. Male Sprague-Dawley rats underwent sham surgery or cecal ligation and puncture (CLP). Twenty-four later, animals were randomized and treated with aPC (1mg/kg) or vehicle (0.9% (w/v) saline) via an indwelling venous catheter at 12 hour intervals for 24 hours. Gene array was performed on hepatic RNA to determine miRNA expression, and predicted mRNA targets determined using a bioinformatics approach. Of 351 rat miRNAs examined by microarray hybridization, 17 were highly expressed during sepsis and restored to basal levels after aPC treatment. In silico analysis identified 9 miRNAs significantly regulating target genes of the focal adhesion pathway. These data suggest aPC treatment coordinates beneficial cytoprotective effects during sepsis by modulating miRNA expression. While translational effects remain to be fully elucidated in a clinical setting, we demonstrate herein the potential experimental and computational benefits for use of microRNA analysis in sepsis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34811" }, "primaryId" : "GEO:GSE34811", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34811" } ] }, "title" : "Gene expression profiling of myelin-phagocytosing macrophages", "dateAssigned" : "2012-01-03T00:00:00.000-06:00", "summary" : "Here we demonstrate, by using genome wide gene expression analysis, that myelin-phagocytosing macrophages have an enhanced expression of genes in pathways involved in migration, phagocytosis and inflammation. More interestingly, we show that myelin internalization induces the expression of genes involved in liver X receptor signaling and cholesterol efflux. In vitro validation shows that myelin-phagocytosing macrophages indeed have an increased capacity to dispose intracellular cholesterol. Additionally, myelin suppresses the production of pro-inflammatory mediators, like nitric oxide and IL-6, by macrophages in a similar manner as a liver X receptor agonist. Our data show that myelin modulates the phenotype of macrophages by nuclear receptor activation, which may subsequently affect lesion progression in multiple sclerosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22984598" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34868" }, "primaryId" : "GEO:GSE34868", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE34868" } ] }, "title" : "Immunodominant myelin basic protein fragments induce mechanical hypersensitivity.", "dateAssigned" : "2012-01-04T00:00:00.000-06:00", "summary" : "An insulating myelin sheath ensures saltatory conduction of mechanosensory A afferents. Myelin damage results in the electrical instability of A fibers and the ability to generate pain in response to light touch/pressure (mechanical allodynia). We have hypothesized and then established that the release of T cell epitopes of myelin basic protein (MBP) enables nociceptive circuitry in myelinated fibers. Thus, mass spectrometry analysis of the rat sciatic nerve proteome followed by bioinformatics examination of the datasets revealed a loss of MBP and activation of T-helper cell signaling in the nerves undergoing chronic constriction injury (CCI). Matrix metalloproteinase-9 (MMP-9) proteolysis resulted in the MBP digest peptides, including the MBP84-104 and MBP68-86 regions, which exhibit prominent immunogenic epitopes. Myelin-forming Schwann cells and paranodal areas accumulated MHCII, MMP-9 and the degraded MBP at the sciatic nerve injury site. Administration of the immunodominant MBP84-104 and MBP68-86 peptides but not of the control peptides in a naïve rat sciatic nerve produced robust mechanical allodynia. Allodynia was accompanied by the T cell infiltration and an increase in MHCII, IL-17A and TNF- levels at the nerve injection site and the segmental ganglia. The pro-nociceptive activity of the synthetic MBP84-104 diminished in athymic nude rats lacking T cells. SB-3CT, an antagonist of MMP-9, inhibited mechanical allodynia, neuroinflammation and spinal sensitization after CCI. Collectively, our novel data implicate, for the first time, MMP-mediated cleavage of MBP and the resulting MBP digest fragments as a major cause of neuropathic pain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22676642" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35048" }, "primaryId" : "GEO:GSE35048", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35048" } ] }, "title" : "Sirolimus induced phosphaturia", "dateAssigned" : "2012-01-12T00:00:00.000-06:00", "summary" : "Male Wistar rats received sirolimus or vehicle for 7 days (1.5mg/kg) and were placed in individual metabolic cages for eight days allowing a 24 hour adaption period to the metabolic cage environment. At the end of the experiments rats were anesthetized by inhalation of Isoflurane/air and blood samples and kidneys were collected.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22859939" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35088" }, "primaryId" : "GEO:GSE35088", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35088" } ] }, "title" : "Regulation of gene expression with thyorid hormone in rats with myocardial infarction", "dateAssigned" : "2012-01-13T00:00:00.000-06:00", "summary" : "Thyroid hormone improves left ventricular remodeling and cardiac performance after myocardial infarction (MI), but the molecular basis is unknown. This study was designed to detect gene expression changes in left ventricular non-infarcted areas at 4 weeks following myocardial infarction with and without thyroid hormone treatment. The results suggest that altered expression of genes for molecular function and biological process may be involved in the beneficial effects of thyroid hormone treatment following myocardial infarction in rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35089" }, "primaryId" : "GEO:GSE35089", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35089" } ] }, "title" : "Molecular Characterization of Laser Microdissected Circumventricular Organs and Third Ventricle Ependyma in the Adult Rat by Microarray Analysis.", "dateAssigned" : "2012-01-13T00:00:00.000-06:00", "summary" : "We used LCM and microarrays to analyze the transcriptomes of three CVOs, the SCO, the subfornical organ (SFO), and the PG, and the third ventricle ependyma in the adult rat in order to better characterize these organs at the molecular level. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22537279" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35132" }, "primaryId" : "GEO:GSE35132", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35132" } ] }, "title" : "Genome-wide analysis of EGR2/SOX10 binding in myelinating peripheral nerve", "dateAssigned" : "2012-01-17T00:00:00.000-06:00", "summary" : "We provide ChIP-Seq analysis of Egr2 and Sox10 transcription factor binding in Schwann cells of rat peripheral nerve", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22492709" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35167" }, "primaryId" : "GEO:GSE35167", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35167" } ] }, "title" : "Global gene expression profiling in PPAR-¿ agonist-treated kidneys in an orthologous rat model of human autosomal recessive polycystic kidney disease", "dateAssigned" : "2012-01-18T00:00:00.000-06:00", "summary" : "Kidneys are enlarged by aberrant proliferation of tubule epithelial cells leading to the formation of numerous cysts, nephron loss, and interstitial fibrosis in polycystic kidney disease (PKD). Pioglitazone (PIO), a PPAR-¿ agonist, decreased cell proliferation, interstitial fibrosis and inflammation, and ameliorated PKD progression in PCK rats. To examine the genetic mechanisms in this efficacy, we analyzed changes in global gene expression. By Gene Set Enrichment Analysis of 30655 genes, 13 of the top 20 down-regulated gene ontology biological process gene sets, and six of the top 20 curated gene set canonical pathways identified to be down-regulated by PIO-treatment were related to cell cycle and proliferation, including EGF, PDGF and JNK pathways. Their relevant pathways were identified using the Kyoto Encyclopedia of Gene and Genomes database. Stearoyl-Coenzyme A desaturase 1 is a key enzyme in fatty acid metabolism found in the top 5 genes down-regulated by PIO treatment. Immunohistochemical analysis revealed that the gene product of this enzyme was highly expressed in PCK kidneys, and decreased by PIO. These data show that PIO alters the expression of genes involved in cell cycle progression, cell proliferation, and fatty acid metabolism.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21147840" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35270" }, "primaryId" : "GEO:GSE35270", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35270" } ] }, "title" : "Whole-Genome Transcriptome Profiling of Microvascular Free Flaps", "dateAssigned" : "2012-01-23T00:00:00.000-06:00", "summary" : "In our study, we developed a venous obstruction rat model in which the superficial inferior epigastric (SIE) vessels to the lower abdominal flaps was separated and artery or vein was ligated, and the flap reattached. Flaps were harvested 4 hours post-op. Total RNA was isolated and gene expression profiles were compared by Affymetrix Whole Genome 230 2.0.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35285" }, "primaryId" : "GEO:GSE35285", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35285" } ] }, "title" : "Defining the Phosphodiesterase Superfamily Members in Rat Brain Microvessels", "dateAssigned" : "2012-01-23T00:00:00.000-06:00", "summary" : "A filtration method followed by microarray analyses allows PDE components to be identified in brain microvessels, and confirmed that PDE4D and PDE5A are the primary forms expressed in rat brain microvessels.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35393" }, "primaryId" : "GEO:GSE35393", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35393" } ] }, "title" : "Skeletal myoblasts protect cardiomyocytes against oxidative stress via c-Met and epidermal growth factor receptor (EGFR)-dependent paracrine pathways", "dateAssigned" : "2012-01-27T00:00:00.000-06:00", "summary" : "To study the effect of myoblast-derived paracrine factors on cardiomyocyte gene expression, microarray analysis was performed from isolated rat fetal cardiomyocyte cultures. These cultures were treated for 24 hours with fresh culture medium (control), skeletal myoblast-conditioned medium, or cardiac fibroblast-conditioned medium.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35555" }, "primaryId" : "GEO:GSE35555", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35555" } ] }, "title" : "Expression data from a model of renal deceased by cardiac death (DCD) donation in rat", "dateAssigned" : "2012-02-05T00:00:00.000-06:00", "summary" : "In DCD organ donation one of the significant problems for the organ is the inflammatory response due to ischaemiua reperfusion injury caused by warm ischaemia prior to retrieval followed by warm reoxygenation upon transplantation. We developed a model where a DCD kidney was retrieved and stoired overnight then the organ was surgically attached to the femoral artery of a recipient rat and blood flow restored for up to six hours to simulate early ischaemia reperfusion injury (IRI). The recipient rats consisted of a control group compared to groups recieveing either low molecular weight heparin or an anti-inflammatory peptide to assess their activity in ameliorating IRI. We used equimolar pooled RNA samples from each group to perform an exploratory microarray experiment.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35598" }, "primaryId" : "GEO:GSE35598", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35598" } ] }, "title" : "Osmolality as a major regulator of the transcriptome and metabolome in kidney collecting duct cells", "dateAssigned" : "2012-02-07T00:00:00.000-06:00", "summary" : "We hypothesized that altered extracellular osmolality per se could affect the transcriptome of the kidney inner medullary collecting duct (IMCD) cells, and hence it might change renal tubular function. The data sets of transcriptomics were incorporated into the \"omic\" data sets of metabolomics. Primary cultured IMCD cells of rat kidney were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 4 d, and then the cells were cultured in the medium with either reduced (300 mOsm/KgH2O) or the same osmolality for 1 or 2 d more.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22686594" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35607" }, "primaryId" : "GEO:GSE35607", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35607" } ] }, "title" : "Genes expressed in age-induced mitochondrial DNA deletion mutation containing / Electron Transport abnormal cells", "dateAssigned" : "2012-02-07T00:00:00.000-06:00", "summary" : "Muscle tissue was longitudinally characterized histologically for electron transport function by staining 1mm of quadriceps muscle at 70 micron intervals for the activities of two complexes in the mitochondrial electron transport chain, Cytochrome C Oxidase and Succinate Dehydrogenase. Unstained serial cryosections were prepared for Laser Capture Microdissection. Target cells from the serial sections were isolated and pooled for RNA extraction, amplification and hybridization on Affymetrix microarrays. We selected homogeneous populations of muscle fibers for expression profiling based upon the presence/absence of electron transport dysfunction caused by the somatic accumulation of mitochondrial DNA deletion mutations.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23516592" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35623" }, "primaryId" : "GEO:GSE35623", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35623" } ] }, "title" : "Functional inactivation of Thyroid Transcription Factor-1 in PCCl3 thyroid cells", "dateAssigned" : "2012-02-08T00:00:00.000-06:00", "summary" : "The expression of a fusion protein composed of the DNA binding domain of TTF-1 and of the strong repressive domain of the Engrailed protein (Engr HD) resulted in a dramatic loss of epithelial cell morphology and in proliferation arrest. These changes were reversed when the inhibition of endogenous TTF-1 was relieved. No change was observed when a similar fusion protein containing point mutations abolishing DNA binding activity (Engr HDm) was produced in the cells. ", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35627" }, "primaryId" : "GEO:GSE35627", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35627" } ] }, "title" : "Expression data from Angiotensin II (Ang II)-treated Rat Vascular Smooth Muscle Cells (RVSMC)", "dateAssigned" : "2012-02-08T00:00:00.000-06:00", "summary" : "We used Rat Affymetrix gene array to profile Ang II-regulated gene in RVSMC and evaluated their role in VSMC dysfunction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22431733" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35664" }, "primaryId" : "GEO:GSE35664", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35664" } ] }, "title" : "High-throughput sequencing of endogenous small RNAs from rat vascular smooth muscle cells with and without Angiotensin II stimulation", "dateAssigned" : "2012-02-09T00:00:00.000-06:00", "summary" : "Angiotensin II (Ang II)-mediated vascular smooth muscle cells (VSMC) dysfunction plays a critical role in cardiovascular diseases. However, the role of microRNAs (miRNAs) in this process is unclear. We used small RNA deep sequencing to profile Ang II-regulated miRNAs in rat VSMC and evaluated their role in VSMC dysfunction. Sequencing results revealed several Ang II-responsive miRNAs and bioinformatics analysis showed that their predicted targets can modulate biological processes relevant to cardiovascular diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22431733" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35697" }, "primaryId" : "GEO:GSE35697", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35697" } ] }, "title" : "Mechanistic evaluation of the insulin response in H4IIE hepatoma cells: New endpoints for toxicity testing?", "dateAssigned" : "2012-02-10T00:00:00.000-06:00", "summary" : "DNA microarray analysis, real-time PCR and flow cytometric cell cycle analysis were used to assess the relevance of the insulin response in H4IIE cells. Insulin dose dependently stimulated H4IIE growth. Time dependency of the insulin response was shown with real-time PCR for the known insulin responsive genes: Fasn, Pck1 and Irs2. Based on these results, microarray analysis was performed on H4IIE cells exposed to insulin (100 nM) for 6h and 24h. Genes related to carbohydrate (glycolysis and gluconeogenesis) and lipid metabolism (glycerolipid metabolism, cholesterol synthesis and fatty acid oxidation) were most profoundly afflicted, in accordance with in vivo insulin action in liver. Since changes in carbohydrate and lipid metabolism are pivotal in the pathogenesis of insulin resistance, the presence of a physiological relevant insulin response in H4IIE cells pleads for further testing of its potential use in research on pollutant-driven insulin resistance.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22652326" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35839" }, "primaryId" : "GEO:GSE35839", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35839" } ] }, "title" : "Environmentally Induced Epigenetic Transgenerational Inheritance of Somatic Transcriptomes", "dateAssigned" : "2012-02-15T00:00:00.000-06:00", "summary" : "We used microarrays to determine genes expressed differentially in rats 11 male or female smatic tissues -male heart, kidney, liver, testis, prostate, seminal vesicles; female heart, kidney, liver, ovary, uterus - due to Vinclozolin treatments of their grand-grandmothers.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23034163" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35841" }, "primaryId" : "GEO:GSE35841", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35841" } ] }, "title" : "Derivation of rat induced pluripotent stem cells that share similarities with embryonic stem cells using a transposon system", "dateAssigned" : "2012-02-15T00:00:00.000-06:00", "summary" : "Here, we employed the PiggyBac (PB) transposon carrying four 2A peptide-linked reprogramming factors for generating rat IPS cells. These stable rat IPS cells are similar to embryonic stem (ES) cells in morphology, proliferation, teratoma formation, expression characteristic pluripotency markers, developmental potential, and germline transmission. Transcriptional profiling of the IPS cells revealed both pathways in common with ES cells from rat and unique signaling pathway to our cells, including Wnt, TGF and Notch. The cell lines and information obtained in this study will accelerate our understanding of the molecular regulation underlying germline pluripotency and pave the way for exploration of cell-based therapies using the rat.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35976" }, "primaryId" : "GEO:GSE35976", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE35976" } ] }, "title" : "Genome wide array analysis of endosseous implant adherent cellular phenotypes", "dateAssigned" : "2012-02-21T00:00:00.000-06:00", "summary" : "Objective: to identify the early molecular processes involved in osseointegration associated with a micro roughened and nanosurface featured implants.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22884725" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36010" }, "primaryId" : "GEO:GSE36010", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36010" } ] }, "title" : "mRNA profiles after experimental ischemia", "dateAssigned" : "2012-02-22T00:00:00.000-06:00", "summary" : "To analyze gene expression we isolated total mRNA from the core, periinfarct and contralateral cortex of 60 sprague-dawley rats after 24 hours or 3 days of permanent middle cerebral artery occlusion (pMCAo). Also ipsilateral and contralateral cortex was obtained from sham-operated and healthy animals. A total of 44 microarrays were performed with RNA pooled from 3 independent animals. For each experimental condition the total n number is of 12.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23284893" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36037" }, "primaryId" : "GEO:GSE36037", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36037" } ] }, "title" : "Use of microarray analyses to determine the effect of hyperoxia and hypoxia on gene expression in early oxygen-induced retinopathy (OIR).", "dateAssigned" : "2012-02-23T00:00:00.000-06:00", "summary" : "Different inbred strains of rats differ in their susceptibility to OIR, an animal model of human retinopathy of prematurity. We examined gene expression profiles in Fischer 344 (F344, resistant to OIR) and Sprague Dawley (SD, susceptible to OIR) rats at the early time points of day 5 (in response to hyperoxia) and day 6 (in response to relative hypoxia) to identify gene pathways related to the underlying genetic cause of the phenotypic differences observed between strains.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36067" }, "primaryId" : "GEO:GSE36067", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36067" } ] }, "title" : "Role of microRNAs in compensatory b-cell mass expansion associated with pregnancy and obesity", "dateAssigned" : "2012-02-24T00:00:00.000-06:00", "summary" : "We found that in rodents, b-cell mass expansion during pregnancy and obesity is associated with changes in the expression of a group of islet microRNAs. We were able to reproduce in isolated pancreatic islets the decrease of miR-338-3p level observed in gestation and obesity by activating the G-protein coupled estrogen receptor GPR30 and the GLP1 receptor. Blockade of miR-338-3p in b-cells using specific anti-miR molecules mimicked gene expression changes occurring during b-cell mass expansion and resulted in increased proliferation and improved survival both in vitro and in vivo. These findings point to a major role for miR-338-3p in compensatory b-cell mass expansion occurring under different insulin resistance states.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22996663" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36101" }, "primaryId" : "GEO:GSE36101", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36101" } ] }, "title" : "Genomic profiles of oxidative stress-induced rat renal cell carcinomas", "dateAssigned" : "2012-02-27T00:00:00.000-06:00", "summary" : "Intraperitoneal administration of ferric nitrilotriacetate (Fe-NTA) initiates Fenton reaction in the renal proximal tubules of rodents that ultimately leads to a high incidence of renal cell carcinoma (RCC) after repeated treatment. We performed high-resolution microarray comparative genomic hybridization to identify characteristics in the genomic profiles of oxidative stress-induced rat RCCs. The results revealed extensive large-scale genomic alterations with a preference for deletion.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22952676" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36109" }, "primaryId" : "GEO:GSE36109", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36109" } ] }, "title" : "Reproducibility of global gene expression in rat lung", "dateAssigned" : "2012-02-27T00:00:00.000-06:00", "summary" : "Expression analyses in 01matsu and 01suzu rat lung. Both prepared under the same conditions, and the comparison is between the reproducibility of the experiment as performed by two different individuals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36122" }, "primaryId" : "GEO:GSE36122", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36122" } ] }, "title" : "Platelet-derived growth factor-alpha (PDGF-a) stimulates intestinal epithelial cell turnover after massive small bowel resection in a rat", "dateAssigned" : "2012-02-28T00:00:00.000-06:00", "summary" : "Numerous cytokines have been shown to affect epithelial cell differentiation and proliferation through epithelial-mesenchymal interaction. Growing evidence suggests that platelet-derived growth factor (PDGF) signaling is an important mediator of these interactions. The purpose of this study was to evaluate the effect of PDGF-a on enterocyte turnover in a rat model of short bowel syndrome (SBS). Male rats were divided into four groups: Sham rats underwent bowel transection, Sham-PDGF-a rats underwent bowel transection and were treated with PDGF-a, SBS rats underwent a 75% bowel resection, and SBS-PDGF-a rats underwent bowel resection and were treated with PDGF-a. Parameters of intestinal adaptation, enterocyte proliferation and apoptosis were determined at sacrifice. Illumina's Digital Gene Expression (DGE) analysis was used to determine PDGF-related gene expression profiling. PDGF-a and PDGF-a receptor (PDGFR-a) expression was determined using Real Time PCR. Western blotting was used to determine p-ERK, Akt1/2/3, bax and bcl-2 protein levels. SBS rats demonstrated a significant increase in PDGF-a and PDGFR-a expression in jejunum and ileum compared to sham animals. SBS-PDGF-a rats demonstrated a significant increase in bowel and mucosal weight, villus height and crypt depth in jejunum and ileum compared to SBS animals. PDGF-a expression in crypts increased in SBS rats (vs sham) and was accompanied by increased cell proliferation following PDGF-a administration. A significant decrease in cell apoptosis in this group was correlated with lower bax protein levels. In conclusion, in a rat model of SBS, PDGF-a stimulates enterocyte turnover, which is correlated with up-regulated PDGF-a receptor expression in the remaining small intestine.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22461028" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36144" }, "primaryId" : "GEO:GSE36144", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36144" } ] }, "title" : "Characterization of chemically induced malignant peripheral nerve sheath tumors (MPNSTs) in the rat by expression profiling", "dateAssigned" : "2012-02-28T00:00:00.000-06:00", "summary" : "Identification of differentially expressed genes in ENU induced MPNSTs and normal tissue from rat Nervus trigeminus by expression profiling", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36174" }, "primaryId" : "GEO:GSE36174", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36174" } ] }, "title" : "LPS-induced expression in rat lung epithelial cells", "dateAssigned" : "2012-02-29T00:00:00.000-06:00", "summary" : "Microarray analysis of mRNA from airway epithelial cells captured by laser microdissection from rat lungs snap-frozen at day 0 and day 2 post LPS exposure was performed to identify inflammatory mediators modulated by LPS exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22461702" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36208" }, "primaryId" : "GEO:GSE36208", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36208" } ] }, "title" : "Transcriptomics Analysis of Lungs and Peripheral Blood of Crystalline Silica Exposed Rats", "dateAssigned" : "2012-03-01T00:00:00.000-06:00", "summary" : "Non-invasive or minimally invasive surrogate approaches to detect/predict target organ toxicity have significant practical applications in occupational toxicology. Presently, using a rat model, we have investigated the potential application of peripheral blood transcriptomics as a practical approach to study the mechanisms of silica-induced pulmonary toxicity. Rats were exposed by inhalation to crystalline silica for one week (15 mg/m3, 6-hours/day, 5 days/week). Pulmonary toxicity and global gene expression profiles of lungs and peripheral blood were determined in the control and silica exposed rats at 32-weeks following termination of silica exposure. A significant elevation in bronchoalveolar lavage fluid (BALF) lactate dehydrogenase (LDH) activity and moderate histological changes in the lungs, including type II pneumocyte hyperplasia and fibrosis, indicated silica-induced pulmonary toxicity in the rats. Similarly, significant infiltration of neutrophils and elevated monocyte chemotactic protein-1 (MCP1) level in the lungs suggested silica-induced pulmonary inflammation in the rats. Microarray analysis of global gene expression profiles identified significant differential expression (>1.5 fold change and FDR p<0.01) of 520 and 537 genes, respectively, in the lungs and blood of the silica exposed rats. Bioinformatics analysis of the differentially expressed genes demonstrated significant similarity in the biological processes, molecular networks, and canonical pathways enriched by silica exposure in the lungs and blood of the rats. Several genes involved in functions relevant to silica-induced pulmonary toxicity such as inflammation, respiratory diseases, cancer, cellular movement, fibrosis, etc, were found significantly differentially expressed in the lungs and blood of the silica exposed rats. The results of this study, in addition to providing molecular insights into the mechanisms underlying silica-induced pulmonary toxicity, suggested the potential application of peripheral blood gene expression profiling as a toxicologically relevant and minimally invasive surrogate approach to study the mechanisms underlying silica-induced pulmonary toxicity. Non-invasive or minimally invasive surrogate approaches to detect/predict target organ toxicity have significant practical applications in occupational toxicology. Presently, using a rat model, we have investigated the potential application of peripheral blood transcriptomics as a practical approach to study the mechanisms of silica-induced pulmonary toxicity. Rats were exposed by inhalation to crystalline silica for one week (15 mg/m3, 6-hours/day, 5 days/week). Pulmonary toxicity and global gene expression profiles of lungs and peripheral blood were determined in the control and silica exposed rats at 32-weeks following termination of silica exposure. A significant elevation in bronchoalveolar lavage fluid (BALF) lactate dehydrogenase (LDH) activity and moderate histological changes in the lungs, including type II pneumocyte hyperplasia and fibrosis, indicated silica-induced pulmonary toxicity in the rats. Similarly, significant infiltration of neutrophils and elevated monocyte chemotactic protein-1 (MCP1) level in the lungs suggested silica-induced pulmonary inflammation in the rats. Microarray analysis of global gene expression profiles identified significant differential expression (>1.5 fold change and FDR p<0.01) of 520 and 537 genes, respectively, in the lungs and blood of the silica exposed rats. Bioinformatics analysis of the differentially expressed genes demonstrated significant similarity in the biological processes, molecular networks, and canonical pathways enriched by silica exposure in the lungs and blood of the rats. Several genes involved in functions relevant to silica-induced pulmonary toxicity such as inflammation, respiratory diseases, cancer, cellular ", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36239" }, "primaryId" : "GEO:GSE36239", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36239" } ] }, "title" : "MicroRNA profiling of the failing heart after myocardial infarction induction and doxorubicin treatment", "dateAssigned" : "2012-03-02T00:00:00.000-06:00", "summary" : "The use of anthracycline antibiotics such as doxorubicin (DOX) has greatly improved the mortality and morbidity of cancer patients. However, the associated risk of cardiomyopathy has limited their clinical application. DOX-associated cardiotoxicity is irreversible and progresses to heart failure (HF). For this reason, a better understanding of the molecular mechanisms underlying these adverse cardiac effects is essential to develop improved regimes that include cardioprotective strategies. MicroRNAs (miRNAs) are short non-coding RNAs that are able to post-trascriptionally regulate gene expression. MiRNAs have been demonstrated to be involved in both cancer and cardiovascular disease. Therefore, we were interested in unveiling the potential role of miRNAs in chemotherapy-induced HF. We used a combination of three different models to recreate this cardiac toxicity (acute in vitro DOX treatment, DOX-induced HF in vivo and a myocardial infarction -MI- leading to failure model) to study the pattern of dysregulated miRNAs. Using RNA from all three conditions, miRNA microarray profiling was performed and a common miRNA signature was identified. Interestingly, these dysregulated miRNAs have been previously identified as involved in the failing heart. Our results suggest that DOX is able to alter the expression of miRNAs implicated in HF, in vitro as well as in vivo.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36256" }, "primaryId" : "GEO:GSE36256", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36256" } ] }, "title" : "Differential expression of miRNA in stretched rat alveolar epithelial cells", "dateAssigned" : "2012-03-04T00:00:00.000-06:00", "summary" : "Cyclic stretch of alveoli is characteristic of mechanical ventilation, and is postulated to be partly responsible for the lung injury and inflammation in ventilator induced lung injury. We propose that miRNAs may regulate some of the stretch response and, therefore, hypothesized that miRNAs would be differentially expressed between stretched and unstretched rat alveolar epithelial cells (RAECs).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22537220" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36446" }, "primaryId" : "GEO:GSE36446", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36446" } ] }, "title" : "Genome-wide analysis of renal gene expression during hyperoxaluria development", "dateAssigned" : "2012-03-12T00:00:00.000-05:00", "summary" : "HLP was used to induce hyperoxaluria. Hyperoxaluria will lead to crystallization and up regulation of various NADPH oxidase subunits followed by increased expression of different specific genes. It is our hypothesis that crystallization induces inflammation of the kidneys via the activation of renin-angiotensin system (RAS) and production of reactive oxygen species (ROS) through NADPH oxidase complex. Apocynin was used to block hyperoxaluria and production of reactive oxygen species (ROS) with the inhibition of NADPH oxidase system as Apocynin inhibits membrane translocation of p47 subunit of NADPH oxidase.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24598804" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36524" }, "primaryId" : "GEO:GSE36524", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36524" } ] }, "title" : "Comparison of hepatocarcinogen-induced gene expression profiles in conventional primary rat hepatocytes with in vivo rat liver", "dateAssigned" : "2012-03-15T00:00:00.000-05:00", "summary" : "At present, substantial efforts are focused on the development of in vitro assays coupled with ”omics” technologies for the identification of carcinogenic substances as an alternative to the classical 2-year rodent carcinogenicity bioassay. A prerequisite for the eventual regulatory acceptance of such assays, however, is the in vivo relevance of the observed in vitro findings.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22484513" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36577" }, "primaryId" : "GEO:GSE36577", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36577" } ] }, "title" : "Chromosomal aberration of asbestos-induced malignant mesothelioma in rats", "dateAssigned" : "2012-03-16T00:00:00.000-05:00", "summary" : "Exposure to asbestos is a risk for malignant mesothelioma in humans. We carried out array comparative genomic hybridization (CGH) analysis in a rat model by repeated intraperitoneal injections of three types of asbestos including chrysotile, crocidolite and amosite. We found a common chromosomal deletion mapped to the chromosome 5q32 locus, containing the genes encoding tumour suppressor genes CDKN2A/2B/ARF. Homozygous deletion of CDKN2A/2B/ARF was observed in the majority (92.6%) of the rat MM samples.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22864872" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36596" }, "primaryId" : "GEO:GSE36596", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36596" } ] }, "title" : "Functional Comparison of Chronological and In Vitro Aging: Differential Role of the Cytoskeleton and Mitochondria in Mesenchymal Stromal Cells", "dateAssigned" : "2012-03-19T00:00:00.000-05:00", "summary" : "Mesenchymal stromal cells (MSCs) are of high relevance for the regeneration of mesenchymal tissues such as bone and cartilage. The promising role of MSCs in cell-based therapies and tissue engineering appears to be limited due to a decline of their regenerative potential with increasing donor age, their limited availability in human tissues and the need of in vitro expansion prior to treatment. We therefore aimed to determine to which degree in vitro aging and chronological aging may be similar processes or if in vitro culture-related changes at the cellular and molecular level are at least altered as a function of donor age. For that purpose we established MSCs cultures from young (yMSCs) and aged (aMSCs) rats that were cultured for more than 100 passages. These long-term MSCs cultures were non-tumorigenic and exhibited similar surface marker patterns as primary MSCs of passage 2. During in vitro expansion, but not during chronological aging, MSCs progressively lose their progenitor characteristics, e.g., complete loss of osteogenic differentiation potential, diminished adipogenic differentiation, altered cell morphology and increased susceptibility towards senescence. Transcriptome analysis revealed that long-term in vitro MSCs cultivation leads to down-regulation of genes involved in cell differentiation, focal adhesion organization, cytoskeleton turnover and mitochondria function. Accordingly, functional analysis demonstrated altered mitochondrial morphology, decreased antioxidant capacities and elevated ROS levels in long-term cultivated yMSCs as well as aMSCs. Notably, only the MSC migration potential and their antioxidative capacity were altered by in vitro as well as chronological aging. Based on specific differences observed between the impact of chronological and in vitro MSC aging we conclude that both are distinct processes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23285157" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36671" }, "primaryId" : "GEO:GSE36671", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36671" } ] }, "title" : "Expression data from an ex vivo ischaemia reperfusion model of renal deceased by cardiac death (DCD) donation in rat", "dateAssigned" : "2012-03-21T00:00:00.000-05:00", "summary" : "We used equimolar pooled RNA samples from each group to perform an exploratory microarray experiment", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36714" }, "primaryId" : "GEO:GSE36714", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36714" } ] }, "title" : "Gene expression changes in anti-diabetic treated Zucker diabetic rats", "dateAssigned" : "2012-03-22T00:00:00.000-05:00", "summary" : "Transcriptional profiling of insulin-sensitive tissues comparing control untreated ZDF rat with ZDF rat treated with three different anti-diabetic drugs and ZLC rat.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36722" }, "primaryId" : "GEO:GSE36722", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36722" } ] }, "title" : "Genomic transcriptional profiling identifies candidates genes for successful aging", "dateAssigned" : "2012-03-22T00:00:00.000-05:00", "summary" : "The inbred LOU/C/Jall rat is currently described as a model of successful aging. These rats have a longer healthy median lifespan than other strains, do not develop obesity, diabetes, or tumor and more importantly they do not show cognitive decline with aging. This is the first study to examine gene expression changes in the inbred LOU/C/Jall rat hippocampus and frontal cortex. Microarray data from LOU/C/Jall rats aged of 5 months were compared to the one measured in rats aged of 26 month. We have identified a set of 15 genes in the hippocampus and 70 genes in the frontal cortex that could be grouped into several clusters of similar expression profiles and that are involved in biological functions, namely regulation of plasticity, inflammatory response, metabolic, catabolic and homeostatic processes, and transcription. Genes were mainly up-regulated in aged brain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36798" }, "primaryId" : "GEO:GSE36798", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36798" } ] }, "title" : "Development of microRNA signatures for acute rejection after liver transplantation using rat model", "dateAssigned" : "2012-03-26T00:00:00.000-05:00", "summary" : "To find out acute rejection (AR) associated microRNAs, we have employed Agilent microRNA microarray as a discovery platform to identify microRNAs with the potential to distinguish AR from controls. We first established a rat Orthotopic liver transplantation (OLT) model with AR, using Brown Norway (BN) rats that received OLT with liver grafts from Lewis rats (Lewis to BN). OLT with BN rats as the donors and recipients were also performed (BN to BN), and these rats served as the control group (non-rejection group, NR group). Then, global microRNA expression profiles of the plasma and grafts were evaluated and validated with high throughout microarray and RT-qPCR.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36929" }, "primaryId" : "GEO:GSE36929", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36929" } ] }, "title" : "Expression data from rat with different quantities of PS", "dateAssigned" : "2012-03-29T00:00:00.000-05:00", "summary" : "Paradoxical sleep function remains unknown although several studies indicate that it might play a role in learning and memory. To investigate what modifications paradoxical sleep may bring at the molecular level in neocortex and in hippocampal formation, we profiled gene expression in these structures in rats with different quantities of PS by cDNA microarrays approach.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36935" }, "primaryId" : "GEO:GSE36935", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE36935" } ] }, "title" : "Role of IGFBP-3 in the Regulation of ß-Cell Mass during Obesity: Adipose Tissue/ ß-Cell Cross Talk", "dateAssigned" : "2012-03-29T00:00:00.000-05:00", "summary" : "In obesity an increase in ß-cell mass occurs to cope with the rise in insulin demand. This ß -cell plasticity is essential to avoid the onset of hyperglycemia, although the molecular mechanisms that regulate this process remain unclear. This study analyzed the role of adipose tissue in the control of ß -cell replication. Using a diet-induced model of obesity, we obtained conditioned media from three different white adipose tissue depots. Only in the adipose tissue depot surrounding the pancreas did the diet induce changes that led to an increase in INS1E cells and the islet replication rate. To identify the factors responsible for this proliferative effect, adipose tissue gene expression analysis was conducted by microarrays and quantitative RT-PCR. Of all the differentially expressed proteins, only the secreted ones were studied. IGF binding protein 3 (Igfbp3) was identified as the candidate for this effect. Furthermore, in the conditioned media, although the blockage of IGFBP3 led to an increase in the proliferation rate, the blockage of IGF-I receptor decreased it. Taken together, these data show that obesity induces specific changes in the expression profile of the adipose tissue depot surrounding the pancreas, leading to a decrease in IGFBP3 secretion. This decrease acts in a paracrine manner, stimulating the ß -cell proliferation rate, probably through an IGF-I-dependent mechanism. This cross talk between the visceral-pancreatic adipose tissue and ß -cells is a novel mechanism that participates in the control of ß -cell plasticity. (Endocrinology 153: 177–187, 2012)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22067319" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37133" }, "primaryId" : "GEO:GSE37133", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37133" } ] }, "title" : "Gene expression profiles in isolated proximal tubules and whole kidneys of rats after cisplatin-administration", "dateAssigned" : "2012-04-10T00:00:00.000-05:00", "summary" : "To clarify the effects of cisplatin (cis-diamminedichloroplatinum II, CDDP) on the gene expression profiles in renal proximal tubules, microarray analyses were carried out using total RNA samples isolated from microdissected proximal tubules and whole kidneys. The molecular events underlying acute kidney injury (AKI) in the proximal tubules of rats with cisplatin-induced nephrotoxicity were successfully clarified with 17,000 transcripts.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37260" }, "primaryId" : "GEO:GSE37260", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37260" } ] }, "title" : "Analysis of potential transcriptomic biomarkers for doxorubicin cardiotoxicity in peripheral blood", "dateAssigned" : "2012-04-13T00:00:00.000-05:00", "summary" : "The aim of this study is the characterize and compare heart and PBMC transcriptomes of rats treated with doxorubicin in order to isolate a list of similarly differentially regulated genes with an ultimate goal to indentify PBMC biomarkers for early prediction of doxirubicinduced cardiotoxicity", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37313" }, "primaryId" : "GEO:GSE37313", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37313" } ] }, "title" : "Vitamin A deficiency results in an uncontrolled immune response and aggravates liver damage during obstructive cholestasis", "dateAssigned" : "2012-04-16T00:00:00.000-05:00", "summary" : "Conclusions: We conclude that vitamin A deficiency dramatically aggravates liver damage caused by obstructive cholestasis. The transcriptome analysis suggests that a disturbed immune response may be the predominant causative factor.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37351" }, "primaryId" : "GEO:GSE37351", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37351" } ] }, "title" : "Apoptosis induction in rat mammary tumor cells by repression of Pla2g4c expression.", "dateAssigned" : "2012-04-17T00:00:00.000-05:00", "summary" : "Although some phospholipase A2 forms, the initiator of the arachidonic acid cascade, contribute to carcinogenesis of many organs, the phospholipase A2 group IVc (Pla2g4c) remains to be clarified. When Pla2g4c expression in Rat mammary tumor-1 E4 (RMT-1) cells was knocked down by using specific siRNAs, cell counts were found to decrease to 40 % of the number of control and apoptotic cells were increased. Whole transcript profiling revealed the up-regulation of lipocalin 2 and down-regulation of epithelical marker genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26013918" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37413" }, "primaryId" : "GEO:GSE37413", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37413" } ] }, "title" : "Genome-wide DNA Microarray Unravels Rapid Changes in the Transcriptome of MK-801 treated Rat Brain", "dateAssigned" : "2012-04-19T00:00:00.000-05:00", "summary" : "Conclusions: Our results reveal that MK-801 triggered i) an increase in the power of gamma oscillations, and ii) simultaneously caused very early changes in gene expressions in the rat brain, representing a first such inventory of gene expression profiles in brain after acute MK-801 treatment.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37476" }, "primaryId" : "GEO:GSE37476", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37476" } ] }, "title" : "Time course of gene expression changes after muscle contraction in spinal cord injured rats", "dateAssigned" : "2012-04-21T00:00:00.000-05:00", "summary" : "Purpose: The goal of this study was to determine the gene expression changes that occur over 7 days in parralyzed muscle in response to isometric contraction elicited by electrical stimulation initiated 4 months after spinal cord injury and to compare such changes to those observed in a normal muscle subjected to overload.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23914941" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37564" }, "primaryId" : "GEO:GSE37564", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37564" } ] }, "title" : "Expression profile of PC12 cells stimulated by nerve growth factor measured by Agilent microarray", "dateAssigned" : "2012-04-24T00:00:00.000-05:00", "summary" : "We analyzed the comprehensive gene expression changes by nerve growth factor (NGF) in PC12 cells using Agilent microarrays. The genes of 1920 NGF treated were up-regulated and 2670 genes were down-regulated significantly compared with the control group. The expression level of genes involved in cell structure and proteolysis were up-regulated. On the other hand, the genes of cell cycle and some metabolism were rather down-regulated. Therefore, it is suggested that it is necessary to stop the cell cycle and down-regulate metabolism to neurite outgrowth.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37600" }, "primaryId" : "GEO:GSE37600", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37600" } ] }, "title" : "The Refilin/Filamin complex regulates filipodia dynamics in oligodendrocyte progenitor cells.", "dateAssigned" : "2012-04-26T00:00:00.000-05:00", "summary" : "Actin assembly and dynamics control the shape, motility and functions of diverse cell types. Programme for controlling theses dynamics is hard-coded into actin binding proteins and regulatory proteins. Refilins (RefilinA and RefilinB) are short lived regulatory proteins that interact with the actin-binding protein Filamin to convert it from an actin branching protein into one that bundles. We here show that different mechanisms converge to increase Refilin level in brain NG2+ precursor cells (polydendrocytes) committed to differentiate into the oligodendrocyte lineage. RefilinA is up-regulated through transcriptional activation during commitment into oligodendrocyte progenitor cells (OPC). RefilinB expression relies on PDGF signalling and is further stabilized by a unique auto-inhibitory domain masking the adjacent conserved PEST degradation signal. In NG2+ precursor cells and OPC, the RefilinB/Filamin complex localizes on filipodia protrusions and filipodial processes. Stable ectopic expression of Refilins in cells stimulates membrane remodelling dynamics linked with filipodia growth. These studies extend the function of the Refilin/FLNA complex to cell membrane remodelling linked with reorganization of underlying actin cytoskeleton. ", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37618" }, "primaryId" : "GEO:GSE37618", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37618" } ] }, "title" : "Glucocorticoid-Dependent Hippocampal Transcriptome in Male Rats: Pathway-Specific Alterations with Aging", "dateAssigned" : "2012-04-26T00:00:00.000-05:00", "summary" : "Although glucocorticoids (GCs) are known to exert numerous effects in the hippocampus, their chronic regulatory functions remain poorly understood. Moreover, evidence is inconsistent regarding the longstanding hypothesis that chronic GC exposure promotes brain aging/Alzheimer's disease. Here, we adrenalectomized male F344 rats at 15-months-of-age, maintained them for 3 months with implanted corticosterone (CORT) pellets producing low or intermediate (glucocorticoid-receptor (GR)-activating) blood levels of CORT, and performed microarray/pathway analyses in hippocampal CA1. We defined the chronic GC-dependent transcriptome as 393 genes that exhibited differential expression between Intermediate- and Low-CORT groups. Short-term CORT (4 days) did not recapitulate this transcriptome. Functional processes/pathways overrepresented by chronic CORT-upregulated genes included learning/plasticity, differentiation, glucose metabolism and cholesterol biosynthesis, whereas processes overrepresented by CORT-downregulated genes included inflammatory/immune/glial responses and extracellular structure. These profiles indicate that GCs chronically activate neuronal/metabolic processes while coordinately repressing a glial axis of reactivity/inflammation. We then compared the GC-transcriptome with a previously-defined hippocampal aging transcriptome, revealing a high proportion of common genes. Although CORT and aging moved expression of some common genes in the same-direction, the majority were shifted in opposite directions by CORT and aging (e.g., glial inflammatory genes downregulated by CORT are upregulated with aging). These results contradict the hypothesis that GCs simply promote brain aging, and also suggest that the opposite-direction shifts during aging reflect resistance to CORT regulation. Therefore, we propose a new model in which aging-related GC resistance develops in some target pathways while GC overstimulation develops in others, together generating much of the brain aging phenotype.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23736296" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37619" }, "primaryId" : "GEO:GSE37619", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37619" } ] }, "title" : "Spalax gene expression profiling of muscle and brain under hypoxia", "dateAssigned" : "2012-04-26T00:00:00.000-05:00", "summary" : "Spalax, an underground fossoral rodant is exposed to chronic hypoxic environments. Measurements of Spalax burrows indicated 7% oxygen and up to 15% CO2. In the laboratory Spalax can survive 3% oxygen up to 14 hours as compared to rats that survive less than 4 hours at these oxygen levels. we have proposed Spalax as a model species for the investigation of hypoxia tolerance. this research has implications for many biomedical phenomena involving ischemic disease, notably heart disease and cancer. In this work we have subjected Spalax to 3%, 6% and 10% O2 levels for varying lengths of time and have profiled expression patterns and differential expression in muscle and brain, two tissues with high energy requirements. For comparison with a terrestrial mammal we have profiled RNA from rats exposed to either 21% or 6% oxygen.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23148642" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37627" }, "primaryId" : "GEO:GSE37627", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37627" } ] }, "title" : "microRNA expression in epicardial mesothelial cells undergoing Epithelial-to-Mesenchymal Transition", "dateAssigned" : "2012-04-27T00:00:00.000-05:00", "summary" : "In this study we have identified a number of miRNAs that potentially play an intrinsic role in cardiac EMT. We speculate that by targeting those miRNA, the onset and long-term progression of cardiac fibrosis can be substantially reduced.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37695" }, "primaryId" : "GEO:GSE37695", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37695" } ] }, "title" : "Poly(A) RNA profiling upon Gld2 knockdown in cultured hippocampal neurons", "dateAssigned" : "2012-05-01T00:00:00.000-05:00", "summary" : "Poly(A) RNA profiling upon Gld2 knockdown in cultured hippocampal neurons", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22727665" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37732" }, "primaryId" : "GEO:GSE37732", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37732" } ] }, "title" : "Impact of oral compost-extract administration on gene expression in the rat gastrointestinal tract", "dateAssigned" : "2012-05-03T00:00:00.000-05:00", "summary" : "Oral administration of an extract of compost fermented with thermophiles to pigs reduces the incidence of stillbirth and promotes piglet growth. However, the mechanism by which compost extract modulates the physiological conditions of the animals remains largely unknown. Here, we investigate the effects of compost extract on the gene expression in the intestine of the rat as a mammalian model. Gene expression analyses of the intestine indicated that several immune-related genes were upregulated following compost exposure. Thus, thermophile-fermented compost can contain microbes and/or substances that activate the gut mucosal immune response in the rat.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37777" }, "primaryId" : "GEO:GSE37777", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37777" } ] }, "title" : "Comprehensive gene expression analysis of cerebral cortices from mature rats after neonatal hypoxic-ischemic brain injury", "dateAssigned" : "2012-05-04T00:00:00.000-05:00", "summary" : "Neonatal hypoxic-ischemic (HI) encephalopathy can lead to severe brain damage and is a common cause of neurological handicaps in adulthood. To elucidate the molecular events occurring in cerebral cortices of mature rats (8 weeks old) after neonatal HI brain insult, we performed comprehensive gene expression and gene network analyses using a DNA microarray system (Agilent 4x44K). A rat model of neonatal HI encephalopathy (Rice model) was obtained by unilateral ligation of the common carotid artery of 7-day-old rats with hypoxia (exposure to 8% oxygen). Due to the HI insult-related breakdown of the ipsilateral hemisphere in the brain, RNAs were prepared from the contralateral cerebral cortices of 8-week-old rats and analyzed by DNA microarray. Biofunctional analysis of differentially regulated genes revealed that many upregulated genes were related to cell death signaling, such as the arachidonic acid cascade. In contrast, many downregulated genes were related to gene expression, reflecting progressive damage by the HI insult, even within the contralateral cerebral hemisphere.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22700374" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37852" }, "primaryId" : "GEO:GSE37852", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37852" } ] }, "title" : "VGF-derived peptide attenuates development of type 2 diabetes via enhancement of islet beta cell survival and function survival and function", "dateAssigned" : "2012-05-08T00:00:00.000-05:00", "summary" : "Deterioration of functional islet ß-cell mass is the final step in progression to Type 2 diabetes. We previously reported that overexpression of Nkx6.1 in rat islets has the dual effects of enhancing glucose-stimulated insulin secretion (GSIS) and increasing ß-cell replication. Here we show that Nkx6.1 strongly upregulates the prohormone VGF in rat islets and that VGF is both necessary and sufficient for Nkx6.1-mediated enhancement of GSIS. Moreover, the VGF-derived peptide TLQP-21 potentiates GSIS in rat and human islets and improves glucose tolerance in vivo. Chronic injection of TLQP-21 in pre-diabetic ZDF rats preserves islet mass and slows diabetes onset. TLQP-21 prevents islet cell apoptosis by a pathway similar to that used by GLP-1, but independent of the GLP-1, GIP, or VIP receptors. Unlike GLP-1, TLQP-21 does not inhibit gastric emptying or increase heart rate. We conclude that a TLQP-21 is a novel agent for enhancing islet ß-cell survival and function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22768837" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37944" }, "primaryId" : "GEO:GSE37944", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE37944" } ] }, "title" : "Sparing of muscle mass and function by passive loading in an experimental intensive care unit model", "dateAssigned" : "2012-05-11T00:00:00.000-05:00", "summary" : "Critically ill intensive care unit (ICU) patients commonly develop severe muscle wasting and impaired muscle function, leading to delayed recovery, with subsequent increased morbidity and financial costs, and decrease quality of life of survivors. Acute Quadriplegic Myopathy (AQM) is one of the most common neuromuscular disorders associated with ICU-acquired muscle weakness. Although there are no available treatments for the ICU-acquired muscle weakness, it has been demonstrated that early mobilization can improve its prognosis and functional outcomes. This study aims at improving our understanding of the effects of passive mechanical loading on skeletal muscle structure and function by using a unique experimental rat ICU model allowing analyses of the temporal sequence of changes in mechanically ventilated and pharmacologically paralyzed animals at durations varying from 6 h to 14 days. Results show that passive mechanical loading alleviated the muscle wasting and the loss of force-generation associated with the ICU intervention, resulting in a doubling of the functional capacity of the loaded vs. unloaded muscles after a 2-week ICU intervention. We demonstrated that the improved maintenance of muscle structure and function is likely a consequence of a reduced oxidative stress, and a reduced loss of the molecular motor protein myosin. A complex temporal gene expression pattern, delineated by microarray analysis, was observed with loading-induced changes in transcript levels of sarcomeric proteins, muscle developmental processes, stress response, ECM/cell adhesion proteins and metabolism. Thus, the results from this study show that passive mechanical loading alleviates the severe negative consequences on muscle structure and function associated with mechanical silencing in ICU patients, strongly supporting early and intense physical therapy in immobilized ICU patients.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23266938" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38037" }, "primaryId" : "GEO:GSE38037", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38037" } ] }, "title" : "Profiling brain cortex from tMCAO rat stroke model", "dateAssigned" : "2012-05-17T00:00:00.000-05:00", "summary" : "This program addresses the gene signature associated with brain (cortex) in the tMCAO rat model for stroke.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22806142" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38038" }, "primaryId" : "GEO:GSE38038", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38038" } ] }, "title" : "Profiling Chung rat model for neuropathic pain", "dateAssigned" : "2012-05-17T00:00:00.000-05:00", "summary" : "This program addresses the gene signature associated with DRG in the Chung rat model for neuropathic pain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22806142" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38056" }, "primaryId" : "GEO:GSE38056", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38056" } ] }, "title" : "Novel long non-coding RNAs are involved in cellular response to angiotensin II signaling", "dateAssigned" : "2012-05-18T00:00:00.000-05:00", "summary" : "Angiotensin II (AngII) is a polypeptide hormone that plays a pivotal role in the regulation of blood pressure. In vascular smooth muscle cells (VSMCs), AngII signaling results in hypertrophy, proliferation, contraction, and migration, which ultimately promote atherosclerosis and hypertensive cardiovascular diseases. Recent studies have shown that fundamental biological processes such as cell proliferation and differentiation are mediated in part by the activities of long non-protein-coding RNAs (lncRNAs). In this study, we sought to identify lncRNAs that are involved in the response to AngII-signaling. Genome-wide analysis of de novo assembled transcripts from rat vascular smooth muscle cells (VSMCs) identified novel lncRNA as well as protein-coding transcripts which have not been previously annotated. The majority of the genomic loci from which these novel transcripts are transcribed are enriched for histone H3 lysine 4 trimethylation and histone H3 lysine 36 trimethylation, two chromatin modifications that are closely associated with actively transcribed regions, further supporting these as bona fide transcripts. Compared with previously annotated rat transcripts, these novel lncRNA transcripts, on average, are shorter in length and are less abundant, consistent with reports from mice and humans. Expression analyses of transcripts from control and AngII-stimulated VSMCs reveal that AngII signaling affects the abundance of both protein-coding transcripts as well as lncRNAs transcripts. Altogether, these data provide new insights into the global effects of AngII signaling and reveal potential novel therapeutic targets for treatment of AngII-associated cardiovascular diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23697773" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38060" }, "primaryId" : "GEO:GSE38060", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38060" } ] }, "title" : "Changes in mammary gene expression and morphology following consumption of soy protein isolate in female Sprague-Dawley rats differs from that produced by 17b-estradiol treatment", "dateAssigned" : "2012-05-20T00:00:00.000-05:00", "summary" : "Soy foods have been suggested to have both positive health benefits and potentially adverse effects largely as a result of their content of isoflavone phytoestrogens. Since soy protein isolate (SPI) contains isoflavones, in addition to purported health benefits, safety concerns have been raised regarding the use of SPI and soy formulas, because of potential estrogenic actions during the neonatal period, including the potential for reproductive toxicity, infertility, and the possibility of increased risk for development and recurrence of estrogen sensitive cancers such as breast cancer. In the current study, we used a rat model to compare the effects of SPI with those of 17b-estradiol (E2), on global gene expression profiles and morphology in the female rat mammary gland. Rats were either fed AIN-93G diets containing casein (CAS) or SPI beginning on postnatal day (PND) 30.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23027806" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38062" }, "primaryId" : "GEO:GSE38062", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38062" } ] }, "title" : "Comparison of the long-term effects of calorie restriction without malnutrition on global gene expression profiles of rat and human skeletal muscle [Rat]", "dateAssigned" : "2012-05-20T00:00:00.000-05:00", "summary" : "With the population of older and overweight individuals on the rise in the Western world, there is an ever greater need to slow the aging processes and reduce the burden of age-associated chronic disease that would significantly improve the quality of human life and reduce economic costs. Caloric restriction (CR), is the most robust and reproducible intervention known to delay aging and to improve healthspan and lifespan across species (1); however, whether this intervention can extend lifespan in humans is still unknown. Here we report that rats and humans exhibit similar responses to long-term CR at both the physiological and molecular levels. CR induced broad phenotypic similarities in both species such as reduced body weight, reduced fat mass and increased the ratio of muscle to fat. Likewise, CR evoked similar species-independent responses in the transcriptional profiles of skeletal muscle. This common signature consisted of three key pathways typically associated with improved health and survival: IGF-1/insulin signaling, mitochondrial biogenesis and inflammation. To our knowledge, these are the first results to demonstrate that long-term CR induces a similar transcriptional profile in two very divergent species, suggesting that such similarities may also translate to lifespan-extending effects in humans as is known to occur in rodents. These findings provide insight into the shared molecular mechanisms elicited by CR and highlight promising pathways for therapeutic targets to combat age-related diseases and promote longevity in humans.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23601134" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38072" }, "primaryId" : "GEO:GSE38072", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38072" } ] }, "title" : "Profiling skin from Carrageenan (CGN) rat model for inflammation pain", "dateAssigned" : "2012-05-21T00:00:00.000-05:00", "summary" : "This program aims at identifying a skin gene signature associated with inflammation pain in rat CGN model", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22806142" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38077" }, "primaryId" : "GEO:GSE38077", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38077" } ] }, "title" : "Profiling muscle from aged rat model for sarcopenia", "dateAssigned" : "2012-05-21T00:00:00.000-05:00", "summary" : "This program aims at identifying a muscle gene signature associated with aging in rat sarcopenia model", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22806142" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38078" }, "primaryId" : "GEO:GSE38078", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38078" } ] }, "title" : "Profiling livers from LPS-treated rats", "dateAssigned" : "2012-05-21T00:00:00.000-05:00", "summary" : "This program addresses the gene signature associated with LPS-treated liver in rat. Specifically, which genes are differentially expressed in livers of the Sprague Dawley rats treated with LPS?", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22806142" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38221" }, "primaryId" : "GEO:GSE38221", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38221" } ] }, "title" : "Genome wide expression analysis of the Hypothalamic control of Mammalian Puberty", "dateAssigned" : "2012-05-24T00:00:00.000-05:00", "summary" : "Gene expression analysis of hypothalami from female animals at different juvenil developmental reproductive stages. Results provide insight into the role of the hypothalamus in controlling the onset of puberty.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38223" }, "primaryId" : "GEO:GSE38223", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38223" } ] }, "title" : "pCREB-dependent transcriptional activation is a mediator of molecular neuroadaptations induced by methamphetamine self-administration in the rat dorsal striatum", "dateAssigned" : "2012-05-24T00:00:00.000-05:00", "summary" : "Neuroplastic changes in the dorsal striatum participate in the transition from casual drug use to habitual and compulsive drug taking. These alterations might also play a critical role in the development of methamphetamine (METH) addiction. Nevertheless, the molecular substrates that underlie habitual METH consumption have yet to be elucidated. Therefore, in the present study, we examined the influence of METH self-administration on the expression of genes and proteins of interest, as potential substrates of METH-induced neuronal plasticity in the dorsal striatum. Rats self-administered METH (0.1 mg/kg/injection, i.v.) during 15 h sessions for 8 d and were euthanized after 2 h, 24 h, or 1 month of abstinence. Compared to yoked saline control, METH self-administration induced increases in the mRNA expression of the transcription factors, c-fos and fosb, the neurotrophic factor, Bdnf, and of the synaptic protein, synaptophysin (Syp) at 2 h after cessation of drug exposure. METH self-administration also caused changes in FosB, BDNF and TrkB protein levels, with increases at 2 and 24 h but decreases observed after 1 month of drug abstinence. Importantly, METH exposure caused increases in the levels of H3K4me3 and pCREB after 2 and 24 h of abstinence. Chromatin immunoprecipitation followed by qPCR was used to clarify the role of these proteins in the regulation of gene expression. We found that METH self-administration caused enrichment of pCREB, but not of H3K4me3, on the promoters of c-fos, fosb, Bdnf and Syp at 2 h after drug cessation. These data indicate that METH-induced activation of their transcription is mediated, in part, by pCREB-dependent epigenetic phenomena. Thus, METH self-administration might trigger epigenetic changes that caused alterations in the expression of genes and proteins serving as substrates for addiction-related synaptic plasticity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38348" }, "primaryId" : "GEO:GSE38348", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38348" } ] }, "title" : "Effects of Developmental Lead Exposure on the Hippocampal Transcriptome.", "dateAssigned" : "2012-05-30T00:00:00.000-05:00", "summary" : "In this study we analyzed the effects of lead-exposure up hippocampal gene expression in males and females exposed to 0ppm, 250ppm and 750ppm lead during two different developmental periods, perinatal (in utero through to weaning at PND21) and postnatal (PND0-PND45). All tissue was taken at PND 55. We used affymetrix Rat Gene 1.0ST arrays to obtain global gene expression data from each animal, with a group size of 4 for all conditions (Total number of Arrays = 40)", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38450" }, "primaryId" : "GEO:GSE38450", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38450" } ] }, "title" : "Analyzing the cytoskeletal transcriptome: sex differences in rat hypothalamus", "dateAssigned" : "2012-06-04T00:00:00.000-05:00", "summary" : "The transcriptomes of young male and (in estrus) female hypothalami were profiled and compared to learn about the sex dichotomy of the cytoskeletal genomic fabric(CGF), defined as the most inter-coordinately and stably expressed gene web whose encoding proteins form the intracellular scaffolding.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38454" }, "primaryId" : "GEO:GSE38454", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38454" } ] }, "title" : "Analysis of the global gene expression in VEGF-B transgenic rat hearts", "dateAssigned" : "2012-06-04T00:00:00.000-05:00", "summary" : "We show that an excess of VEGF-B protects the heart via adaptive cardiac hypertrophy and increased coronary arterial reserve, and by inducing a shift from lipid to glucose metabolism.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24448490" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38455" }, "primaryId" : "GEO:GSE38455", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38455" } ] }, "title" : "Analysis of the global gene expression in the rat hearts transduced with adeno-associated viral vectors coding VEGF-B", "dateAssigned" : "2012-06-04T00:00:00.000-05:00", "summary" : "We show that an excess of VEGF-B protects the heart via adaptive cardiac hypertrophy and increased coronary arterial reserve, and by inducing a shift from lipid to glucose metabolism.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24448490" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38505" }, "primaryId" : "GEO:GSE38505", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38505" } ] }, "title" : "Promoter methylation analysis in rat Pubertal Hypothalamus", "dateAssigned" : "2012-06-05T00:00:00.000-05:00", "summary" : "Promoter methylation analysis of hypothalamc DNA from female rats at different juvenile developmental reproductive stages. Results provide insight into the role of the hypothalamus in controlling the onset of puberty.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23354331" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38570" }, "primaryId" : "GEO:GSE38570", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38570" } ] }, "title" : "Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation (Rat)", "dateAssigned" : "2012-06-07T00:00:00.000-05:00", "summary" : "Analysis of gene expression during differentiation of alveolar epithelial type 2 (AT2) cells into AT1 cells. Timepoints taken at Day 0 (AT2 cell), Days 2, 4, and 6 in culture (differentiating) and Day 8 in culture (AT1-like cells).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23818859" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38584" }, "primaryId" : "GEO:GSE38584", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38584" } ] }, "title" : "Hierarchical regulation in a KRAS pathway-dependent transcriptional network revealed by a reverse-engineering approach (7TF and control)", "dateAssigned" : "2012-06-07T00:00:00.000-05:00", "summary" : "RAS mutations are highly relevant for progression and therapy response of human tumours, but the genetic network that ultimately executes the oncogenic effects is poorly understood. Here we used a reverse-engineering approach in an ovarian cancer model to reconstruct KRAS oncogene-dependent cytoplasmic and transcriptional networks from perturbation experiments based on gene silencing and pathway inhibitor treatments. We measured mRNA and protein levels in manipulated cells by microarray, RT-PCR and Western Blot analysis, respectively. The reconstructed model revealed complex interactions among the transcriptional and cytoplasmic components, some of which were confirmed by double pertubation experiments. Interestingly, the transcription factors decomposed into two hierarchically arranged groups. To validate the model predictions we analysed growth parameters and transcriptional deregulation in the KRAS-transformed epithelial cells. As predicted by the model, we found two functional groups among the selected transcription factors. The experiments thus confirmed the predicted hierarchical transcription factor regulation and showed that the hierarchy manifests itself in downstream gene expression patterns and phenotype.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22864383" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38585" }, "primaryId" : "GEO:GSE38585", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38585" } ] }, "title" : "Hierarchical regulation in a KRAS pathway-dependent transcriptional network revealed by a reverse-engineering approach (RAS-ROSE and ROSE with siRNA)", "dateAssigned" : "2012-06-07T00:00:00.000-05:00", "summary" : "RAS mutations are highly relevant for progression and therapy response of human tumours, but the genetic network that ultimately executes the oncogenic effects is poorly understood. Here we used a reverse-engineering approach in an ovarian cancer model to reconstruct KRAS oncogene-dependent cytoplasmic and transcriptional networks from perturbation experiments based on gene silencing and pathway inhibitor treatments. We measured mRNA and protein levels in manipulated cells by microarray, RT-PCR and Western Blot analysis, respectively. The reconstructed model revealed complex interactions among the transcriptional and cytoplasmic components, some of which were confirmed by double pertubation experiments. Interestingly, the transcription factors decomposed into two hierarchically arranged groups. To validate the model predictions we analysed growth parameters and transcriptional deregulation in the KRAS-transformed epithelial cells. As predicted by the model, we found two functional groups among the selected transcription factors. The experiments thus confirmed the predicted hierarchical transcription factor regulation and showed that the hierarchy manifests itself in downstream gene expression patterns and phenotype.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22864383" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38595" }, "primaryId" : "GEO:GSE38595", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38595" } ] }, "title" : "Analysis of postnatal gene expression in a transgenic rat kidney", "dateAssigned" : "2012-06-08T00:00:00.000-05:00", "summary" : "We have generated a transgenic rat model with postnatal pathology. In order to investigate the potential contribution of changes in kidney gene expression to the pathology, we have conducted microarray-based gene expression profiling of postnatal kidney. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23001561" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38599" }, "primaryId" : "GEO:GSE38599", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38599" } ] }, "title" : "Global microRNAs profile and signaling pathways in the development of hypertrophy", "dateAssigned" : "2012-06-08T00:00:00.000-05:00", "summary" : "The aberrantly expressed differences of microRNAs in the cardiac hypertrophy model between sham surgery and TAC surgery methods were successfully detected. The global miR expression profile, comprehensive prediction of miR targets and signaling pathway analysis during cardiac hypertrophy were conducted in depth.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38607" }, "primaryId" : "GEO:GSE38607", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38607" } ] }, "title" : "Transcriptome-wide gene expression of the heart of neonatal rats with polygenic cardiac hypetrophy", "dateAssigned" : "2012-06-08T00:00:00.000-05:00", "summary" : "Identification of genes differentially expressed between the neonatal heart of a genetic rat model of cardiac hypertrophy (the Hypertrophic Heart Rat, HHR) and the control (the Normal Heart Rat, NHR) using Affymetrix GeneChip® Rat Gene 1.0 ST Arrays.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28615213" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38645" }, "primaryId" : "GEO:GSE38645", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38645" } ] }, "title" : "Gene expression profiling of CD4+myelin basic protein specific T cells", "dateAssigned" : "2012-06-11T00:00:00.000-05:00", "summary" : "We found that on their way to the CNS T cells fundamentally reprogram their gene expression profile, by down-regulating their activation program and up-regulating cell locomotion molecules.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22914092" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38655" }, "primaryId" : "GEO:GSE38655", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38655" } ] }, "title" : "Exosomal tumor microRNA modulates premetastatic organ cells [Agilent]", "dateAssigned" : "2012-06-12T00:00:00.000-05:00", "summary" : "Exososmes, potent intercellular communicators, are supposed to contribute to metastasis formation, which we confirmed for exosomes of the metastatic rat pancreatic adenocarcinoma line BSp73ASML that promote metastatic settlement in lymph nodes and lung of poorly metastatic BSp73ASML cells with a selective CD44v4-v7 (BSp73ASML-CD44vkd) knockdown. To define the molecular pathway(s), whereby exosomes contribute to premetastatic niche preparation, we profiled mRNA miRNA of BSp73ASMLwt and BSp73ASML-CD44vkd- exosomes and evaluated the impact on potential target cells. BSp73ASML exosomes are recovered in the draining lymph node after subcutaneous injection. In vitro, they preferentially bind and are taken-up by lymph node stroma cells (LnStr) and lung fibroblasts (LuFb) that were chosen as exosome targets. BSp73ASMLwt and BSp73ASML-CD44kd exosomes contain a restricted repertoire of mRNA and miRNA, hwere the lattter differe significantly between the two lines and even more pronounced, exosomes derived thereof with a not yet explored dominance of tumor-suppressor miRNA in ASML-CD44kd cells and exosomes. Both, exosomal mRNA and miRNA are recovered in target cells and exosome-uptake is accompanied by significant changes in gene expression. We didn't observe a correlation between exosomal mRNA and changes in target cell mRNA or proteins. Instead transferred miRNA significantly affected target cell mRNA translation as demonstrated for selected, most abundant ASML exosomal miRNA besides others, miR-494 known target MAL (myelin and lymphocytes protein)/cadherin17, and miR-542-3p which targets TRAF/cadherin17. Furthermore, MMP transcription suggested to accompany cadherin17 dwon-regulation was upregulated in miR-494 or miR542-3p transfected or exosome co-cultured LnStr. Taken together, tumor exosomes target in vivo non-transformed cells in premetastatic organs. Exosome uptake induced altered target celll gene expression is strongly promoted by exosomal miRNA where we demonstrate for the first time that exosomes/exosomal miRNA from a metastasizing tumor line can modulate stroma cells from premetastatic organs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23479506" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38695" }, "primaryId" : "GEO:GSE38695", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38695" } ] }, "title" : "Exacerbated oxidative stress in the fasting liver according to fuel partitioning", "dateAssigned" : "2012-06-13T00:00:00.000-05:00", "summary" : "Complete starvation may prove lethal due to excessive loss of body proteins. However, it is still not completely understood whether responses to food deprivation are time-dependently induced or triggered in relation with the successive phases of protein sparing and wasting that characterize prolonged fasting. As the liver has a wide range of vital functions, we examined the hepatic regulatory mechanisms elicited during prolonged fasting. We showed that fasting-induced transcriptome/proteome changes occur in close relation with fuel partitioning, independently of ATP levels. Omics data suggesting a worsening of oxidative stress during the proteolytic stage of fasting, this was further validated using biochemical assays. Low levels of antioxidant factors were indeed paralleled by their decreased activity, which could be impaired by low NADPH levels. Oxidative damages on lipids and proteins were accordingly increased only during late fasting. At this stage, the gene/protein expression of several chaperones was also repressed. Together with the impairment of metabolic achievements, a vicious cycle involving protein misfolding and oxidative stress could jeopardize liver functions when the proteolytic stage of fasting is reached. Thus, monitoring of liver impairments should help to better manage or treat catabolic and/or oxidative stress conditions, such as ageing and degeneration.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24920225" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38710" }, "primaryId" : "GEO:GSE38710", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38710" } ] }, "title" : "Transcriptome-wide microRNA expression of the heart of neonatal rats with polygenic cardiac hypetrophy", "dateAssigned" : "2012-06-14T00:00:00.000-05:00", "summary" : "Identification of microRNAs differentially expressed between the neonatal heart of a genetic rat model of cardiac hypertrophy (the Hypertrophic Heart Rat, HHR) and the control (the Normal Heart Rat, NHR) using the Agilent Rat miRNA Microarray Kit Release 16.0.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38802" }, "primaryId" : "GEO:GSE38802", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38802" } ] }, "title" : "MicroRNA expression profiles associated with anti-schistosome features in Microtus fortis", "dateAssigned" : "2012-06-19T00:00:00.000-05:00", "summary" : "Microtus fortis (M. fortis) is the only mammal in which the growth, development and maturation of schistosomes (Schistosoma japonicum) is prevented, resulting in the failure of the parasite to mature and complete its life cycle. MicroRNAs (miRNAs) are a class of endogenous, non-coding small RNAs, has been found to introduce a whole new layer of gene regulation in eukaryotes. The anti-schistosomiasis mechanosm of M. fortis may require the participation of miRNA-mediated gene expression. In the present study, the difference pathological change of different tissue such as liver, spleen and lung of M. fortis were observed by using haematoxylin-eosin staining. Also, the miRNA expression in different tissue of M. fortis and mice before challenge and 10 days post-infection with schistosomes were first compared using microRNA microarray analysis. Histological analyses showed that S. japonicum infection in M. fortis resulted in more intensive inflammatory response and pathologic change than mice. The microarray investigations showed that 388 miRNAs detected common expressed in the two species, and 11 miRNAs in liver, 25 miRNAs in spleen and 28 miRNAs in lung differentially expressed in non-permissive M. fortis while increased, decreased or nearly fixed in mice. Further studies of the differentially expressed miRNAs demonstrated that many important signal pathway were triggered after the S. japonicum infection in M. fortis rather than the mouse, such as the metabolism of some nutrient material such as fatty-acid, cholesterol, lipid, insulin, and carbohydrate; immune response such as B and T cell differentiation, monocyte differentiation, the inflammation, NF-kappaB binding, even the in innate immune system; Cell differentiation and apoptosis such as erythrocytic differentiation and targeting proapoptotic and antiapoptotic proteins. These results may provide new insights into general mechanisms of regulation in non-permissive M. fortis, exploit the potential miRNA regulatory networks and the interaction between parasites and different hosts, which provide valuable new information on schistosome biology and valuable information for the better understanding of schistosome development and host-parasite interactions.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38807" }, "primaryId" : "GEO:GSE38807", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38807" } ] }, "title" : "Translational microarray analysis of liver samples treated with PredTox hepatotoxic compound FP014SC", "dateAssigned" : "2012-06-19T00:00:00.000-05:00", "summary" : "Liver samples were lysed (15 mM Tris-HCl (pH 8.0), 300 mM NaCl and 15 mM MgCl2, plus inhibitors (1 mg/ml heparin 100 µg/ml cycloheximide and 80 U RNAsin)), added to a 10-50% sucrose gradient and ultracentrifuged at 182,000x g for 2 hours. The gradient was aliquotted into 16 1ml fractions and added to Tri reagent (Sigma). RNA was extracted as per the manufacturer's instructions and then sub-pooled into fractions corresponding to monosomes, light polysomes, medium polysomes and heavy polysomes, according to ribosomal density (more ribosomal occupancy = higher translational activity = heavier, and therefore, located in the more dense fractions). Microarray analysis was performed by hybridising control (vehicle treated) monosomes against test (high-dose treated) monosomes on one microarray, control light polysomes against test light polysomes on a second microarray, and so forth for each sub-pool of fractions. Following microarray analysis there were a maximum of four values for each mRNA, corresponding to the proportional representation of that mRNA within each sub-pool of fractions. By calculating the change in values, i.e. degree of slope, across the monosomal region, the light polysomal region, the medium polysomal region and the dense polysomal region it was possible to determine any translational change in activity. In addition, the overall transcriptional change could be analysed for each mRNA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23586759" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38834" }, "primaryId" : "GEO:GSE38834", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38834" } ] }, "title" : "Differential gene expression profiling of cultured neu-transformed versus spontaneously-transformed rat cholangiocytes and of corresponding cholangiocarcinomas", "dateAssigned" : "2012-06-20T00:00:00.000-05:00", "summary" : "Characterization of preclinical models of intrahepatic cholangiocarcinoma progression that reliably recapitulate altered molecular features of the human disease. Here, we performed comprehensive gene expression profiling of cholangiocarcinoma tumors arising from bile duct inoculation of different grade malignant rat cholangiocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:20816680" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38859" }, "primaryId" : "GEO:GSE38859", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38859" } ] }, "title" : "Expression data from pain model: rat L5 sensory ganglia after local inflammation", "dateAssigned" : "2012-06-21T00:00:00.000-05:00", "summary" : "We observed significant regulation in a large number of genes (23% of observed transcripts), and examined 221 (3%) with a fold-change of 1.5-fold or more in more detail. Immune-related genes were the largest category in this group and included members of the complement system as well as several pro-inflammatory cytokines. However, these upregulated cytokines had no prior links to peripheral pain in the literature other than through microarray studies, though most had previously described roles in CNS (especially neuroinflammatory conditions) as well as in immune responses.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38889" }, "primaryId" : "GEO:GSE38889", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38889" } ] }, "title" : "A novel 3-D organotypic culture model by co-culturing alpha-SMA positive CAF and cholangiocarcinoma cells in a collagen matrix", "dateAssigned" : "2012-06-22T00:00:00.000-05:00", "summary" : "We developed a novel 3-D organotypic culture model by co-culturing a-SMA positive CAF and cholangiocarcinoma cells in a collagen matrix.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28315313" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38942" }, "primaryId" : "GEO:GSE38942", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38942" } ] }, "title" : "VSL#3 protects against development of visceral pain in the neonatal maternal separation model: A whole genome microarray study", "dateAssigned" : "2012-06-26T00:00:00.000-05:00", "summary" : "Conclusions: This study indicates that VSL#3 is effective in reducing visceral pain in an experimental model of IBS by induction or suppression of pain-modulating genes. These observations provide support for the use of VSL#3 in the treatment of painful conditions related to IBS.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23691109" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38950" }, "primaryId" : "GEO:GSE38950", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE38950" } ] }, "title" : "Comprehensive expression analysis of primary hepatocytes under four different culture conditions", "dateAssigned" : "2012-06-26T00:00:00.000-05:00", "summary" : "Primary hepatocytes have been widely explored as cell sources for the study of in vitro drug metabolism and pharmacokinetics (DMPK). Aiming toward establishing an in vitro drug screening method, the current study illustrated a comprehensive increase in the DMPK-related gene expression of nanopillar (NP)-cultured 3D-spheroid. To examine the expressional changes in DMPK-related genes under four different conditions, namely, NP-, sandwich (SW)-, monolayer (ML)-cultured rat hepatocytes, and freshly isolated hepatocytes, genome-wide gene-expression analysis using a DNA microarray was performed. Among the DMPK-related genes, cytochrome P450, UDP-glucuronosyltransferase, and transporter genes were focused on. Principal component analysis showed that the global gene expression profile in sample from NP culture is closer to that from freshly isolated hepatocytes than that from SW culture. The expressions of almost all Cyp 1 to 3 and Ugt genes of NP-cultured 3-D spheroid were higher than those of ML and SW. The expression of Abcc2 gene whose translation product has a critical role in excretion of metabolized bile acids in hepatocyte to bile canaliculi was three times higher in NP than in ML. From these results, 3-D spheroid formed by the NP culture was suggested to possess higher ability of metabolism and excretion than conventional 2-D monolayer culture. The NP culture has a potential as an alternative culturing technique for evaluating metabolism and toxicity toward the development of new drugs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39119" }, "primaryId" : "GEO:GSE39119", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39119" } ] }, "title" : "Gene Expression Changes in the Spinal Cords of Lewis Rats with Myelin Basic Protein-Induced Experimental Autoimmune Encephalomyelitis (EAE)", "dateAssigned" : "2012-07-05T00:00:00.000-05:00", "summary" : "In these data sets we include the exon and gene expression data obtained from total RNA preparations from the spinal cords of female Lewis rats sacrificed at the clinical peak of MBP induced EAE and age matched , untreated, healthy controls. This data was used to obtain 2265 mapped IDS wich identified 1190 known genes which were differentially expressed in the spinal cord in EAE compared to healthy animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23139791" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39120" }, "primaryId" : "GEO:GSE39120", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39120" } ] }, "title" : "Exon Expression Changes in the Spinal Cords of Lewis Rats with Myelin Basic Protein-Induced Experimental Autoimmune Encephalomyelitis (EAE)", "dateAssigned" : "2012-07-05T00:00:00.000-05:00", "summary" : "In these data sets we include the exon expression data obtained from total RNA preparations from the spinal cords of female Lewis rats sacrificed at the clinical peak of MBP induced EAE and age matched , untreated, healthy controls.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39212" }, "primaryId" : "GEO:GSE39212", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39212" } ] }, "title" : "INS1-EGFP-L10a stable cell lines treated with Thapsigargin", "dateAssigned" : "2012-07-10T00:00:00.000-05:00", "summary" : "When unfolded proteins accumulate to irremediably high levels within the endoplasmic reticulum (ER), intracellular signaling pathways called the unfolded protein response (UPR) become hyperactivated to cause programmed cell death. We discovered that thioredoxin-interacting protein (TXNIP) is a critical node in this “Terminal UPR”. TXNIP becomes rapidly induced by hyperactivated IRE1a, an ER bifunctional kinase/endoribonuclease (RNase). IRE1a controls TXNIP mRNA stability by reducing levels of a TXNIP destabilizing micro-RNA, miR-17. In turn, elevated TXNIP protein activates the NLRP3 inflammasome, causing Caspase-1 cleavage and interleukin 1b (IL-1b) secretion. Txnip gene deletion reduces pancreatic b-cell death during ER stress, and suppresses diabetes caused by proinsulin misfolding in the Akita mouse. Finally, small molecule IRE1a RNase inhibitors suppress TXNIP production to block IL-1b secretion. In summary, the IRE1a-TXNIP pathway is used in the terminal UPR to promote sterile inflammation and programmed cell death, and may be targeted to develop new treatments for degenerative diseases driven by ER stress.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22883233" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39225" }, "primaryId" : "GEO:GSE39225", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39225" } ] }, "title" : "Chip-chip investigation of the effcts of phthalate plastisizers on fetal rat testes", "dateAssigned" : "2012-07-10T00:00:00.000-05:00", "summary" : "ChIP microarrays were used to investigate whether dibutylphthalate (DBP)-mediated repression of SF1-regulated genes was associated with changes in transcription factor binding to genes involved in DBP-induced testicular maldevelopment. The repressive effect of DBP on SF1 regulated gene expression in fetal testes correlates with inhibition of SF1 binding to steroidogenic gene promoters.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23358192" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39344" }, "primaryId" : "GEO:GSE39344", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39344" } ] }, "title" : "New insights into the molecular mechanisms of 1,3-dinitrobenzene-induced testicular toxicity", "dateAssigned" : "2012-07-13T00:00:00.000-05:00", "summary" : "Several studies have shown that 1,3-dinitrobenzene (DNB) causes injury to Sertoli cells and induces apoptosis in the surrounding germinal cells in male laboratory rats ; however, the mechanisms by which DNB functions are not well understood. In this context, we have conducted studies using standard parameters and molecular tools to better understand the pathogenesis of the testicular effects produced by DNB, as well as its mode of action. Wistar rats were orally exposed to 0.1-8 mg DNB/kg/day for 4 days. Testosterone concentrations were not affected at any dose level, but marked histopathological lesions in the testes were recorded at 4 mg/kg/day. Global transcriptomic analysis of rat testes revealed cell cycle and cell death as the major biological processes affected. In particular, we identified an alteration in the expression of genes associated with cell cycle progression (mitotic roles of polo-like kinase).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39350" }, "primaryId" : "GEO:GSE39350", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39350" } ] }, "title" : "Gene expression profiles of non-genotoxic hepatocarcinogens and hepatotoxicants in rat liver", "dateAssigned" : "2012-07-13T00:00:00.000-05:00", "summary" : "Liver tumors in rodents are frequently induced by non-genotoxic carcinogens. These hepatocarcinogens generally activate hepatic nuclear receptors (e.g., CAR and PXR), resulting in a cascade of signals causing modifications in the expression of genes responsible for several processes involved in carcinogenesis. Evaluation of the carcinogenic potential of chemicals is a regulatory requirement but is time-consuming and expensive. Consequently, several short-term in vivo and in vitro approaches, using molecular tools, have been proposed as predictive models for non-genotoxic hepatocarcinogens. The objective of our study was to discriminate between chemicals that are either non-genotoxic hepatocarcinogens or merely hepatotoxicants and also between CAR and PXR modulators on the basis of their gene expression profiles. Thus, we treated rats for seven days with the hepatoxicants, diclofenac and diazepam, or with several CAR and PXR modulators, which were mainly hepatocarcinogens. Different hepatic gene expression profiles were obtained not only between the hepatotoxicants and the non-genotoxic hepatocarcinogens but also between the CAR activators phenobarbital, phenytoin and 1,1-bis-(4-chlorophenyl)-2,2-dichloroethene which were grouped together, and the two PXR activators pregnenolone 16a-carbonitrile and clotrimazole. Diethylstilbestrol had an expression profile that was quite distinct from the other PXR activators, suggesting that this compound is certainly not a classic PXR modulator. Moreover, some differences were observed between phenytoin (not considered as a hepatocarcinogen), and the other two CAR activators. Our data therefore indicate that discrimination is possible between hepatocarcinogens and hepatotoxicants, between CAR and PXR modulators and also between compounds within the same class of modulators using a short-term transcriptomic approach.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39378" }, "primaryId" : "GEO:GSE39378", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39378" } ] }, "title" : "Hepatic transcriptome of rats treated with vehicle or fipronil (3 mg/kg/d per os for 14 days)", "dateAssigned" : "2012-07-16T00:00:00.000-05:00", "summary" : "Fipronil (CAS #: 120068-37-3), a widely used insecticide, has been described as a thyroid disruptor in rat inducing a marked increase in thyroxine (T4) clearance resulting in a decrease in T4 plasma concentration. These effects seem to require the bioactivation of fipronil via its biotransformation into fipronil sulfone by cytochromes P450 (CYP). Here, we hypothesized that fipronil-induced thyroid disruption may, at least in part, result from the induction of hepatic enzymes involved in the metabolism of thyroid hormones. Thus, we used microarrays to perform a genome-wide analysis of the effects of fipronil on gene expression in rat liver.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23962444" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39525" }, "primaryId" : "GEO:GSE39525", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39525" } ] }, "title" : "5 Day Oral Study of A-998679 in Male Sprague Dawley Rats (liver)", "dateAssigned" : "2012-07-20T00:00:00.000-05:00", "summary" : "Male Sprague-Dawley rats [Crl:CD®(SD)IGS BR], weighing ~250 g at study initiation were obtained from Charles River Laboratories, Inc. (Wilmington, MA). Rats were housed singly in ventilated, stainless steel, wire-bottom hanging cages and fed non-certified Rodent Chow (Harlan Labs, Madison, WI) and water ad libitum and acclimated for at least 5 days after arrival. Rats were randomly assigned to various treatment groups (3 rats/group) and were dosed once daily by oral gavage with vehicle (0.2% hydroxypropylmethylcellulose at a dose volume of 10 ml/kg) or with 30, 100, or 200 mg/kg of A-998679. All rats were fasted overnight after their last dose, weighed and sacrificed under isoflurane anesthesia. Liver and small intestine (jejunum) were flash frozen in liquid nitrogen and stored at -80°C until processing for gene expression profiling on the Affymetrix platform.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23112805" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39700" }, "primaryId" : "GEO:GSE39700", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39700" } ] }, "title" : "miRNA profile of rat vascular smooth muscle cell stimulated by 2.6 mM high-phosphate", "dateAssigned" : "2012-07-27T00:00:00.000-05:00", "summary" : "We compared time-series miRNA expression profile in high-phosphate–stimulated rat vascular smooth muscle cells at 0, 3, and 12 hr respectively.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39788" }, "primaryId" : "GEO:GSE39788", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39788" } ] }, "title" : "Mapping of Three Genetic Determinants of Susceptibility to Estrogen-Induced Mammary Cancer within the Emca8 Locus on Rat Chromosome 5", "dateAssigned" : "2012-07-31T00:00:00.000-05:00", "summary" : "We are using the ACI rat model of 17beta-estradiol induced mammary cancer to define the mechanisms through which estrogens contribute to breast cancer development; identify and functionally characterize the genetic variants that determine susceptibility; and define the hormone-gene-environment interactions that influence development of mammary cancer in this physiologically relevant rat model. Female ACI rats are uniquely susceptible to development of mammary cancer when treated continuously with physiologic levels of 17beta-estradiol. Induction of mammary cancer in female ACI rats occurs through a mechanism that is largely dependent upon estrogen receptor-alpha. Interval mapping analyses of progeny generated in intercrosses between susceptible ACI rats and resistant Brown Norway (BN) rats revealed seven quantitative trait loci (QTL), designated Emca3 (Estrogen-induced mammary cancer) through Emca9, each of which harbors one or more genetic determinants of mammary cancer susceptibility. Genes that reside within Emca8 on RNO5 and were differentially expressed between 17beta-estradiol treated ACI and ACI.BN-Emca8 congenic rats were identified as Emca8 candidates.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23151807" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39850" }, "primaryId" : "GEO:GSE39850", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39850" } ] }, "title" : "5 Day Oral Study of A-998679 in Male Sprague Dawley Rats (Jejunum)", "dateAssigned" : "2012-08-02T00:00:00.000-05:00", "summary" : "Male Sprague-Dawley rats [Crl:CD®(SD)IGS BR], weighing ~250 g at study initiation were obtained from Charles River Laboratories, Inc. (Wilmington, MA). Rats were housed singly in ventilated, stainless steel, wire-bottom hanging cages and fed non-certified Rodent Chow (Harlan Labs, Madison, WI) and water ad libitum and acclimated for at least 5 days after arrival. Rats were randomly assigned to various treatment groups (3 rats/group) and were dosed once daily by oral gavage with vehicle (0.2% hydroxypropylmethylcellulose at a dose volume of 10 ml/kg) or with 30, 100, or 200 mg/kg of A-998679. All rats were fasted overnight after their last dose, weighed and sacrificed under isoflurane anesthesia. Liver and small intestine (jejunum) were flash frozen in liquid nitrogen and stored at -80°C until processing for gene expression profiling on the Affymetrix platform.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23112805" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39979" }, "primaryId" : "GEO:GSE39979", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39979" } ] }, "title" : "Expression data from cultured rat astrocytes", "dateAssigned" : "2012-08-08T00:00:00.000-05:00", "summary" : "The objective of this study is to search for calcium signal-dependent expression changes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23798419" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39980" }, "primaryId" : "GEO:GSE39980", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE39980" } ] }, "title" : "Effect of zonisamide co-administration with levodopa on global gene expression in the striata of rats with Parkinson’s disease", "dateAssigned" : "2012-08-08T00:00:00.000-05:00", "summary" : "The anti-epileptic drug zonisamide is reported to exert beneficial effects in patients with Parkinson's disease. To elucidate the pathophysiological mechanisms underlying the anti-parkinsonism effects of zonisamide, we examined the effect of zonisamide co-administered with levodopa in the striata of rats with 6-hydoroxydopamine hemiparkinsonism by using a DNA microarray for genome-wide gene expression profiling. We found that the expression of some genes related to metabolism and nervous system development and function were upregulated by zonisamide; expression of these genes was downregulated by levodopa. Furthermore, many genes related to the immune system and inflammation were downregulated by zonisamide, and their expression was upregulated by levodopa. These results indicate that zonisamide has a protective effect when co-administered with levodopa.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23103374" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40117" }, "primaryId" : "GEO:GSE40117", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40117" } ] }, "title" : "Analyses of transcriptomic responses generated by hepatocarcinogens in a battery of liver-based in vitro models", "dateAssigned" : "2012-08-14T00:00:00.000-05:00", "summary" : "For assessing the cancer-causing potential for humans of a chemical compound, the conventional approach is the use of the 2-year rodent carcinogenicity bioassay, thus alternatives such as in vitro toxicogenomics are highly desired. In the present study, the transcriptomics responses following exposure to genotoxic (GTX) and non-genotoxic (NGTX) hepatocarcinogens and non-carcinogens (NC) in five liver-based in vitro models, namely conventional and epigenetically-stabilized cultures of primary rat hepatocytes, the human hepatoma-derived HepaRG and HepG2 cell lines and the human embryonic stem cell-derived hepatocyte-like cells hES-Heps are examined and compared.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23393228" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40170" }, "primaryId" : "GEO:GSE40170", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40170" } ] }, "title" : "Flow dependent gene expression in the rat aorta under physiological conditions", "dateAssigned" : "2012-08-16T00:00:00.000-05:00", "summary" : "Objective: Shear forces play a key role in the maintenance of vessel wall integrity. Current understanding regarding shear-dependent gene expression is mainly based on in vitro or in vivo observations with experimentally deranged shear, hence reflecting acute molecular events in relation to flow. Our objective was to combine computational fluid dynamic (CFD) simulations with global microarray analysis to study flow-dependent vessel wall biology in portions of the entire aorta under physiological conditions. Methods and Results: Animal-specific WSS magnitude and vector direction were estimated using CFD based on aortic geometry and flow information acquired by MRI. Two distinct flow pattern regions were identified in the normal rat aorta; the distal part of the inner curvature being exposed to low WSS and a non-uniform vector direction, and a region along the outer curvature being subjected to markedly higher levels of WSS and a uniform vector direction. Microarray analysis identified numerous novel mechanosensitive genes, including Hand2, trpc4 and slain2, and confirmed well-known ones, such as klf2 and BMP4. Three genes were further validated for protein , including Hand2, which showed higher expression in the endothelium in regions exposed to disturbed flow. Gene ontology analysis revealed an over-representation of genes involved in transcriptional regulation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23284944" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40251" }, "primaryId" : "GEO:GSE40251", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40251" } ] }, "title" : "High-fat or ethinyl-estradiol intake during pregnancy increases mammary cancer risk in several generations of offspring", "dateAssigned" : "2012-08-21T00:00:00.000-05:00", "summary" : "Maternal exposures during pregnancy influence the risk of many chronic adult-onset diseases in the offspring. We investigated whether feeding pregnant rats a high fat (HF) or ethinyl-estradiol (EE2)-supplemented diet affects carcinogen-induced mammary cancer risk in daughters, granddaughters and great-granddaughters. Here we show that mammary tumorigenesis is higher in daughters and granddaughters of HF rat dams and in daughters, granddaughters and great-granddaughters of EE2 rat dams. Outcross experiments indicate that increased mammary cancer risk is transmitted to HF granddaughters equally through the female or male germlines, but it is only transmitted to EE2 granddaughters through the female germline. The effects of maternal EE2 exposure on offspring's mammary cancer risk are associated with alternations in the DNA methylation machinery and methylation patterns in mammary tissue of all three EE2 generations. We conclude that dietary and estrogenic exposures in pregnancy increase breast cancer risk in multiple generations of offspring, possibly through non-genetic means", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22968699" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40336" }, "primaryId" : "GEO:GSE40336", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40336" } ] }, "title" : "Effect of Acetominophen on Rat Primary Hepatocytes.", "dateAssigned" : "2012-08-23T00:00:00.000-05:00", "summary" : "Primary rat hepatocytes were treated for 24 and 48 hours with two doses (500 uM and 5 mM) of acetominophen and 1% DMSO vehicle control. Five replicates of each treatment were performed. Cells were then extracted and RNA processed for microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25475144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40337" }, "primaryId" : "GEO:GSE40337", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40337" } ] }, "title" : "Effect of Dioctyl Phthalate on Rat Primary Hepatocytes.", "dateAssigned" : "2012-08-23T00:00:00.000-05:00", "summary" : "Primary rat hepatocytes were treated for 24 and 48 hours with two doses (250 uM and 1 mM) of dioctyl phthalate and 1% DMSO vehicle control. Five replicates of each treatment were performed. Cells were then extracted and RNA processed for microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25475144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40338" }, "primaryId" : "GEO:GSE40338", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40338" } ] }, "title" : "Effect of Sodium Valproate on Rat Primary Hepatocytes.", "dateAssigned" : "2012-08-23T00:00:00.000-05:00", "summary" : "Primary rat hepatocytes were treated for 24 and 48 hours with two doses (500 uM and 10 mM) of sodium valproate and water vehicle control. Five replicates of each treatment were performed. Cells were then extracted and RNA processed for microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25475144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40339" }, "primaryId" : "GEO:GSE40339", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40339" } ] }, "title" : "Effect of Phenobarbital on Rat Primary Hepatocytes.", "dateAssigned" : "2012-08-23T00:00:00.000-05:00", "summary" : "Primary rat hepatocytes were treated for 24 and 48 hours with two doses (300 uM and 3 mM) of phenobarbital and water vehicle control. Five replicates of each treatment were performed. Cells were then extracted and RNA processed for microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25475144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40340" }, "primaryId" : "GEO:GSE40340", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40340" } ] }, "title" : "Effect of Beta-Naphthoflavone on Rat Primary Hepatocytes.", "dateAssigned" : "2012-08-23T00:00:00.000-05:00", "summary" : "Primary rat hepatocytes were treated for 24 and 48 hours with two doses 1 uM and 100 mM) of beta-naphthaflavone and 1% DMSO vehicle control. Five replicates of each treatment were performed. Cells were then extracted and RNA processed for microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25475144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40341" }, "primaryId" : "GEO:GSE40341", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40341" } ] }, "title" : "Effect of Chlorpromazine HCl on Rat Primary Hepatocytes.", "dateAssigned" : "2012-08-23T00:00:00.000-05:00", "summary" : "Primary rat hepatocytes were treated for 24 and 48 hours with two doses (0.8 uM and 20 uM) of chlorpromazine HCl and 1% DMSO vehicle control. Five replicates of each treatment were performed. Cells were then extracted and RNA processed for microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25475144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40342" }, "primaryId" : "GEO:GSE40342", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40342" } ] }, "title" : "Effect of Diisononyl Phthalate on Rat Primary Hepatocytes.", "dateAssigned" : "2012-08-23T00:00:00.000-05:00", "summary" : "Primary rat hepatocytes were treated for 24 and 48 hours with two doses (25 mM and 100 mM) of diisononyl phthalate and 1% DMSO vehicle control. Five replicates of each treatment were performed. Cells were then extracted and RNA processed for microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25475144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40344" }, "primaryId" : "GEO:GSE40344", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40344" } ] }, "title" : "Effect of Clofibrate on Rat Primary Hepatocytes.", "dateAssigned" : "2012-08-23T00:00:00.000-05:00", "summary" : "Primary rat hepatocytes were treated for 24 and 48 hours with two doses (60 uM and 1 mM) of clobibrate and 1% DMSO vehicle control. Five replicates of each treatment were performed. Cells were then extracted and RNA processed for microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25475144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40346" }, "primaryId" : "GEO:GSE40346", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40346" } ] }, "title" : "Effect of WY-14643 on Rat Primary Hepatocytes.", "dateAssigned" : "2012-08-23T00:00:00.000-05:00", "summary" : "Primary rat hepatocytes were treated for 24 and 48 hours with two doses 8 uM and 200 uM) of WY-14643 and 1% DMSO vehicle control. Five replicates of each treatment were performed. Cells were then extracted and RNA processed for microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25475144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40347" }, "primaryId" : "GEO:GSE40347", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40347" } ] }, "title" : "Effect of Methapyrilene on Rat Primary Hepatocytes.", "dateAssigned" : "2012-08-23T00:00:00.000-05:00", "summary" : "Primary rat hepatocytes were treated for 24 and 48 hours with two doses (3 uM and 100 uM) of methaphyriline and 1% DMSO vehicle control. Five replicates of each treatment were performed. Cells were then extracted and RNA processed for microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25475144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40381" }, "primaryId" : "GEO:GSE40381", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40381" } ] }, "title" : "Expression data from HSCs", "dateAssigned" : "2012-08-27T00:00:00.000-05:00", "summary" : "Hepatic stellate cells (HSCs) experience phenotypic transformation, from the quiescent phenotype to the activated one, after different etiologies of liver injury. Liver fibrosis is then occurred upon the activation of HSCs. miR-16 deficiency is identified to be an important characteristic of HSCs activation. We used Affymetrix rat 230 2.0 arrays (Affymetrix, Santa Clara, U.S.A.) to uncover the global alternations of transcriptome under miR-16 restoration.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40421" }, "primaryId" : "GEO:GSE40421", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40421" } ] }, "title" : "Generation of oligodendroglial cells by direct lineage conversion", "dateAssigned" : "2012-08-28T00:00:00.000-05:00", "summary" : "We report the generation of induced oligodendrocyte precursor cells (iOPCs) by direct lineage conversion. Forced expression of the three transcription factors Sox10, Olig2 and Zfp536 was sufficient to convert mouse and rat fibroblasts into iOPCs with morphologies and gene expression signatures that resemble OPCs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23584610" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40454" }, "primaryId" : "GEO:GSE40454", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40454" } ] }, "title" : "Mechanisms and rescue strategies of Calcineurin inhibitor mediated tolerance abrogation", "dateAssigned" : "2012-08-29T00:00:00.000-05:00", "summary" : "To ensure safety tolerance induction protocols are accompanied by conventional immunosuppressive drugs IS. But IS such as calcineurin inhibitors CNI can interfere with tolerance induction. We investigated the effect of an additional CNI treatment on anti-CD4 mAb-induced tolerance induction upon rat kidney transplantation. Additional CNI treatment induced deteriorated graft function and chronic rejection characterised by alloantibody production, intragraft plasma cells and C3d deposition. Microarray analysis revealed enhanced intragraft expression of the B cell chemokine CXCL13 upon additional CNI treatment. In contrast PNOC, a B cell-related gene highly expressed in operational tolerant kidney transplant recipients, was decreased in grafts of anti-CD4 mAb+CsA-treated recipients suggesting an altered balance of B regulatory genes. Transient B cell depletion or transfer of Tregs three weeks after transplantation could inhibit intragraft B cell accumulation, alloantibody production and ameliorate chronic rejection. These data represent unexpected findings and should be taken into consideration when designing new clinical trials. To safe the benefit of CNI in controlling memory T cell responses we need strategies for a therapeutic optimization. We show here that early B cell depletion or transfer of Tregs may be one approach to arrest B cell accumulation, activation and graft destruction.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40490" }, "primaryId" : "GEO:GSE40490", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40490" } ] }, "title" : "Hippocampal gene expression profiling in a rat model of posttraumatic epilepsy reveals temporal upregulation of lipid metabolism-related genes", "dateAssigned" : "2012-08-30T00:00:00.000-05:00", "summary" : "Traumatic brain injury occasionally causes posttraumatic epilepsy. To elucidate the molecular events responsible for posttraumatic epilepsy, we established a rodent model that involved the injection of microliter quantities of FeCl3 solution into the amygdalar nuclear complex. We previously compared hippocampal gene expression profiles in the traumatic epilepsy model and normal rats at 5 days after brain injury (acute phase) and observed the role of inflammation. In this study, we focused on later stages of epileptogenesis. We compared gene expression profiles at 5, 15 (sub-chronic phase), and 30 days (chronic phase) after brain injury to identify temporal changes in molecular networks involved in epileptogenesis. A total of 81 genes was significantly (at least 2-fold) up- or downregulated over the course of disease progression. We found that genes related to lipid metabolism, namely, Apoa1, Gh, Mc4r, Oprk1, and Pdk4, were temporarily upregulated in the sub-chronic phase. Changes in lipid metabolism regulation might be related to seizure propagation during epileptogenesis. This temporal description of hippocampal gene expression profiles throughout epileptogenesis provides clues to potential markers of disease phases and new therapeutic targets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23585123" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40497" }, "primaryId" : "GEO:GSE40497", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40497" } ] }, "title" : "Temporal induction of immunoregulatory processes coincides with age-dependent resistance to viral-induced type 1 diabetes [Rat]", "dateAssigned" : "2012-08-30T00:00:00.000-05:00", "summary" : "In applying this approach to the BN rat, we observed that samples collected from both sub-strains at 60 days of age induced transcription of genes encoding cytokines, immune receptors, and signaling molecules consistent with a their shared susceptibility and immune activation. The DRlyp/lyp signature was differentiated from that of the DR+/+ by more robust induction of many interleukin (IL)-1–regulated genes. Treatment of DRlyp/lyp rats with IL-1 receptor antagonist (IL-1RN) delayed onset and, in part, normalized the signature, suggesting that this approach may prove useful in monitoring the effect of therapeutic interventions in human T1D. Consistent with the presence of TREG cells in DR+/+ rats, we observed induction of a signature possessing negative regulators of transcription and inflammation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23739610" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40500" }, "primaryId" : "GEO:GSE40500", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40500" } ] }, "title" : "Expression data from endthelial cells in ductus arteriosus and aorta in rat fetuses or neonates", "dateAssigned" : "2012-08-30T00:00:00.000-05:00", "summary" : "Since ductus arteriosus (DA) has unique characteristics comparing other vessels, we hypothesized that ECs were the primary target to investigate the molecular mechanisms of DA-specific vasoconstriction and vascular remodeling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24086288" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40506" }, "primaryId" : "GEO:GSE40506", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40506" } ] }, "title" : "Genome-wide mapping of Olig2 targets in primary oligodendrocytes", "dateAssigned" : "2012-08-30T00:00:00.000-05:00", "summary" : "Myelination by oligodendrocytes in the central nervous system (CNS) is essential for proper brain function, yet the molecular determinants that control this process remain poorly understood. The basic helix-loop-helix transcription factors Olig1 and Olig2 promote myelination, whereas bone morphogenetic protein (BMP) and Wnt/ß-catenin signaling inhibit myelination. Here we show that these opposing regulators of myelination are functionally linked by the Olig1/2 common target Smad-interacting protein-1 (Sip1). We demonstrate that Sip1 is an essential modulator of CNS myelination. Sip1 represses differentiation inhibitory signals by antagonizing BMP receptor-activated Smad activity while activating crucial oligodendrocyte-promoting factors. Importantly, a key Sip1-activated target, Smad7, is required for oligodendrocyte differentiation and partially rescues differentiation defects caused by Sip1 loss. Smad7 promotes myelination by blocking the BMP- and ß-catenin-negative regulatory pathways. Thus, our findings reveal that Sip1-mediated antagonism of inhibitory signaling is critical for promoting CNS myelination and point to new mediators for myelin repair.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22365546" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40534" }, "primaryId" : "GEO:GSE40534", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40534" } ] }, "title" : "Expression profiling in ductus arteriosus and aorta of Brown-Norway and Fischer344 rats", "dateAssigned" : "2012-08-31T00:00:00.000-05:00", "summary" : "We analyzed the fold difference between BN and F344 rats in ductus arteriosus in order to identify the down-regulated and up-regulated genes specifically in BN rat's DA. The differences in aorta was also examined for additional comparison.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40552" }, "primaryId" : "GEO:GSE40552", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40552" } ] }, "title" : "DBCP Exposed Rat Testis Transcript Content", "dateAssigned" : "2012-09-03T00:00:00.000-05:00", "summary" : "Rats were exposed to sub-chronic low doses of the the germ cell toxicant 1,2-dibromo-3-chloropropane (DBCP) or corn oil (control for DBCP), for 3 months. Some rats in each group underwent 3 months of post-exposure recovery.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40642" }, "primaryId" : "GEO:GSE40642", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40642" } ] }, "title" : "Pdx1 overexpression sensitizes to IL-1b-induced apoptosis", "dateAssigned" : "2012-09-06T00:00:00.000-05:00", "summary" : "Cytokines have been shown to play a key role in the destruction of beta cells. In the rat insulinoma cell line (INS-1ab) overexpressing pancreatic duodenum homeobox 1 (Pdx1) increases sensitivity to Interleukin 1b (IL-1b). To elucidate mechanisms of action underlying Pdx1 driven potentiation of beta-cell sensitivity to IL-1ß, we performed a microarray analysis of INS-1ab cells with and without Pdx1 overexpression exposed to IL-1ß between 2h and 24h.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23000401" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40713" }, "primaryId" : "GEO:GSE40713", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40713" } ] }, "title" : "Mammary Gland Morphology and Gene Expression Signature of Prepubertal Male and Female Rats Following Exposure to Exogenous Estradiol", "dateAssigned" : "2012-09-09T00:00:00.000-05:00", "summary" : "In order to properly understand whether xenoestrogens act as estrogens, it is essential to possess a solid portrait of the physiological effects of exogenous estradiol. Because the estrogen-dependent gene expression is one of the primary biomarkers of estrogenic action, we have assessed effects of three doses of exogenous estradiol (0.1, 1.0 and 10 µg/kg of body weight/day) on the mammary gland morphology and gene expression profiles by microarray analysis of prepubertal male and female rats of both sexes compared to untreated controls. Estradiol was administered subcutaneously with minipumps from weaning at PND21 to the end of the experiment at PND33. The data suggest that the male mammary is a sensitive tissue for estrogenicity assessment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24046281" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40779" }, "primaryId" : "GEO:GSE40779", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40779" } ] }, "title" : "The expression profiles of miRNAs in the heart with glucose fluctuation compared with sustained hyperglycemia.", "dateAssigned" : "2012-09-11T00:00:00.000-05:00", "summary" : "We examined miRNAs expression profiles in rat hearts. The expression of five of 350 scanned miRNAs significantly differed between rat hearts exposed to vehicle and diabetic rat hearts. The expression of 31 miRNAs significantly differed between vehicle and diabetes with fluctuations in glucose levels, and that of 22 miRNAs significantly differed between diabetic hearts and diabetic hearts with glucose fluctuations.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26497329" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40795" }, "primaryId" : "GEO:GSE40795", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40795" } ] }, "title" : "Transcriptomic Dose Response Changes in Female Mouse and Rat Lungs following Chloroprene Exposure", "dateAssigned" : "2012-09-12T00:00:00.000-05:00", "summary" : "ß-chloroprene (2-chloro-1,3-butadiene), a monomer used in the production of neoprene elastomers, is of regulatory interest due to the production of multi-organ tumors in mouse and rat cancer bioassays. A significant increase in female mouse lung tumors was observed at the lowest exposure concentration of 12.8 ppm while a small, but not statistically significant, increase was observed in female rats only at the highest exposure concentration of 80 ppm. The metabolism of chloroprene results in the generation of reactive epoxides and the rate of overall chloroprene metabolism is highly species dependent. To identify potential key events in the mode-of-action of chloroprene lung tumorigenesis, dose response and time course gene expression microarray measurements were made in the lungs of female mice and female rats. The gene expression changes were analyzed using both a traditional analysis of variance approach followed by pathway enrichment analysis and a pathway-based benchmark dose (BMD) analysis approach. Pathways related to glutathione biosynthesis and metabolism were the primary pathways consistent with cross-species differences in tumor incidence and transcriptional BMD values for the pathway were more similar to differences in tumor response than were estimated target tissue dose surrogates based on the total amount of chloroprene metabolized per unit mass of lung tissue per day. The closer correspondence of the transcriptional changes with the tumor response are likely due to their reflection of the overall balance between metabolic activation and detoxication reactions whereas the current tissue dose surrogate reflects only oxidative metabolism.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23125180" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40937" }, "primaryId" : "GEO:GSE40937", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE40937" } ] }, "title" : "ARF6 bi-directionally regulates the dendritic spine formation depending on neuronal maturation and activity", "dateAssigned" : "2012-09-17T00:00:00.000-05:00", "summary" : "Recent studies reported contradictory results regarding the role of ADP-ribosylation factor 6 (ARF6), a small GTPase known to regulate actin cytoskeleton, in dendritic spine development and maintenance. We readdress this question, and found that ARF6 either positively or negatively regulates dendritic spine formation depending on neuronal maturation and activity. ARF6 activation facilitates filopodia to spines transition, increasing the spine formation in developing neurons while it decreases spine density in matured neurons. Consistently, genome-wide microarray analysis revealed that Arf6 activation in developing and matured neurons leads to opposite expression patterns of a subset of genes that are involved in neuronal morphology.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25605715" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41173" }, "primaryId" : "GEO:GSE41173", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41173" } ] }, "title" : "Environmentally Induced Epigenetic Transgenerational Inheritance of Altered Sertoli Cell Transcriptome and Epigenome: Molecular Etiology of Male Infertility [Affymetrix]", "dateAssigned" : "2012-09-26T00:00:00.000-05:00", "summary" : "Environmental toxicants have been shown to induce the epigenetic transgenerational inheritance of adult onset disease, including testis disease and male infertility. The exposure of a gestating female during the period of gonadal sex determination has been shown to promote sperm epimutations, differential DNA methylation regions (DMR), that transmit transgenerational disease to subsequent generations. The current study was designed to determine the impact of an altered sperm epigenome on the subsequent development of an adult somatic cell (Sertoli cell) that influences the onset of a specific disease (male infertility). A gestating female rat (F0 generation) was exposed to the agriculture fungicide vinclozolin during gonadal sex determination and then the subsequent F3 generation progeny used for the isolation of Sertoli cells and assessment of testis disease. As previously observed, a spermatogenic cell apoptosis was observed. The Sertoli cells that provide the physical and nutritional support for the spermatogenic cells were isolated and alterations in gene expression examined. Over 400 genes were differentially expressed in the F3 generation control versus vinclozolin lineage Sertoli cells. A number of specific signaling pathways and cellular processes were identified to be transgenerationally altered. One of the key metabolic processes affected was pyruvate/lactate production that is directly linked to spermatogenic cell viability. The Sertoli cell epigenome was also altered with over 100 promoter differential DNA methylation regions (DMR) modified in the vinclozolin F3 generation Sertoli cell. The genomic features and overlap with the sperm DMR were investigated. Observations demonstrate that the transgenerational sperm epigenetic alterations subsequently alters the development of a specific somatic cell (Sertoli cell) epigenome and transcriptome that then has a role in the adult onset disease (male infertility). The environmentally induced epigenetic transgenerational inheritance of testis disease appears to be a component of the molecular etiology of male infertility.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23555832" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41217" }, "primaryId" : "GEO:GSE41217", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41217" } ] }, "title" : "Acute Stress Induced Increase in Histone H3 Lys 9 Trimetylation in Rat Hippocampus", "dateAssigned" : "2012-09-28T00:00:00.000-05:00", "summary" : "We utilized ChIP Seq to examine the the genomic localization of the increase in H3K9 trimethylation we had previously observed in the hippocampus as a consequence of acute restraint stress in rats (Hunter et. al PNAS 2009).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23043114" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41262" }, "primaryId" : "GEO:GSE41262", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41262" } ] }, "title" : "Microarray gene expression profiles of adipose-derived mesenchymal stem cells from LEW and PVG rats upon 24h and 48h LPS stimulation", "dateAssigned" : "2012-10-01T00:00:00.000-05:00", "summary" : "We have extended our investigation to differential immunogenicity between tolerogenic PVG rats and immunogenic LEW rats by analyzing gene expression in adipose-derived mesenchymal stem cells (ASCs) with LPS stimulation. Furthermore, to establish a direct link between gene expression and immunogenic functional annotation, ASCs from LEW and PVG rats were obtained, and the effects of inherent difference and LPS treatment on global gene expression were evaluated using microarray analyses.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23613728" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41388" }, "primaryId" : "GEO:GSE41388", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41388" } ] }, "title" : "Systematic Evaluation of Medium-Throughput mRNA Abundance Platforms", "dateAssigned" : "2012-10-05T00:00:00.000-05:00", "summary" : "Profiling of mRNA abundances with high-throughput platforms such as microarrays and RNA-Seq has become an important tool in both basic and biomedical research. However these platforms remain prone to systematic errors, and have challenges in clinical and industrial application. As a result it is standard practice to validate a subset of key results using alternate technologies. Similarly, clinical and industrial applications typically involve transitions from high-throughput discovery platform to medium-throughput validation ones. These medium-throughput validation platforms have high technical reproducibility and reduced sample input needs, and low sensitivity to sample-quality (e.g. for processing FFPE specimens). Unfortunately, while medium-throughput platforms have proliferated, there are no comprehensive comparisons of them. Here we present ABI's OpenArray and qPCR systems.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23169800" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41420" }, "primaryId" : "GEO:GSE41420", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41420" } ] }, "title" : "A comparative analysis of genistein and daidzein in affecting lipid metabolism in rat liver", "dateAssigned" : "2012-10-09T00:00:00.000-05:00", "summary" : "The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19430610" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41452" }, "primaryId" : "GEO:GSE41452", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41452" } ] }, "title" : "Gene expression in the whole brains of two spontaneously hypertensive rat strains at 3 and 6 weeks of age", "dateAssigned" : "2012-10-10T00:00:00.000-05:00", "summary" : "We examined gene expression profiles in the rat whole brains using genome-wide microarray technology, and determined gene expression profiles in 3 rat strains: normotensive WKY, spontaneously hypertensive rats (SHR), and stroke-prone SHR (SHRSP). To identify candidate genes involved in the genesis of hypertension in the SHR strains, we compared the gene expression levels at 3 and 6 weeks of age, isolated 407 genes showing a more than 4-fold increase or a less than 1/4-fold decrease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24452243" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41453" }, "primaryId" : "GEO:GSE41453", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41453" } ] }, "title" : "Gene expression in the kidneys of two spontaneously hypertensive rat strains at 3 and 6 weeks of age", "dateAssigned" : "2012-10-10T00:00:00.000-05:00", "summary" : "We examined gene expression profiles in the rat kidneys using genome-wide microarray technology, and determined gene expression profiles in 3 rat strains: normotensive WKY, spontaneously hypertensive rats (SHR), and stroke-prone SHR (SHRSP). To identify candidate genes involved in the genesis of hypertension in the SHR strains, we compared the gene expression levels at 3 and 6 weeks of age, isolated 407 genes showing a more than 4-fold increase or a less than 1/4-fold decrease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26165378" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41462" }, "primaryId" : "GEO:GSE41462", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41462" } ] }, "title" : "Antisense exon profiling across human, mouse, and rat", "dateAssigned" : "2012-10-10T00:00:00.000-05:00", "summary" : "Transcription profiling of antisense transcripts of 10 tissues each from human, mouse, and rat.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23577827" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41464" }, "primaryId" : "GEO:GSE41464", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41464" } ] }, "title" : "Sense exon profiling across human, mouse, and rat", "dateAssigned" : "2012-10-10T00:00:00.000-05:00", "summary" : "Transcription profiling of sense transcripts of 10 tissues each from human, mouse, and rat.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23577827" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41537" }, "primaryId" : "GEO:GSE41537", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41537" } ] }, "title" : "MicroRNA expression in neonatal and adult rat cardiomyocytes", "dateAssigned" : "2012-10-12T00:00:00.000-05:00", "summary" : "Expression profiles of microRNAs in neonatal (isolated from day0 newborn rats) and adult rat cardiomyocytes (isolated from 2month old rats)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23222520" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41540" }, "primaryId" : "GEO:GSE41540", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41540" } ] }, "title" : "Genes induced after BDV infection in Sprague Dawley and Lewis rats", "dateAssigned" : "2012-10-12T00:00:00.000-05:00", "summary" : "Borna Disease Virus (BDV) is a neurotropic virus that persistently infects neurons in the central nervous system of various hosts, including rats. Although BDV is known to be an IFN sensitive virus, determination of the cellular mRNA transcript levels revealed the induction of IFN-stimulated genes in organotypic rat hippocampus slice cultures, raising the question how BDV evades this innate immune response. Using rat Mx protein as a specific marker for IFN-induced gene products, we could show that neurons lack detectable levels of Mx in these BDV infected cultures, whereas astrocytes and microglial cells were Mx positive. Neurons remained Mx negative after treatment of uninfected hippocampus cultures as well as primary dissociated neuronal cultures with high concentrations of IFN-a. This non-responsiveness correlated with a lack of a detectable nuclear translocation of pSTAT1 in rat neurons. Consistently, IFN treatment of BDV-infected rat neurons did not prevent the establishment of a viral persistence in the neuronal tissue. However, IFN treatment efficiently prevented vesicular stomatitis virus (VSV) replication, indicating that these cells can mount a weak innate immune response. In contrast, IFN treatment of mouse neurons resulted in the upregulation of Mx1 proteins and inhibition of BDV replication, indicating species-specific differences in the IFN response in neurons between mice and rats. Rat neurons may therefore represent the ideal cell type for BDV to evade the innate immune in the central nervous system.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23793543" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41552" }, "primaryId" : "GEO:GSE41552", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41552" } ] }, "title" : "Hypertensive SHR vs WKY, RVLM, PVN, SON, NIL", "dateAssigned" : "2012-10-12T00:00:00.000-05:00", "summary" : "We have used Affymetrix microarray-driven gene profiling to comprehensively describe the expression of mRNAs in the brainstem and hypothalamus in the adult male spontaneously hypertensive rat (SHR) as compared to its normotensive parental Wistar-Kyoto (WKY) strain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41572" }, "primaryId" : "GEO:GSE41572", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41572" } ] }, "title" : "Molecular mechanisms of pulmonary response progression in crystalline silica exposed rats", "dateAssigned" : "2012-10-15T00:00:00.000-05:00", "summary" : "The capability to detect target organ toxicity as well as to determine the molecular mechanisms underlying such toxicity by employing surrogate biospecimens that can be obtained by a non-invasive or minimally invasive procedure has significant advantage in occupational toxicology. Pulmonary toxicity and global gene expression profile in the lungs, peripheral blood and bronchoalveolar lavage (BAL) cells were determined in rats at 44-weeks following pulmonary exposure to crystalline silica (15 mg/m3, 6-hours/day, 5 days). A significant elevation in lactate dehydrogenase activity and albumin content observed in the BAL fluid suggested the induction of pulmonary toxicity in the silica exposed rats. Similarly, the observation of histological alterations, mainly type II pneumocyte hyperplasia and fibrosis, in the lungs further confirmed silica-induced pulmonary toxicity in the rats. A significant increase in the number of neutrophils and elevated monocyte chemotactic protein 1 level in the BAL fluids suggested silica-induced pulmonary inflammation in the rats. Determination of global gene expression profile in the lungs, BAL cells, and peripheral blood of the silica exposed rats identified 144, 236, and 51 significantly differentially expressed genes (SDEGs), respectively, compared with the corresponding control samples. Bioinformatics analysis of the SDEGs demonstrated a remarkable similarity in the biological functions, molecular networks and canonical pathways that were significantly affected by silica exposure in the lungs, BAL cells and blood of the rats. Induction of inflammation was identified, based on the bioinformatics analysis of the significantly differentially expressed genes in the lungs, blood and BAL cells, as the major molecular mechanism underlying the silica-induced pulmonary toxicity. The findings of our study demonstrated the potential application of global gene expression profiling of peripheral blood and BAL cells as a valuable minimally invasive approach to study silica-induced pulmonary toxicity in rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28317464" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41579" }, "primaryId" : "GEO:GSE41579", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41579" } ] }, "title" : "A master cistromic circuit governing hepatic fibrogenesis [expression array]", "dateAssigned" : "2012-10-15T00:00:00.000-05:00", "summary" : "Liver fibrosis is a reversible wound-healing response to liver injury and hepatic stellate cells (HSCs) are central cellular players that mediate hepatic fibrogenesis. However, the molecular mechanisms that govern this process remain unclear. Expression profiling was used to explore the potential impact of VDR signaling in TGFß1 and TGFß1+1,25(OH)2D3-treated primary rat HSCs. Notably, 1,25(OH)2D3 treatment attenuated the culture-induced activation of HSCs, such that the transcriptome of treated cells closely resembled that of freshly isolated quiescent cells (Figure 2A), and co-treatment of 1,25(OH)2D3 together with TGFß resulted in considerable repression of a large set of TGFß induced genes. We also demonstrated that in primary mouse HSCs, calcipotriol potently repressed fibrotic gene expression, suggesting that the anti-TGFß properties of VDR agonists are likely conserved across mammalian species.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23622244" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41637" }, "primaryId" : "GEO:GSE41637", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41637" } ] }, "title" : "Evolutionary dynamics of gene and isoform regulation in mammalian tissues", "dateAssigned" : "2012-10-17T00:00:00.000-05:00", "summary" : "Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear. To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth. We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific. Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators. Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23258891" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41709" }, "primaryId" : "GEO:GSE41709", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41709" } ] }, "title" : "Perinatal Calorie Restriction with IUGR Perturbs Hepatic Circadian Cycling in Rat Male Offspring", "dateAssigned" : "2012-10-19T00:00:00.000-05:00", "summary" : "Aside from the perinatal complications associated with low birth weight, individuals born with intra-uterine growth restriction suffer from chronic diseases late in life that ultimately lead to a shortened lifespan. These late life metabolic sequelae of low birth weight include obesity and metabolic syndrome, diabetes mellitus, cardiovascular disease, hypertension, stroke, dyslipidemia, and non-alcoholic fatty liver disease/steatohepatitis. Animal models employing perinatal calorie restriction recapitulate the observations made in humans. Interestingly, if continued calorie restriction is employed post-natally the late life sequelae of intra-uterine growth restriction are ameliorated. These observations linking both fetal and early post natal growth to later health is now termed the developmental origins of health and disease. To further our understanding of the mechanism of how early growth affects late life health we have employed Affymetrix microarray-based expression profiling to characterize hepatic gene expression in a rat model of maternal semi-nutrient restriction. In these experiments we have limited maternal calorie intake to 50% of normal so as to create 3 groups of animals: Control (Con) male offspring born to mothers who were fed normally throughout gestation and lactation; intra-uterine calorie restricted male offspring (IUCR) born to mothers who had 50% restriction of calories from e11 to e21; and combined intra-uterine and post-natal calorie restriction (IPCR) male offspring who were born to mothers who received calorie restriction during both fetal growth (e11 to e21) and post-natally (p1-p21). Livers were collected at p21(day 21 of life) for Con and IPCR groups (IUCR withheld owing to ‘catch up” growth), and at p450 (day 450 of life) for Con, IUCR, and IPCR. The profiling data reveals clear alteration of circadian cycling at P21, and subtle changes for circadian gene expression at p450. In addition, a clear transcriptional response is found during active calorie restriction at p21 but an absence of a transcriptional response late in life at p450.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41734" }, "primaryId" : "GEO:GSE41734", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41734" } ] }, "title" : "Effect of Lactobacillus brevis 119-2 isolated from turnip “Tsuda kabu” on hepatic cholesterol level in cholesterol-administrated rat", "dateAssigned" : "2012-10-22T00:00:00.000-05:00", "summary" : "In previous in vitro study, we reported potential mechanism of cholesterol-lowering effect of Lactobacillus brevis119-2 (119-2) isolated from turnip “Tsuda kabu” is due to incorporation of cholesterol into 119-2 cell. In this study, we analyzed serum cholesterol and hepatic gene expression of Sprague-Dawley (SD) rat fed diet containing cholesterol with or without 119-2 for 2 weeks, to evaluate the cholesterol-lowering effect of 119-2 in vivo. Serum cholesterol of SD rat fed diet with 119-2 significantly decreased compared to SD rat fed diet without 119-2, and both viable and dead 119-2 indicated the effect. The result of hepatic gene analysis using DNA microarray suggested that potential mechanism of the cholesterol-lowering effect of 119-2 in vivo is inhibiting the activity of 3-hydroxy-3-methylglutaryl-CoA reductase by Insig (insulin induced gene) that is endoplasmic reticulum membrane protein, and catabolizing cholesterol to bile acid by Cyp7a1 (cytochrome P450 a1) that is the rate-limiting enzyme in the synthesis of bile acid from cholesterol. In addition, we concluded feeding 119-2 decreased serum low density lipoprotein (LDL) cholesterol by overexpression of Ldlr (LDL receptor gene). On the other hand, feeding Lactobacillus acidophilus ATCC43121 (ATCC) increased high density lipoprotein (HDL) cholesterol by over expression of Abca1 (ATP binding cassette sub-family A member 1 gene) and Angplt3 (Angiopoietin-like 3). These results suggested that 119-2 decrease the risk of atherosclerosis by serum cholesterol-lowering effect and improving effect of fatty liver and the LH (LDL cholesterol / HDL cholesterol) ratio.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23415664" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41735" }, "primaryId" : "GEO:GSE41735", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41735" } ] }, "title" : "To elucidate the role of estradiol- 17ß (E2) in the regulation of corpus luteum function", "dateAssigned" : "2012-10-22T00:00:00.000-05:00", "summary" : "Corpus luteum (CL) is a transient endocrine tissue formed from the remnants of the ovarian follicle after ovulation. In response to gonadotropin surge, the ovulating follicle undergoes dramatic changes in expression of genes and differentiation of follicular cells into luteal cells. In several species, of the several genes that are down- regulated post ovulation, Cyp19A1 that codes for aromatase, essential for biosynthesis of estradiol- 17ß (E2), also get down- regulated but appears to get up- regulated at later time points in the estrous cycle to have critical role in E2 secretion. In primates and rodents, higher expression and higher E2 levels has been observed in CL. Surprisingly, in the recently carried out gene expression profiling of PGF2a- induced luteolysis studies in the bovine species [GSE27961], it was observed that expression of one of the earliest genes that was down- regulated was Cyp19A1 in the CL. However, the specific role of E2 in the regulation of CL function remains poorly defined. Thus, in the present study, efforts were made to examine the temporal changes in the global gene expression profile in the CL of pregnant rats after treatment with aromatase inhibitor (AI), Anastrozole, and E2 supplementation. The results obtained will further expand our knowledge on E2 target/responsive genes and the basic mechanism(s) that regulates the CL function. Key words: CL, E2, AI, Gene expression", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41800" }, "primaryId" : "GEO:GSE41800", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41800" } ] }, "title" : "Rapid changes of gene expression in rat adipose tissue when food was removed", "dateAssigned" : "2012-10-23T00:00:00.000-05:00", "summary" : "When food was removed for 6 hours, 43 genes, including Angptl4, changed their expression more than two-fold.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23176178" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41832" }, "primaryId" : "GEO:GSE41832", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41832" } ] }, "title" : "Gene Expression Profiles in Skeletal Muscle and Liver of Type 2 Diabetes Rats", "dateAssigned" : "2012-10-25T00:00:00.000-05:00", "summary" : "Analyzing changes in gene expression in liver and skeletal muscle from streptozotocin-diabetic rats. From the 9,929 expressed genes across the genome, 1,305 and 997 differentially expressed genes (DEGs, P < 0.01) were identified in comparisons of skeletal muscle and liver, respectively. Interestingly, large numbers of DEGs (200) were common to both comparisons, which was clearly more than the predicted number (131 genes, P < 10-4). Further interpretation of gene ontology used three over-representation analysis software (WebGestalt, Expander and GATHER). All the tools detected one KEGG pathway (MAPK signaling) and two GO biological processes (response to stress and cell death), with enrichment of DEGs in both tissues. In addition, PPI (protein-protein interaction) networks constructed using human homologs not only revealed the tendency of DEGs to form a highly connected module, but also suggested a “hub” role of MAPK related genes (such as MAPK14) in the pathogenesis of T2D.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41836" }, "primaryId" : "GEO:GSE41836", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41836" } ] }, "title" : "Estrus Synchronization and Ovarian Hyper Stimulation Treatments Have Negligible Effects on Cumulus Oocyte Complexes Gene Expression: Induction of Ovulation Causes Major Expression Changes", "dateAssigned" : "2012-10-25T00:00:00.000-05:00", "summary" : "The effects of exogenous hormones used for estrus synchronization, and ovarian hyper stimulation on cumulus oocyte complexes (COCs) gene expression in sexually mature rats were determined using microarrays. Gene expression in COCs collected from GnRH (Gtrt), GnRH+eCG (G+Etrt), and GnRH+eCG+hCG (G+E+Htrt) treatments were compared to COCs from naturally cycling (NC) rats. There was no significant difference in gene expression among NC, Gtrt and G+Etrt. Over 2600 genes were significantly different between NC and G+E+Htrt (P<0.05). Genes encoding proteins that are involved in prostaglandin synthesis (Ptgs2, Pla2g4a, Runx1); cholesterol biosynthesis (Hmgcr, Sc4mol, Dhcr24); receptors that allow cholesterol uptake (Ldlr, Scarb1); regulate progesterone synthesis (Star); inactivate estrogen (Sult1e1); and downstream effectors of LH signal (Pgr, Cebpb, Creb3l1, Areg, Ereg, Adamts1) were upregulated in G+E+Htrt. Genes encoding proteins that are involved in DNA replication (Ccne2, Orc5l, Rad50, Mcm6); reproductive developmental process and granulosa cell expansion (Gdf9, Bmp15, Amh, Amhr2, Bmpr1b, Tgfb2, Foxl2, Pde3a, Esr2, Fshr, Ybx2, Ccnd2, Ccnb1ip1, Zp3); maternal effect genes that are important for embryo development (Zar1, Npm2, Nlrp5, Dnmt1, H1foo, Zfp57); amino acid degradation and ketogenesis (Hmgcs2 , Cpt1b) were downregulated in G+E+Htrt. These results on rat model show that hormones used for estrus synchronization (Gtrt) and ovarian hyper stimulation (G+Etrt) had minimal effects on gene expression. However, induction of ovulation (G+E+Htrt) caused major changes in gene expression of rat COCs. This study provides comprehensive information about regulated genes during late follicle development and ovulation induction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23239112" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41901" }, "primaryId" : "GEO:GSE41901", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41901" } ] }, "title" : "Comparison of the effects of Tris (2-ethylhexyl) trimellitate (TOTM) on gene expression associated with testicular maldevelopment (TMD) in male rat foetal testes by transcription profiling", "dateAssigned" : "2012-10-29T00:00:00.000-05:00", "summary" : "Certain phthalate esters have previously been shown to be involved in the induction of rat testicular mal-development (TMD) through effects on the expression of genes in pathways involved in steroidogenesis and testes development. In order to assess the effects of a potential alternate plasticizer, tris(2-ethylhexyl)trimellitate (TOTM), rats were exposed daily, in utero, to TOTM in order to assess the potential of this compound to induce developmental effects on the fetal testes. Pregnant rats were exposed between gestational day 12 and 19 and fetal testes RNA was analysed using whole genome microarrays. The effects of TOTM on the expression of genes in pathways involved in steroidogenesis and testes development were examined. The effects of TOTM were also compared with di(2-ethylhexyl)phthalate (DEHP), mono(2-ethylhexyl)phthalate (MEHP), an active metabolite of DEHP, and 2-ethylhexanol (2-EH), which were used as positive and negative controls, respectively. MEHP & DEHP (500mg/kg) caused a repression of genes in TMD pathways involved in cholesterol synthesis and transport (HMGCS, HMGCR, StAR, SCARB1, FDFT1, FDPS), steroidogenesis (Cyp11a, HSD3B1, SC4MOL) and testes development (INSL3, INHA). 2-EH caused minor repression of some of the genes in the TMD pathway. This was rationalised on the basis that 2-EH, a DEHP metabolite, is also a weak PPARa agonist. It has been shown that in utero treatment with DBP will repress the genes from fetal testes involved in steroidogenesis and that this effect is associated with direct DBP-mediated binding of PPARa to the promoters of these genes (Plummer et. al. 2010). TOTM did not cause a significant repression of genes in the TMD pathway. Based on these data, it is highly unlikely that TOTM will cause testicular dysgenesis in rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41902" }, "primaryId" : "GEO:GSE41902", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE41902" } ] }, "title" : "Expression data from rat liver stem-like WB-F344 cells treated with 3,3’,4,4’,5-pentachlorobiphenyl (PCB 126)", "dateAssigned" : "2012-10-29T00:00:00.000-05:00", "summary" : "Although the tumor promoting effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), coplanar polychlorinated biphenyls (PCBs) and related compounds in liver tissue are primarily attributed to activation of the aryl hydrocarbon receptor (AhR), the underlying molecular mechanisms are still unclear. Liver progenitor (oval) cells have been suggested to constitute a potential target for hepatocarcinogenic chemicals. To better understand AhR-driven pathways we analyzed the transcriptional program in response to coplanar PCB 126 in rat liver progenitor WB-F344 cells using high density microarrays. After 6h treatment, we identified 145 significantly deregulated genes considered to be direct AhR-dependent target genes. The number of differentially regulated genes increased to 658 and 968 genes after 24h and 72h, respectively. Gene ontology analysis revealed that these genes were primarily involved in drug and lipid metabolism, cell cycle and growth control, cancer developmental processes, cell-cell communication and adhesion. Interestingly, the Wnt and TGF-beta signaling pathways, both being involved in developmental and tumorigenic processes, belonged to the most affected pathways. AhR and ARNT-dependent regulation of selected target genes of interest was then confirmed using TCDD as a model AhR agonist, together with pharmacological inhibition of the AhR and by RNA-interference techniques. We demonstrated AhR-dependent regulation of emerging and novel AhR target genes, such as Fst, Areg, Hbegf, Ctgf, Btg2, and Foxq1. Among them, the transcription factor Foxq1, recently suggested to contribute to tumor promotion and/or progression, was found to be regulated at both mRNA and protein levels by AhR/ARNT activation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23196670" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42081" }, "primaryId" : "GEO:GSE42081", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42081" } ] }, "title" : "Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos", "dateAssigned" : "2012-11-06T00:00:00.000-06:00", "summary" : "Casanova EA, Okoniewski MJ, Cinelli P. Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos.PLoS One. 2012;7(10):e47107. doi: 10.1371/journal.pone.0047107. Epub 2012 Oct 15.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23077551" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42091" }, "primaryId" : "GEO:GSE42091", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42091" } ] }, "title" : "Mutant TDP-43 in Astrocytes Kills Motor Neurons in Rats through Neurotoxic Gain and Neuroprotective Loss in Astrocytes", "dateAssigned" : "2012-11-06T00:00:00.000-06:00", "summary" : "Mutation in TDP-43 is causative to amyotrophic lateral sclerosis (ALS). TDP-43 is a multifunctional ribonucleoprotein and is reproted to regulate thousands of genes in neurons, but how astrocytes contribute to TDP-43 pathogenesis is not known. This study examined how mutant TDP-43 in astrocytes kills motor neurons and causes ALS phenotypes. Primary astrocytes were isolated from transgenic rats expressing mutant TDP-43 or from control rats without mutant TDP-43 expression. Cultured astrocytes were induced to express mutant human TDP-43 and their gene expression profiles were determined by microarray assays. Microarray analysis revealed that hundreds of genes were altered in astrocytes in response to mutant TDP-43 expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23714777" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42177" }, "primaryId" : "GEO:GSE42177", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42177" } ] }, "title" : "Expression data for effect of p300 knockdown and Doxorubicin treatment in cardiac myocytes", "dateAssigned" : "2012-11-09T00:00:00.000-06:00", "summary" : "We used microarray to compare the transcriptomes of cardiac myocytes transfected with anti-p300 or non-silencing siRNA beforebefore and after exposure to Doxorubicin.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42207" }, "primaryId" : "GEO:GSE42207", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42207" } ] }, "title" : "Rodent trophoblast epigenome", "dateAssigned" : "2012-11-09T00:00:00.000-06:00", "summary" : "We characterized the trophoblast stem cell epigenome and gene expression profiles in rat and mouse.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23396136" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42295" }, "primaryId" : "GEO:GSE42295", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42295" } ] }, "title" : "Osteoarthritis-related changes in gene expression in knee articular chondrocytes in a rat model of osteoarthritis.", "dateAssigned" : "2012-11-14T00:00:00.000-06:00", "summary" : "Cartilage destruction in osteoarthritis (OA) results from disturbed chondrocyte metabolism. Here, we used microarrays to show that TGF alpha and CCL2 are simultaneously upregulated in a rat model of OA and cooperate to drive cartilage degradation. The goals of the experiments included here were to a) characterize gene expression in knee joint articular chondrocytes at various stages of development of OA (2 and 8 weeks after surgical induction of OA), and b) to establish trends in gene expression among groups of genes related to the TGF alpha-EGFR axis, over time, in OA. The model chosen to study these results has been previously validated (Appleton, CT et al, 2007, Arthritis Rheum) and used to describe similar gene expression results at a different time point (4 weeks) after induction of OA. The rat model of OA involves surgical destabilization of the knee joint, followed by forced low-intensity mobilization over several weeks; a sham surgery is used as the control (representing a healthy non-OA knee joint) wherein a surgical incision is made but not structural (i.e. ligamentous) modification is made to the joint. Altogether, our data indicate that TGF and CCL2 cooperate to drive cartilage degradation in osteoarthritis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42393" }, "primaryId" : "GEO:GSE42393", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42393" } ] }, "title" : "Formaldehyde-induced changes in microRNA signaling [Agilent]", "dateAssigned" : "2012-11-19T00:00:00.000-06:00", "summary" : "MicroRNAs (miRNAs) are critical regulators of gene expression, yet much remains unknown regarding miRNA changes resulting from environmental exposures and whether they influence pathway signaling across various tissues and time. To gain knowledge on these novel topics, we set out to investigate in vivo miRNA responses to inhaled formaldehyde, an important air pollutant known to disrupt miRNA expression profiles. Rats were exposed by inhalation to either 0 or 2 ppm formaldehyde (6 hours/day) for 7 days, 28 days, or 28 days followed by a 7 day recovery. Genome-wide miRNA expression profiles and associated signaling pathways were assessed within the nasal respiratory mucosa, circulating mononuclear white blood cells (WBC), and bone marrow (BM).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24304932" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42394" }, "primaryId" : "GEO:GSE42394", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42394" } ] }, "title" : "Formaldehyde-induced changes in microRNA signaling [Affymetrix]", "dateAssigned" : "2012-11-19T00:00:00.000-06:00", "summary" : "In addition to gaining knowledge on in vivo miRNA responses to formaldehyde, we set out to relate these miRNA responses to transcriptional profiles modified by formaldehyde. Rats were exposed by inhalation to either 0 or 2 ppm formaldehyde (6 hours/day) for 28 days. Genome-wide transcriptional profiles and associated signaling pathways were assessed within the nasal respiratory mucosa and circulating mononuclear white blood cells (WBC).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24304932" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42411" }, "primaryId" : "GEO:GSE42411", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42411" } ] }, "title" : "Whole-transcriptome analysis identifies re-expression of fetal splice variants in cardiac hypertrophy", "dateAssigned" : "2012-11-20T00:00:00.000-06:00", "summary" : "Cardiac hypertrophy has been well-characterized at the level of transcription. During cardiac hypertrophy, genes normally expressed primarily during fetal heart development are re-expressed, and this fetal gene program is believed to be a critical component of the hypertrophic process. Recently, alternative splicing of mRNA transcripts has been shown to be temporally regulated during heart development, leading us to consider whether fetal patterns of splicing also reappear during hypertrophy.We hypothesized that patterns of alternative splicing occurring during heart development are recapitulated during cardiac hypertrophy. Here we present a whole-transcriptome study of isoform expression during pressure-overload cardiac hypertrophy induced by 10 days of transverse aortic constriction (TAC) in rats and in developing fetal rat hearts compared to sham-operated adult rat hearts, using high-throughput sequencing of poly(A) tail mRNA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23688780" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42438" }, "primaryId" : "GEO:GSE42438", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42438" } ] }, "title" : "PTHRP/Adenylate cyclase promotes parietal whereas Wnt/ß-catenin signaling promotes visceral endoderm differentiation of rat XEN cells.", "dateAssigned" : "2012-11-21T00:00:00.000-06:00", "summary" : "In this study we showed that rat XEN cells grown in the presence of a GSK3 inhibitor exhibited enhanced formation of cell contacts and decreased motility. In contrast, treatment with forskolin induced the PE formation and epithelial-mesenchymal transition (EMT) in rat XEN cells. Using microarray and real-time PCR assays, we found that VE versus PE formation of rat XEN cells was correlated with change in expression levels of VE or PE marker genes. Similar to forskolin, EMT was prompted upon treatment of rat XEN cells with recombinant parathyroid hormone related peptide (PTHRP), an activator of the cAMP pathway in vivo. Taken together, our data suggest that rat XEN cells are PrE-like cells. The activation of Wnt pathway in rat XEN cells leads to the acquisition of VE characteristics, whereas the activation of the PTHRP/cAMP pathway leads to EMT and the formation of PE.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23038778" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42447" }, "primaryId" : "GEO:GSE42447", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42447" } ] }, "title" : "Activation of the chromatin-remodeling factor Smarca4/Brg1 cooperates with Olig2 to establish oligodendrocyte identity and control CNS myelination [ChIP-seq]", "dateAssigned" : "2012-11-21T00:00:00.000-06:00", "summary" : "We investigate the role of Brg1 and Olig2 during oligodendrocyte differentiation by combining gene conditional knockout and next generation sequencing technology. We generate genome-wide maps of RNA polymerase II (RPolII), Brg1 (Smarca4), Olig2 and histone modifications in primary rat oligodendrocyte precursor cells (iOLs), differentiating oligodendrocytes and mature oligodendrocytes.We found that Brg1 is intensely regulated by RPolII at the initiation of oligodedrocyte differentiation. The genomic distribution of Brg1 in differentiating oligodendrocytes is pre-directed by Olig2 in iOLs. The dynamic interaction of Brg1 and chromatin is correlate with the distinct stages of gene expression during maturation. Finally, we show that Brg1 and Olig2 localization predict critical genes controling CNS myeliantion. Our study represents the first detailed analysis of genomic landscape during the oligodendrocyte development and provides a framework for further understanding of molecular mechanisms underlying oligodendrocyte lineage progression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23332759" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42455" }, "primaryId" : "GEO:GSE42455", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42455" } ] }, "title" : "microRNA expression in Mestenteric lymph samples from rat models of acute pancreatitis", "dateAssigned" : "2012-11-21T00:00:00.000-06:00", "summary" : "We used Affymetrix microRNA arrays to assess the differences in mesenteric lymph fluid miRNAs in a taurocholate induced rat model of pancreatitis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24509209" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42497" }, "primaryId" : "GEO:GSE42497", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42497" } ] }, "title" : "Genome wide profiling of FOXE1 binding sites in PCCL3 rat cells", "dateAssigned" : "2012-11-26T00:00:00.000-06:00", "summary" : "FoxE1 transcriptional profiling of rat PCCL3 cells comparing wild type cells with FoxE1 silenced cells and scramble treated with FoxE1 silenced cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23675434" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42532" }, "primaryId" : "GEO:GSE42532", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42532" } ] }, "title" : "Expression data from leptin administration to Lepob/Lepob mice and Lepmkyo/Lepmkyo rats", "dateAssigned" : "2012-11-27T00:00:00.000-06:00", "summary" : "We used microarray to detailed the expression of gene in liver in the status of leptin deficiency, and leptin administration. As leptin deficient status, we use Lepmkyo/Lepmkyo rats or Lepob/Lepob mice and their wild type littermates.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23800849" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42578" }, "primaryId" : "GEO:GSE42578", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42578" } ] }, "title" : "Changes in Gene Expression within the Ventral Tegmental Area Following Loss-of-Control Alcohol Drinking by Alcohol-Preferring (P) Rats", "dateAssigned" : "2012-11-28T00:00:00.000-06:00", "summary" : "The objective of this study was to determine changes in gene expression in the ventral tegmental area (VTA) following loss-of-control alcohol drinking by alcohol-preferring (P) rats. Adult female P rats (n = 7) were given concurrent access to 10, 20 and 30% EtOH for four 1-hr sessions daily for 10 weeks followed by 2 cycles of 2 weeks of abstinence and 2 weeks of EtOH access. Rats were killed by decapitation 3 hr after the 4th daily EtOH-access session at the end of the second 2-week relapse period. An age-matched water control group of female P rats (n = 8) was also killed. RNA was prepared from micropunch samples of the VTA from individual rats; analyses were conducted with Affymetrix Rat 230.2 chips. Ethanol intakes were 1.5-2.5 g/kg per sessions, resulting in blood levels >200 mg% at the end of the 4th session. There were 211 named genes that were significantly different (FDR = 0.1) between the water and EtOH groups. Bioinformatics analyses indicated alterations in (a) transcription factors that reduced excitation-coupled transcription and promoted exocitotic neuronal damage involving clusters of genes associated with Nfkbia, Fos and Srebf1; (b) genes that reduced cholesterol and fatty acid synthesis, and increased protein degradation; and (c) genes involved in cell-to-cell interactions and regulation of the actin cytoskeleton. Among the named genes, there were 62 genes in common with differences between alcohol-naïve P and non-preferring (NP) rats, with 43 of the genes changing in the opposite direction following excessive binge-like drinking. These genes are involved in a pro-inflammatory response, and enhanced response to glucocorticoids and steroid hormones. Overall, the results of this study indicated that excessive binge-like alcohol drinking by P rats may be altering the expression of genes that promote neuronal damage.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42579" }, "primaryId" : "GEO:GSE42579", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42579" } ] }, "title" : "Gene expression in the right ventricle of Rattus norvegicus during development of right ventricular heart failure and treatment", "dateAssigned" : "2012-11-28T00:00:00.000-06:00", "summary" : "Right ventricular heart failure (RVF) associated with pulmonary hypertension (PH) is characterized by a distinct gene expression pattern when compared with functional compensatory hypertrophy. Carvedilol treatment after RVF has been established reduces right ventricle (RV) hypertrophy and improves the RV function. In addition, carvedilol treatment has been shown to alter the gene expression of select genes. We sought to identify, on a genome-wide basis, the effect of carvedilol on gene expression. RVF was induced in male Sprague-Dawley rats by the combination of VEGF-receptor blockade and chronic hypoxia; thereafter, one group was treated with carvedilol. RNA was isolated from the RV and subjected to microarray analysis. A prediction analysis of the carvedilol-treated RVs showed that carvedilol treated RVs most resembled in their expression pattern the RVF pattern. However, an analysis beyond the boundaries of the prediction set revealed a small set of genes associated with carvedilol reversal of RVF. Pathway analysis of this set of genes revealed expression changes of genes involved in cardiac hypertrophy, mitochondrial dysfunction, protein ubiquitination, and sphingolipid metabolism. Genes encoding proteins in the cardiac hypertrophy and protein ubiquitination pathways were downregulated in the RV by carvedilol, while genes encoding proteins in the mitochondrial dysfunction and sphingolipid metabolism pathways were upregulated by carvedilol.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23632417" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42611" }, "primaryId" : "GEO:GSE42611", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42611" } ] }, "title" : "An Organ Culture System to Model Early Degenerative Changes of the Intervertebral Disc: II Profiling Global Gene Expression Changes", "dateAssigned" : "2012-11-29T00:00:00.000-06:00", "summary" : "Gene expression analysis was performed using a microarray to identify differential gene expression between experimental and control groups.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42676" }, "primaryId" : "GEO:GSE42676", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42676" } ] }, "title" : "Functional genomics in perinatal asphyxia and fetal asphyctic preconditioning in the brain", "dateAssigned" : "2012-12-03T00:00:00.000-06:00", "summary" : "Fetal asphyctic (FA) preconditioning is effective in attenuating brain damage incurred by a subsequent perinatal asphyctic insult. Unraveling mechanisms of this endogenous neuroprotection, activated by FA preconditioning, is an important step towards new clinical strategies for asphyctic neonates. Genomic reprogramming is thought to be, at least in part, responsible for the protective effect of preconditioning. Therefore, we investigated whole genome differential expression in the preconditioned rat brain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24885038" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42693" }, "primaryId" : "GEO:GSE42693", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42693" } ] }, "title" : "Comparative study of sesame lignans affecting gene expression profile and fatty acid oxidation in rat liver", "dateAssigned" : "2012-12-03T00:00:00.000-06:00", "summary" : "The impact of sesamin, episesamin and sesamolin (sesame lignans) on hepatic gene expression profiles was compared with a DNA microarray. Male Sprague-Dawley rats were fed experimental diets containing 0.2% sesamin, episesamin or sesamolin, and a control diet free of lignans for 15 d. Compared to a lignan-free diet, a diet containing sesamin, episesamin and sesamolin caused 1.5- and 2-fold changes in the expression of 128 and 40, 526 and 152, and 516 and 140 genes, respectively. The lignans modified not only the mRNA levels of many enzymes involved in hepatic fatty acid oxidation, but also those of proteins involved in the transportation of fatty acids into hepatocytes and their organelles, and regulate hepatic concentrations of carnitine, CoA and malonyl-CoA. It is apparent that sesame lignans stimulate hepatic fatty acid oxidation by affecting the gene expression of various proteins regulating hepatic fatty acid metabolism. We also observed that lignans modified the gene expression of various proteins involved in hepatic lipogenesis, cholesterogenesis and glucose metabolism. The changes were generally greater with episesamin and sesamolin than with sesamin. In terms of the amounts accumulated in serum and the liver, the lignans ranked in the order sesamolin, episesamin and sesamin. The differences in bio-availability among these lignans appear to be important to their divergent physiological activities.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:19352061" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42767" }, "primaryId" : "GEO:GSE42767", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42767" } ] }, "title" : "Investigation of endothelial cell gene dysregulation in early pulmonary arterial hypertension disease model", "dateAssigned" : "2012-12-06T00:00:00.000-06:00", "summary" : "Endothelial cell (EC) dysfunction plays a key role in the pathogenesis of pulmonary arterial hypertension (PAH). To avoid cell cultures and whole lung tissue samples, we have, for the first time, used CD31 antibody coated magnetic beads in conjunction with genome scale RNA expression microarrays to profile ECs in vivo at any stage of PAH. We hypothesized that targeting early stages of the disease would identify novel mediators of PAH and genes linked to bone morphogenetic protein receptor 2 (BMPR2) signaling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24433082" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42776" }, "primaryId" : "GEO:GSE42776", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42776" } ] }, "title" : "Genome-wide analysis of acetylated H4K5 binding offers new insights into the acute and chronic effects of METH on gene expression in the dorsal striatum", "dateAssigned" : "2012-12-06T00:00:00.000-06:00", "summary" : "In contrast to the acute METH-induced transcriptional changes, chronic METH administration produces differential changes in IEG responses and blunts the striatal effects of a single METH injection (McCoy et al., 2011). These observations suggested that chromic METH might have caused changes in the molecular machinery that controls the acute effects of the drug. Gene transcription is regulated by complex interactions of transcription factors with regulatory elements [14,15]. During resting states, DNA is compacted in a way that interferes with the binding of transcription factors whereas DNA becomes more accessible during activation of cells by various stimuli [16]. DNA is indeed packaged into chromatin whose fundamental subunit, the nucleosome, is made of 4 core histones, histones H2A, H2B, H3, and H4 that form an octomer (2 of each histone) surrounded by 146 bp of DNA [17]. The N-tails of histones possess lysine residues that can be reversibly acetylated or deacetylated by several histone acetyltransferases (HATs) or by histone deacetylases (HDACs), respectively [18,19]. These changes promote alterations in gene expression by modifying chromatin conformation and enabling or inhibiting recruitment of regulatory factors onto DNA sequences [20]. Herein, we report that the acute, but not the chronic, transcriptional effects of METH are mediated, for the most part, by increased DNA binding of histone H4 acetylated at lysine 5 (H4K5ac). These results suggest that other factors, including histone and/or DNA methylation, might play a more important role in mediating the molecular effects of chronic METH exposure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42780" }, "primaryId" : "GEO:GSE42780", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42780" } ] }, "title" : "epithelia and fibroblasts gene profile in 4NQO induced tongue carcinogenesis", "dateAssigned" : "2012-12-06T00:00:00.000-06:00", "summary" : "Nine groups of rat tongue epithelia and submucosal fibroblasts RNA samples respectively, including three from normal control, three from dysplasia, and three from carcinoma (3 rats per group) were collected for gene microarray hybridization.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26831400" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42793" }, "primaryId" : "GEO:GSE42793", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42793" } ] }, "title" : "Intracranial self-stimulation regulates gene expression in rat hippocampus", "dateAssigned" : "2012-12-06T00:00:00.000-06:00", "summary" : "Rats were implanted with a monopolar stainless steel electrode aimed at the lateral hypothalamus in the right hemisphere. Hippocampal gene expression was analyzed 4.5h post treatment comparing rats subjected to acute self-stimulation (2500 stimulation trains; ICSS group) with sham-operated rats (with electrode placement but placed in the ICSS without stimulation during 40 min.; Sham group).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23898803" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42855" }, "primaryId" : "GEO:GSE42855", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42855" } ] }, "title" : "Tongue tissue gene profile in 4NQO induced tongue carcinogenesis before and after IL-1Ra interference", "dateAssigned" : "2012-12-11T00:00:00.000-06:00", "summary" : "Nine groups of rat tongue tissue RNA samples, including three from normal control, three from 4NQO induced tongue tissue, and three from 4NQO induced and IL-1Ra interference tongue tissue (3 rats per group) were collected for gene microarray hybridization.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26831400" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42897" }, "primaryId" : "GEO:GSE42897", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42897" } ] }, "title" : "Expression data from rat INS-1E cells", "dateAssigned" : "2012-12-13T00:00:00.000-06:00", "summary" : "We used microarrays to look for gene set(s) that are regulated by BRD0476.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26042473" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42940" }, "primaryId" : "GEO:GSE42940", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE42940" } ] }, "title" : "postnatal fluoxetine evoked gene expression changes in the rat hippocampus", "dateAssigned" : "2012-12-14T00:00:00.000-06:00", "summary" : "to understand the consequences of chronic exposure to fluoxetine during postnatal life on global transcriptional changes withing the rat hippocamps", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43013" }, "primaryId" : "GEO:GSE43013", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43013" } ] }, "title" : "Gene Expression Defines Natural Changes in Mammalian Lifespan", "dateAssigned" : "2012-12-19T00:00:00.000-06:00", "summary" : "Mammals differ more than hundred fold in maximum lifespan, which can be altered in either direction during evolution, but the molecular basis for natural changes in longevity is not understood. Divergent evolution of mammals also led to extensive changes in gene expression within and between lineages. To understand the relationship between lifespan and variation in gene expression, we carried out RNA-seq-based gene expression analyses of liver, kidney and brain of 33 diverse species of mammals. Our analysis uncovered parallel evolution of gene expression and lifespan, as well as the associated life history traits, and identified the processes and pathways involved. These findings provide direct insights into how Nature reversibly adjusts lifespan and other traits during adaptive radiation of lineages.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25677554" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43053" }, "primaryId" : "GEO:GSE43053", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43053" } ] }, "title" : "The multikinase inhibitor Sorafenib targets mitochondria and synergizes with glycolysis blockade for cancer cell killing.", "dateAssigned" : "2012-12-20T00:00:00.000-06:00", "summary" : "Objective: identify novel and relevant aspects of Sorafenib action on liver cancer cells. We found that in rat hepatocholangiocarcinoma (LCSC-2) cells, exposure to the MEK/multikinase inhibitor sorafenib did not inhibit ERK phosphorylation nor induced appreciable cell death in the low micromolar range; instead, the drug elicited a raise of intracellular reactive oxygen species (ROS) accompanied by a severe decrease of oxygen consumption and intracellular ATP levels, all changes consistent with mitochondrial damage. Moreover, Sorafenib induced depolarization of isolated rat liver mitochondria, indicating a possible direct effect on the organelle. Microarray analysis of gene expression in sorafenib-trated cells revealed a metabolic reprogramming toward aerobic glycolysis, that likely accounts for resitance to drug toxicity in this cell line. Importantly, cytotoxicity was strongly potentiated by glucose withdrawal from the culture medium or by the glycolytic inhibitor 2-deoxy-glucose, a finding also confirmed in the highly malignant melanoma cell line B16F10. Mechanistic studies revealed that ROS are pivotal to cell killing by the Sorafenib + 2DG combination, and that a low content of intracellular oxidants is associated with resistance to the drug; instead, Thr172phosphorylation/activation of the AMP-activated protein kinase (AMPK), induced by Sorafenib, may exert protective effects, since cytotoxicity was enhanced by an AMPK specific inhibitor and prevented by the AMPK activator Metformin. Overall, this study identifies novel and relevant aspects of Sorafenib action on liver cancer cells, including mitochondrial damage, induction of ROS and a metabolic cell reprogramming towards “glucose addiction”, potentially exploitable in therapy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25779766" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43066" }, "primaryId" : "GEO:GSE43066", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43066" } ] }, "title" : "In the livers of rats treated with thioacetamide for 28 days", "dateAssigned" : "2012-12-20T00:00:00.000-06:00", "summary" : "We investigated the early stage of hepatocarcinogenesis using global expression analyses.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43251" }, "primaryId" : "GEO:GSE43251", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43251" } ] }, "title" : "NanoString analysis of a rat liver mRNA panel following TCDD treatment", "dateAssigned" : "2013-01-02T00:00:00.000-06:00", "summary" : "Profiling of mRNA abundances with high-throughput platforms such as microarrays and RNA-Seq has become an important tool in both basic and biomedical research. However these platforms remain prone to systematic errors, and have challenges in clinical and industrial application. As a result it is standard practice to validate a subset of key results using alternate technologies. Similarly, clinical and industrial applications typically involve transitions from high-throughput discovery platform to medium-throughput validation ones. These medium-throughput validation platforms have high technical reproducibility and reduced sample input needs, and low sensitivity to sample-quality (e.g. for processing FFPE specimens). Unfortunately, while medium-throughput platforms have proliferated, there are no comprehensive comparisons of them. Here we fill that gap by comparing two key medium-throughput platforms – NanoString’s nCounter Analysis System and ABI’s OpenArray System – to gold-standard quantitative real-time RT-PCR.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24355419" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43375" }, "primaryId" : "GEO:GSE43375", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43375" } ] }, "title" : "Striatal molecular signature of subchronic subthalamic nucleus high frequency stimulation in parkinsonian rat", "dateAssigned" : "2013-01-09T00:00:00.000-06:00", "summary" : "Striatal gene expression profile was assessed in rats with nigral DOPAmine neuron lesion, either treated or not, using agilent microarrays and qPCR verification. The treatments consisted in anti-akinetic STN-HFS (5 days), chronic L-DOPA treatment inducing dyskinesia (LIDs) or the combination of the two treatments that exacerbated LIDs. STN-HFS modulated 71 genes with functional or biochemical annotation, including genes sharing the GO terms regulation of growth, regulation of apoptosis, extracellular region. Ttr, Igf2, Sostdc1 and Nr4A3 (Nor-1), are among the 5 genes showing the highest specific upregulation. Down-regulated genes include Prkcd, Sirt5 and Bbc3. These results show that genes involved in neuroprotection and/or neurogenesis are key components of STN-HFS action in the striatum. STN-HFS and LDOPA treatment share very few common gene regulation features suggesting that the molecular substrates underlying their striatal action are mostly different. In addition to genes already reported to be associated with LIDs (Pdyn, Trh, Grm4/mGlu4, Cnr1/CB1), the comparison between DOPA and DOPA/STN-HFS identifies immunity-related genes: C1s, Rt1-Da and Irf7a, as potential players in L-DOPA side effects.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43404" }, "primaryId" : "GEO:GSE43404", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43404" } ] }, "title" : "Heat acclimation memory: Does the de-acclimated transcriptome reveal epigenetic processes of transcriptional regulation?", "dateAssigned" : "2013-01-10T00:00:00.000-06:00", "summary" : "We used microarray to uncover hallmark pathways in the induction of heat-acclimation-mediated memory, focusing on markers of epigenetic processes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25237184" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43413" }, "primaryId" : "GEO:GSE43413", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43413" } ] }, "title" : "Expression data from the telencephalon of wild-type and rSey2/rSey2 rats", "dateAssigned" : "2013-01-10T00:00:00.000-06:00", "summary" : "To identify candidate target genes of Pax6, we performed transcriptome analyses of wild-type (WT) and Pax6 homozygous mutant rats (rSey2/rSey2) telencephalons at E11.5 within a day of onset of Pax6 expression. In our transcriptome analyses, down-regulated genes in the rSey2/rSey2 rat exhibited larger fold changes, whereas up-regulated genes had relatively small fold changes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23679989" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43464" }, "primaryId" : "GEO:GSE43464", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43464" } ] }, "title" : "Gene Bionetworks that Regulate Ovarian Primordial Follicle Assembly", "dateAssigned" : "2013-01-11T00:00:00.000-06:00", "summary" : "We used microarrays to determine genes expressed differentially between control and P0 ovaries treated with 7 growth factors: AMH, CTGF, estradiol (E2), Activin-a, FGF2, progesterone (P4), and TNFa.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23875758" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43496" }, "primaryId" : "GEO:GSE43496", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43496" } ] }, "title" : "Gene expression of rat PSCs cultured on plastic, matrigel and collagen", "dateAssigned" : "2013-01-15T00:00:00.000-06:00", "summary" : "Activated pancreatic stellate cells produce the fibrotic matrix in chronic pancreatitis and pancreatic cancer. In vitro protocols examining PSC biology have usually involved PSCs cultured on plastic, a non-physiological surface. However, PSCs cultured on physiological matrices e.g. MatrigelTM (normal basement membrane) and collagen (fibrotic pancreas), may have distinctly different behaviours compared to cells cultured on plastic. Therefore, we aimed to compare PSC gene expression after culture on plastic, MatrigelTM and collagen I.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23868411" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43516" }, "primaryId" : "GEO:GSE43516", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43516" } ] }, "title" : "Gene expression changes under cyclic mechanical stretch in rat retinal Muller cells", "dateAssigned" : "2013-01-15T00:00:00.000-06:00", "summary" : "We used microarrays to identify patterns of gene expression changes induced by cyclic mechanical stretching in Muller cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23723984" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43547" }, "primaryId" : "GEO:GSE43547", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43547" } ] }, "title" : "Genome-wide analysis of hypothalamic gene expression in prenatally undernourished male rat offspring under high fat diet", "dateAssigned" : "2013-01-16T00:00:00.000-06:00", "summary" : "Based on the developmental origin of health of disease hypothesis, we previously showed that prenatal 70% maternal food restriction (FR30) predisposes the offspring to development of pathologies in adulthood. In the present study, we focused on the hypothalamus gene expression profile of standard and high fat (HF)-fed FR30 adult offspring.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23523777" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43559" }, "primaryId" : "GEO:GSE43559", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43559" } ] }, "title" : "Environmentally Induced Transgenerational Epigenetic Reprogramming of Primordial Germ Cells and Subsequent Germline [Affymetrix]", "dateAssigned" : "2013-01-16T00:00:00.000-06:00", "summary" : "The combined observations demonstrate ancestral exposure of a gestating female during fetal gonadal sex determination can promote transgenerational alterations in the primordial germ cell and subsequent male germline epigenetic and transcriptional programming. This altered germline programming leads to the epigenetic transgenerational inheritance of disease and phenotypic variation. Observations support the role of the primordial germ cell programming in the molecular mechanism involved and provides insights into the molecular mechanisms that control the epigenetic transgenerational inheritance phenomena. Results suggest a cascade of epigenetic and transcriptional events during germ cell development is needed to obtain the mature germline epigenome that is then transmitted transgenerationally.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23869203" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43671" }, "primaryId" : "GEO:GSE43671", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43671" } ] }, "title" : "Time-Dependent Gene Profiling Indicates the Presence of Different Phases for Ischemia/Reperfusion Injury in Retina", "dateAssigned" : "2013-01-22T00:00:00.000-06:00", "summary" : "The purpose of the present study was to investigate time-dependent changes in gene expression, following induction of IR in the rat retina, and to characterize the affected pathways, networks and processes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25210480" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43723" }, "primaryId" : "GEO:GSE43723", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43723" } ] }, "title" : "The change of gene expression profile of primary rat hepatocytes after treatment with interferon alpha.", "dateAssigned" : "2013-01-24T00:00:00.000-06:00", "summary" : "We used Affymetrix Rat Genome 230 2 microarrays to determine gene expression profiles in primary rat hepatocytes after interferon alpha treatment and untreated cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43744" }, "primaryId" : "GEO:GSE43744", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43744" } ] }, "title" : "Comparison of Gene Expression between Peri-implant Soft Tissue and Oral Mucosal Tissue", "dateAssigned" : "2013-01-24T00:00:00.000-06:00", "summary" : "The mucosal penetration area formed by implant placement is critical problems of dental implant treatment, because epithelial barrier is broken and it can become a source of inflammation. To clarify the influence and risk caused by dental implant treatment in peri-implant soft tissue, we compared to gene expression profile of peri-implant soft tissue and oral mucosal tissue with microarray analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43748" }, "primaryId" : "GEO:GSE43748", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43748" } ] }, "title" : "Transcriptional profiles of psychostimulant reinforcement in rats", "dateAssigned" : "2013-01-25T00:00:00.000-06:00", "summary" : "Drug-induced alterations in transcriptional regulation play a central role in establishing the persistent neuroplasticities that occur during drug addiction. Additionally, changes in gene expression associated with drug administration provide valuable insight into the molecular basis of drug abuse. The molecular mechanisms that underlie susceptibility to psychostimulant addiction remain unknown. Identifying the common gene transcriptional responses to psychostimulants can provide a mechanistic insight to elucidate the molecular nature of drug dependence.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23783774" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43832" }, "primaryId" : "GEO:GSE43832", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43832" } ] }, "title" : "Overexpression of PLIN5 in skeletal muscle promotes oxidative gene expression and intramyocellular lipid content without compromising insulin sensitivity", "dateAssigned" : "2013-01-28T00:00:00.000-06:00", "summary" : "Aims/hypothesis: While lipid deposition in skeletal muscle is considered to be involved in obesity-associated insulin resistance, neutral intramyocellular lipid (IMCL) accumulation per se does not necessarily induce insulin resistance. We previously demonstrated that overexpression of the lipid droplet coat protein perilipin 2 augments intramyocellular lipid content while improving insulin sensitivity. Another member of the perilipin family, perilipin 5 (PLIN5), is predominantly expressed in oxidative tissues like skeletal muscle. Here we investigated the effects of PLIN5 overexpression – in comparison with effects of PLIN2 – on skeletal muscle lipid levels, gene expression profiles and insulin sensitivity. Methods: Gene electroporation was used to overexpress PLIN5 in tibialis anterior muscle of rats fed a high fat diet. Eight days after electroporation, insulin-mediated glucose uptake in skeletal muscle was measured by means of a hyperinsulinemic euglycemic clamp. Electron microscopy, fluorescence microscopy and lipid extractions were performed to investigate IMCL accumulation. Gene expression profiles were obtained using microarrays. Results: TAG storage and lipid droplet size increased upon PLIN5 overexpression. Despite the higher IMCL content, insulin sensitivity was not impaired and DAG and acylcarnitine levels were unaffected. In contrast to the effects of PLIN2 overexpression, microarray data analysis revealed a gene expression profile favoring FA oxidation and improved mitochondrial function. Conclusions/interpretation: Both PLIN2 and PLIN5 increase neutral IMCL content without impeding insulin-mediated glucose uptake. As opposed to the effects of PLIN2 overexpression, overexpression of PLIN5 in skeletal muscle promoted expression of a cluster of genes under control of PPARa and PGC1a involved in FA catabolism and mitochondrial oxidation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23353597" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43846" }, "primaryId" : "GEO:GSE43846", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE43846" } ] }, "title" : "Expression data from cyclically stretched engineered neonatal rat ventricuar myocyte (NRVM) tissues", "dateAssigned" : "2013-01-29T00:00:00.000-06:00", "summary" : "We used micoarrays to determine the effects of longitudinal and transvserse cyclic stretch on gene expression in engineered NRVM cardiac tissues. We found that cyclic stretch induced up-regulation of several known indicators of heart faliure, independent of the direction of stretch.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23716679" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44031" }, "primaryId" : "GEO:GSE44031", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44031" } ] }, "title" : "Transcriptome Profiling of Hippocampal CA1 After Early Life Seizure-Induced Preconditioning May Elucidate New Genetic Therapies for Epilepsy", "dateAssigned" : "2013-02-03T00:00:00.000-06:00", "summary" : "Injury of the CA1 subregion induced by a single injection of kainic acid (1×KA) is attenuated when juvenile animals (P20) have a history of two sustained neonatal seizures on P6 and P9. To identify gene candidates involved in the spatially protective effects produced by early life conditioning seizures, we profiled and compared the transcriptomes of CA1 subregions from control, 1×KA, and 3×KA treated animals. More genes were regulated following 3×KA (9.6%) than after 1×KA (7.1%). Following 1×KA, genes supporting oxidative stress, growth, development, inflammation, and neurotransmission were upregulated (e.g., Cacng1, Nadsyn1, Kcng1, Aven, S100a4, GFAP, Vim, Hrsp12, Grik1). After 3×KA, protective genes were differentially over-expressed (e.g., Cat, Gpx7, GAD1, Hspa12A, Foxn1, adenosine A1 receptor, Ca2+ adaptor and homeostatic proteins, Cacnb4, Atp2b2, anti-apoptotic Bcl-2 gene members, intracellular trafficking protein, Grasp, suppressor of cytokine signaling (Socs3)). Distinct anti-inflammatory interleukins not observed in adult tissues (e.g., IL6 transducer, IL23 and IL33 or their receptors (ILF2)) were also over-expressed. Several transcripts were validated by real-time polymerase chain reaction (QPCR) and immunohistochemistry. QPCR showed that casp 6 was increased after 1×KA but reduced after 3×KA; pro-inflammatory gene cox1 was either upregulated or unchanged after 1×KA but reduced by ~70% after 3×KA. Enhanced GFAP immunostaining following 1×KA was selectively attenuated in the CA1 subregion after 3×KA. The observed differential transcriptional responses may contribute to early life seizure-induced pre-conditioning and neuroprotection by reducing glutamate receptor-mediated Ca2+ permeability of the hippocampus and redirecting inflammatory and apoptotic pathways which could lead to new genetic therapies for epilepsy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23551718" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44045" }, "primaryId" : "GEO:GSE44045", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44045" } ] }, "title" : "Secreted Frizzled-Related Protein 5 is Downregulated in Obesity and Promotes ß-Cell Proliferation [10 days]", "dateAssigned" : "2013-02-04T00:00:00.000-06:00", "summary" : "Obesity is associated with an increase in ß-cell mass in response tothe rising demand for insulin. ß-cell plasticity is essential to maintaining glucose homeostasis, however,the cellular and molecular mechanisms by which ß-cell mass is regulated remain poorly understood.Recently, we described the existence of a crosstalk between the peripancreatic adipose tissue and ß-cells as a novel mechanism that participates in the regulation of ß-cell plasticity. Here, we identify the secreted frizzled-related protein (Sfrp) 5 as down-regulated in the pancreatic islets of obese rats as well as in the pancreatic islets of human obese patients. Our results demonstrate that the silencing of Sfrp5 induces an increase in ß-cell proliferation, which we correlate with the activation of Wnt signaling and of the MAPK and PI3 kinase pathways. Together, these findings expand our understanding of the mechanisms underlying ß-cell proliferation under conditions of obesity. Furthermore, this study opens new insights into the specific targeting of Sfrp5 as a novel therapeutic strategy for balancing ß-cell mass.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24006088" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44046" }, "primaryId" : "GEO:GSE44046", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44046" } ] }, "title" : "Secreted Frizzled-Related Protein 5 is Downregulated in Obesity and Promotes ß-Cell Proliferation [30 days]", "dateAssigned" : "2013-02-04T00:00:00.000-06:00", "summary" : "Obesity is associated with an increase in ß-cell mass in response tothe rising demand for insulin. ß-cell plasticity is essential to maintaining glucose homeostasis, however,the cellular and molecular mechanisms by which ß-cell mass is regulated remain poorly understood.Recently, we described the existence of a crosstalk between the peripancreatic adipose tissue and ß-cells as a novel mechanism that participates in the regulation of ß-cell plasticity. Here, we identify the secreted frizzled-related protein (Sfrp) 5 as down-regulated in the pancreatic islets of obese rats as well as in the pancreatic islets of human obese patients. Our results demonstrate that the silencing of Sfrp5 induces an increase in ß-cell proliferation, which we correlate with the activation of Wnt signaling and of the MAPK and PI3 kinase pathways. Together, these findings expand our understanding of the mechanisms underlying ß-cell proliferation under conditions of obesity. Furthermore, this study opens new insights into the specific targeting of Sfrp5 as a novel therapeutic strategy for balancing ß-cell mass.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24006088" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44056" }, "primaryId" : "GEO:GSE44056", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44056" } ] }, "title" : "Gene expression data from lateral ventricle choroid plexuses of developing and adult rats", "dateAssigned" : "2013-02-04T00:00:00.000-06:00", "summary" : "Choroid plexuses (CP) develop early during development. They form a barrier between the blood and the cerebrospinal fluid, and fulfill important protective and nutritive functions. We used Affymetrix microarrays to assess whether CP of the lateral ventricles (LVCP) have similar functions in developing and adult brain. We identified distinct families of protective and transport genes and found that most of these genes were already well expressed during development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23843944" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44072" }, "primaryId" : "GEO:GSE44072", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44072" } ] }, "title" : "Genome-wide analysis and comparison of E15 and adult rat lateral ventricular choroid plexus epithelial cells.", "dateAssigned" : "2013-02-05T00:00:00.000-06:00", "summary" : "Transcriptome analysis of lateral ventricular choroid plexus epithelial cells of embryonic day 15 (E15) and adult control Sprague-Dawley rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23843944" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44106" }, "primaryId" : "GEO:GSE44106", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44106" } ] }, "title" : "MiRNA/gene profiling unveils early molecular changes and NRF2 activation in a rat model recapitulating human HCC", "dateAssigned" : "2013-02-06T00:00:00.000-06:00", "summary" : "Studies on gene and/or microRNA (miRNA) dysregulation in the early stages of hepatocarcinogenesis are hampered by the difficulty of diagnosing early lesions in humans. Experimental models recapitulating human hepatocellular carcinoma (HCC) are then entailed to perform this analysis. We performed miRNA and gene expression profiling to characterize the molecular events involved in the multistep process of hepatocarcinogenesis in the Resistant-Hepatocyte rat model. A high percentage of dysregulated miRNAs/genes in HCC were similarly altered in early preneoplastic lesions positive for the stem/progenitor cell marker cytokeratin-19, indicating that several HCC-associated alterations occur from the very beginning of the carcinogenic process. Our analysis also identified miRNA/gene-target networks aberrantly activated at the initial stage of hepatocarcinogenesis. Activation of the NRF2 pathway and up-regulation of the miR-200 family were among the most prominent changes. The relevance of these alterations in the development of HCC was confirmed by the observation that NRF2 silencing impaired while miR-200a overexpression promoted HCC cell proliferation in vitro. Moreover, T3-induced in vivo inhibition of the NRF2 pathway accompanied the regression of cytokeratin-19 positive nodules, suggesting that activation of this transcription factor contributes to the onset and progression of preneoplastic lesions towards malignancy. The finding that 78% of genes and 57% of dysregulated miRNAs in rat HCC have been previously associated to human HCC as well underlines the translational value of our results. Conclusions: this study indicates that most of the molecular changes found in HCC occur in the very early stages of hepatocarcinogenesis. Among these, the NRF2 pathway plays a relevant role and may represent a new therapeutic target. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23857252" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44108" }, "primaryId" : "GEO:GSE44108", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44108" } ] }, "title" : "Cardiac phase-targeted dynamic load on left ventricle differentially regulates phase-sensitive gene expressions and pathway activation", "dateAssigned" : "2013-02-06T00:00:00.000-06:00", "summary" : "Each heart was assigned to one of the following three conditions: phasic systolic overload (SO), phasic diastolic overload (DO), and no loading throughout the cardiac cycle (control; CN). We created SO by isovolumic contraction (peak systolic LVP > 170 mmHg) at a constant diastolic volume with end-diastolic pressure (EDP) equals 0 mmHg. For DO, we increased LVV in diastole so that EDP reached 40 mmHg, and unloaded quickly in systole to minimize LVP generation. At the end of 3 hours, the myocardium from each heart was collected for subsequent analyses.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24004468" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44112" }, "primaryId" : "GEO:GSE44112", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44112" } ] }, "title" : "Time dependent expression profiles of mRNAs in rat milk", "dateAssigned" : "2013-02-06T00:00:00.000-06:00", "summary" : "We have reported that mRNAs are present in bovine milk. But, it is unknown the roles of milk mRNAs. To clarify the roles of milk mRNAs, experimental animal such as rat study would be needed. However, it is unclear whether rat milk also contains mRNAs. Thus, we have employed microarray to show that rat milk also contains mRNAs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24533154" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44113" }, "primaryId" : "GEO:GSE44113", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44113" } ] }, "title" : "Time dependent expression profiles of microRNAs in rat milk", "dateAssigned" : "2013-02-06T00:00:00.000-06:00", "summary" : "We have reported that microRNAs are present in human and bovine milk. But, it is unknown the roles of milk miRNAs. To clarify the roles of milk miRNAs, experimental animal such as rat study would be needed. However, it is unclear whether rat milk also contains miRNAs. Thus, we have employed microarray to show that rat milk also contains miRNAs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24533154" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44144" }, "primaryId" : "GEO:GSE44144", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44144" } ] }, "title" : "Development of gene expression signatures for senecionine exposure", "dateAssigned" : "2013-02-07T00:00:00.000-06:00", "summary" : "Senecionine is among the most well-studied pyrrolizidine alkaloids, which have caused intense and lasting attention for their significant hepatotoxicity. To develop gene expression approach to senecionine exposure, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to be biomarkers after senecionine exposure. Rat liver tissues after 36 h of senecionine treatment (i.g., 35 mg/kg body weight) were collected and analyzed comparing with control samples (i.g., sodium chloride solution). Differentially expressed genes were identified through Fold-change filtering and subjected to GO term using gene ontology project (http://www.geneontology.org/) to uncover the co-expression network on the basis of biological process and molecular function. By setting the fold change at = 2 and p value =0.05, 46 down-regulated signaling pathways and 50 up-regulated pathways were found, including bile secretion, primary bile acid biosynthesis, and ABC transporters. Expression of 13 genes referred to bile acids metabolism was quantified from the same tissue samples by real-time PCR, confirming senecionine exposure after 36 h could result in compromised bile acid homeostasis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44150" }, "primaryId" : "GEO:GSE44150", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44150" } ] }, "title" : "Transcriptome Profiling of Rattus norvegicus Embryonic Stem Cells by RNA-Sequencing", "dateAssigned" : "2013-02-07T00:00:00.000-06:00", "summary" : "In order to establish a rat embryonic stem cell transcriptome, mRNA from rESC cell line DAc8, the first male germline competent rat ESC line to be described and the first to be used to generate a knockout rat model was characterized using RNA sequencing (RNA-seq) analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44179" }, "primaryId" : "GEO:GSE44179", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44179" } ] }, "title" : "Role of micro-RNAs in pathophysiology of diabetic cardiomyopathy.", "dateAssigned" : "2013-02-08T00:00:00.000-06:00", "summary" : "Diabetic cardiomyopathy (DCM), occurs independent of Hypertension, Coronary artery disease, or any other known cardiac disease and is characterized by myocardial fibrosis, myocytes loss and hypertrophy. The molecular mechanisms leading to these diseased cardiac phenotype are still being elucidated. A small number of studies have demonstrated that altered expression of several microRNAs are associated with ischemia , mechanical overload, or cardiovascular biology; however, much work is still required to identify individual or group of microRNAs and their role in the pathophysiology of diabetic cardiomyopathy. The aim of present study was to identify the expression of individual or group of microRNAs associated with myocytes hypertrophy and myocardial fibrosis during DCM. MicroRNAs expression profiles were studied in myocardium from High Fat diet and streptozotocin (STZ) induced diabetic (n=4) and non-diabetic (n=2) Wistar rats. All normalized and filtered microRNAs (n=780) processed for differential expression study using unpaired T-test in Gene spring in which unpaired comparison has been performed as test vs. control. After unpaired T-test, total 72 microRNAs were found to be significantly expressed with P-value =0.05. Differentially expression analysis was performed and at fold Change cut off = 1.0, all 780 microRNA passed and 39 out of 780 microRNAs were differentially expressed on fold Change cut-off =1.5. These results indicate that during the development and progression of DCM, various microRNAs were differentially expressed and may participate in the regulation of various signaling pathways leading to myocytes hypertrophy, apoptosis and cardiac fibrosis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44241" }, "primaryId" : "GEO:GSE44241", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44241" } ] }, "title" : "A short-term maternal separation in early neonate rats markedly increases intestinal permeability, induces bacterial translocation to systemic organs and impacts gene expression in the liver", "dateAssigned" : "2013-02-11T00:00:00.000-06:00", "summary" : "Intestinal paracellular permeability (IPP) is high at birth and is involved in gut barrier maturation and liver development. Chronic maternal separation (MS) in early life alters intestinal barrier function in adulthood. However, only transient MS commonly occurs in human newborns, but whether a single episode of MS in early postnatal days (PND) affects the maturation of the gut-liver axis has not been explored. The aim of the current study was to evaluate the effect of a single MS of short duration in neonate rats on epithelial barrier integrity in the gut and on gene expression in the liver. Male and female pups were separated from their dams for 4h or not (controls) at PND10 or PND20. Total intestinal paracellular permeability (IPP) was measured through mucosal-to-plasma passage of oral FITC-Dextran 4 KD with or without ML7, a blocker of myosin light chain kinase (MLCK), or Mifepristone (RU486), an antagonist of the glucocorticoid receptor. Dose response to dexamethasone (DEX) on IPP was studied at PND10 and PND20. Bacterial translocation (BT) was assessed in mesenteric lymph nodes (MLN), liver and spleen in the presence or absence of ML7. The hepatic transcriptome was studied using Agilent microarrays and qPCR on PND10 rats pretreated or not with ML7. At PND10, control pups showed basal BT to MLN while liver and spleen were sterile. A short-term MS procedure increased IPP and plasma corticosterone levels, resulted in BT to the liver and spleen and had a clear impact on the hepatic transcriptome. Most notably, several genes involved in cell division were downregulated by MS. In PND10 rats, MS-induced increase of IPP and BT were blocked by ML7 or RU486, thus demonstrating a role of the MLCK pathway and of increased plasma levels of corticosterone in these effects of MS. All these effects of MS were absent in PND20 rats. Consistently, PND20 rats were found less sensitive to DEX exposure than PND10 rats. These results show that the early life period is a critical window for a short-term mother-infant separation, which can alter the development of the gut-liver axis and facilitate bacterial passage to systemic organs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44289" }, "primaryId" : "GEO:GSE44289", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44289" } ] }, "title" : "Biphasic functional regulation in hippocampus of rat with chronic cerebral hypoperfusion induced by permanent occlusion of bilateral common carotid artery", "dateAssigned" : "2013-02-13T00:00:00.000-06:00", "summary" : "We measured temporal changes of gene expression in hippocampus of rat after BCCAo using time-course microarray analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44317" }, "primaryId" : "GEO:GSE44317", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44317" } ] }, "title" : "Flutamide treated rat hepatocytes in microfluidic biochips", "dateAssigned" : "2013-02-14T00:00:00.000-06:00", "summary" : "We investigated the effects of the flutamide (FLU) -induced liver injury in primary rat hepatocytes using our liver microfluidic biochips. Flutamide is used a non-steroidal anti-androgenic drug. Two flutamide concentrations, 10µM and 100µM, were used to expose the hepatocytes for 24h under perfusion.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44372" }, "primaryId" : "GEO:GSE44372", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44372" } ] }, "title" : "Gene expression profile in visceral-pancreatic adipose tissue from control rats fed a standard chow diet and obese rats fed a high-caloric cafeteria diet for 30 days.", "dateAssigned" : "2013-02-18T00:00:00.000-06:00", "summary" : "The aim of this study was to integrate transcriptomic, proteomic and metabolomic data to unravel the cross-talk between adipose tissue and pancreatic islets during evolution of obesity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24633677" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44373" }, "primaryId" : "GEO:GSE44373", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44373" } ] }, "title" : "Gene expression profile in pancreatic islets from control rats fed a standard chow diet and obese rats fed a high-caloric cafeteria diet for 30 days.", "dateAssigned" : "2013-02-18T00:00:00.000-06:00", "summary" : "The aim of this study was to integrate transcriptomic, proteomic and metabolomic data to unravel the cross-talk between adipose tissue and pancreatic islets during evolution of obesity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24006088" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44375" }, "primaryId" : "GEO:GSE44375", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44375" } ] }, "title" : "Next generation sequencing in ZS rats", "dateAssigned" : "2013-02-18T00:00:00.000-06:00", "summary" : "Next generation sequencing in a rat model of diabetic nephropathy was employed to study in depth the pathogenic alterations involved in progressive diabetic kidney damage. We employed the obese, diabetic ZS rat, a model that develops renal failure and fibrosis, the hallmarks of human disease. We then used RNA-seq to examine in a comprehensive manner the combined effects of renal cells and infiltrating inflammatory cells acting as a pathophysiological unit.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23757392" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44560" }, "primaryId" : "GEO:GSE44560", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44560" } ] }, "title" : "Identification of genes involved in cell differentiation of rat oral epithelial cell line ROE2", "dateAssigned" : "2013-02-21T00:00:00.000-06:00", "summary" : "The use of in vitro cell culture systems has been of central importance for research of physiology, pharmacology, and toxicology, and functions at the cellular and molecular levels. We have developed an immortalized oral epithelial cell line ROE2 from fetal transgenic rats harboring temperature-sensitive simian virus 40 large T-antigen. Here, to identify genes involved in ROE2 cell differentiation, global-scale gene expression analysis was carried out using a GeneChip® system.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24521861" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44562" }, "primaryId" : "GEO:GSE44562", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44562" } ] }, "title" : "Fibroblast growth factor 9 inhibits remyelination via an off target effect on astrocytes in multiple sclerosis", "dateAssigned" : "2013-02-21T00:00:00.000-06:00", "summary" : "We identify multiple downstream events induced by FGF9 associated with this effect including increased expression of leukaemia inhibitory growth factor (LIF) and FGF2, both of which are shown to inhibit myelination if present in excess. These studies identify FGF9-dependent signal transduction in astrocytes as a novel target for therapeutic strategies designed to enhance remyelination by endogenous OPC in MS.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25907862" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44699" }, "primaryId" : "GEO:GSE44699", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44699" } ] }, "title" : "Rat Pancreatic Tissue From Animals Fed Either an Iron Deficient or Iron Loaded vs. Iron Adequate Diet", "dateAssigned" : "2013-02-26T00:00:00.000-06:00", "summary" : "Microarray analysis of pancreatic tissue comparing gene expression in rats fed an iron deficient or iron loaded diet vs. iron adequate diet. Goal was to determine changes in gene expression in response to iron status.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44786" }, "primaryId" : "GEO:GSE44786", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44786" } ] }, "title" : "Rat mammary cancer (spontaneous, radiation, MNU, PhIP, radiation + MNU, radiation + PhIP) (high corn oil diet)", "dateAssigned" : "2013-03-01T00:00:00.000-06:00", "summary" : "Although various mechanisms have been inferred for combinatorial actions of multiple carcinogens, these mechanisms have not been well demonstrated in experimental carcinogenesis models. We evaluated mammary carcinogenesis initiated by combined exposure to various doses of radiation and chemical carcinogens. Female rats at 7 weeks of age were ¿-irradiated (0.2–2 Gy) and/or exposed to 1-methyl-1-nitrosourea (20 or 40 mg/kg, single intraperitoneal injection) or 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (40 mg/kg/day by gavage for 10 days) and were observed until 50 weeks of age. The incidence of mammary carcinoma increased steadily as a function of radiation dose in the absence of chemicals; mathematical analysis supported an additive increase when radiation was combined with a chemical carcinogen, irrespective of the chemical species and its dose. Hras mutations were characteristic of carcinomas that developed after chemical carcinogen treatments and were overrepresented in carcinomas induced by the combination of radiation and MNU (but not PhIP), indicating an interaction of radiation and MNU at the level of initiation. The expression profiles of seven classifier genes, previously shown to distinguish two classes of rat mammary carcinomas, categorized almost all examined carcinomas that developed after individual or combined treatments with radiation (1 Gy) and chemicals as belonging to a single class; more comprehensive screening using microarrays and a separate test sample set failed to identify differences in gene expression profiles among these carcinomas. These results suggest that a complex, multilevel interaction underlies the combinatorial action of radiation and chemical carcinogens in the experimental model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24778018" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44826" }, "primaryId" : "GEO:GSE44826", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44826" } ] }, "title" : "MicroRNA sequence and expression analysis of rat liver tissue exposed to aflatoxin B1 by deep sequencing", "dateAssigned" : "2013-03-04T00:00:00.000-06:00", "summary" : "We report the application of illumina deep sequencing technology for high-throughput profiling of microRNA in aflatoxin B1 treated rat liver tissue, as well as normal liver tissue. miRNAs of miR-17-92 cluster, thought to be tumor activating miRNAs, were down-regulated. miR-34a, considered to be a tumor suppressor, was up-regulated.Novel miRNAs and miRNA base alteration caused by SNP or editing were predicted and summarized.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44858" }, "primaryId" : "GEO:GSE44858", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44858" } ] }, "title" : "PRENATAL EXPOSURE TO CORTICOSTEROIDS: HYPOTHALAMIC CHANGES RELEVANT FOR POSTNATAL BEHAVIORAL IMPAIRMENTS", "dateAssigned" : "2013-03-05T00:00:00.000-06:00", "summary" : "Prenatal exposure to synthetic corticosteroids can significantly alter postnatal development through changes in neurotransmitters, peptides and their receptors, and thus having long-lasting behavioral effects. Some of these changes have been observed in animal experiments, others also in humans prenatally exposed to synthetic corticosteroids. Here, we focused on transcriptomic changes within the ARC of rats prenatally exposed to either betamethasone or saline. The expression of transcriptome has been assessed by novel computational tools to determine complex changes that may have life-long effects on phenotype, i.e., behavior. Total of 18,094 unigenes were quantified in the hypothalamic ARC of P14 male and female rats prenatally exposed to betametasone used in this experiment. Out of these genes, Kyoto Encyclopedia for Genes and Genomes (http://www.genome.jp) selected 112 for the dopaminergic synapse, 75 for the GABAergic and 97 for the glutamatergic synapse. We further analyzed composition, topology and modulatory networks of the genomic fabric of the dopaminergic, GABAergic, and glutamatergic synapse (the transcriptome of the most interconnected and stably expressed gene network responsible for specific transmission). Finally we investigated the “transcriptomic landscape” of the GSF in the ARC of P14 males (M) and females (F) prenatally (G15) exposed to betamethasone (B) or saline (S). We combined in one measure (PWR = Pair-Wise Relevance) expression levels, controls and coordination of all pairs that can be formed by synapse genes with the other synapse genes, higher PWRs indicating larger influence of that gene pair to the fabric modulation. We found that prenatal exposure to betamethasone caused sex-dependent changes in the dopaminergic/GABA/glutamatergic synapse genes:. In males, 10 dopaminergic (9%), 4 GABAergic (5%) and 5 glutamatergic synapse genes (5%) were down-regulated. While in females, 9 dopaminergic (8%), 3 GABAergic (4%) and 6 glutamatergic (6%) synapse genes were downregulated. The data indicate that in both sexes the dopaminergic synapse was the most affected. In contrast, in control animals, no significant differences between male and female were present in these synapse genes. Since the most noticeable transcritpomic changes were found in the transcriptome of DA glutamatergic synapse, we investigated the expression of tyrosine-hydroxylase (TH) NMDA receptor subunits in the ARC. The western blot analyses and immunohistochemistry confirmed the sex-specific differences between prenatally betamethasone-exposed and saline-exposed P15 rats. Accordingly to the changes in gene expression, prenatal exposure to synthetic corticosteroids was associated with postnatal changes in behavior and susceptibility to certain types of seizures. While we did not find any significant impairements in normal behavioral patterns (open field activity), there was a sex-specific change in the novel object recognition test. We found that behavioral lateralization in females is lost after prenatal betamethasone exposure and both male and female prenatally betamethasone exposed rats were avoiding novelty. This trait is similar to children with autism and suggests that certain elements of autistic behaviors can be present after prenatal exposure to synthetic corticosteroids. Additionally, there were changes in the search patterns in the Morris water maze as well as in the Barnes maze. In conclusion, our work is consistent with findings of profound reprogramming changes in the brain after prenatal corticosteroid exposure associated with alterations cognitive functions and seizure susceptibility.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44903" }, "primaryId" : "GEO:GSE44903", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44903" } ] }, "title" : "Gene expression profiling of a hypoxic seizure model of epileptogenesis in the rat.", "dateAssigned" : "2013-03-05T00:00:00.000-06:00", "summary" : "Gene expression in the control samples was found to be consistent with known processes of neuronal maturation in the rat for the given time window. The hypoxic seizure response was found to be saliently enriched for components of the PI3K/mTOR and Wnt signaling pathways, alongside gene sets representative of glutamatergic, synaptic and axonal processes, perhaps regulated as a downstream consequence of activation of these pathways. Wnt signaling components were also found enriched in the more specifically epileptogenic NBQX-responsive gene set. While activation of the mTOR pathway is consistent with its known role in epileptogenesis and strengthens the case for mTOR or PI3K pathway inhibitors as potential anti-epileptogenic drugs, investigation of the role of Wnt signaling and the effect of cognate inhibitors offers a parallel avenue of research toward anti-epileptogenic treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24086344" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44962" }, "primaryId" : "GEO:GSE44962", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE44962" } ] }, "title" : "Minor compensatory changes in SAGE Mdr1a (P-gp), Bcrp, and Mrp2 knockout rats do not detract from their utility in the study of transporter-mediated pharmacokinetics.", "dateAssigned" : "2013-03-07T00:00:00.000-06:00", "summary" : "Mdr1a-, Bcrp-, and Mrp2-knockout rats are a more practical species for ADME studies than murine models and previously demonstrated expected alterations in pharmacokinetics of various probe substrates. At present, gene expression and pathology changes were systematically studied in small intestine, liver, kidney, and brain tissue from male SAGE Mdr1a-, Bcrp-, and Mrp2-knockout rats versus wild-type Sprague Dawley controls. Gene expression data supported the relevant knockout genotype. As expected, Mrp2-knockout rats were hyperbilirubinemic and exhibited upregulation of hepatic Mrp3. Overall, few alterations were observed within 137 ADME-relevant genes. The two most consequential changes were upregulation of intestinal carboxylesterase in Mdr1a-knockouts and catechol-O-methyltransferase in all tissues of Bcrp-knockout rats. Previously reported upregulation of hepatic Mdr1b P-glycoprotein in proprietary Wistar Mdr1a-knockout rats was not observed in the SAGE counterpart investigated herein. Relative liver and kidney weights were 22-53% higher in all three knockouts, with microscopic increases in hepatocyte size in Mdr1a- and Mrp2-knockout rats, and glomerular size in Bcrp- and Mrp2-knockouts. Increased relative weight of clearing organs is quantitatively consistent with reported increases in clearance of drugs that are not substrates of the knocked-out transporter. Overall, SAGE knockout rats demonstrated modest compensatory changes, which do not preclude their general application to study transporter-mediated pharmacokinetics. However until future studies elucidate the magnitude of functional change, caution is warranted in rare instances of extensive metabolism by catechol-O-methyltransferase in Bcrp-knockouts and intestinal carboxylesterase in Mdr1a-knockout rats, specifically for molecules with free catechol groups and esters subject to gut wall hydrolysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23569176" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45006" }, "primaryId" : "GEO:GSE45006", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45006" } ] }, "title" : "Genome-Wide Gene Expression Profiling of Spinal Cord Injury in Rat", "dateAssigned" : "2013-03-11T00:00:00.000-05:00", "summary" : "The aneurysm clip impact-compression model of spinal cord injury (SCI) in animals mimics the primary mechanism of SCI in human, i.e. acute impact and persisting compression; and its histo-pathological and behavioural outcomes are extensively similar to the human SCI. In order to understand the distinct molecular events underlying this injury model, an analysis of global gene expression of the acute, subacute and chronic stages of a moderate to severe injury to the rat spinal cord was conducted using a microarray gene chip approach.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45021" }, "primaryId" : "GEO:GSE45021", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45021" } ] }, "title" : "Real-time quantitative PCR analysis of rat diaphragm before and after acute cervical spinal cord injury", "dateAssigned" : "2013-03-11T00:00:00.000-05:00", "summary" : "Male Sprague Dawley adult rats were subjected to a cervical hemisection at C2 (C2HS). Costal diaphragm (both ipsilesional and contralesional sides) were assessed under control conditions (sham surgery) and at 1 and 7 days post-C2HS. We used SA Biosciences Rat Skeletal Muscle Development and Disease RT2 Profiler PCR Array to quantitate gene expression of muscle atrophy and regeneration-relevant genes from the uninjured and injured tissues on the indicated sides and at the indicated timepoints post-lesion.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24341999" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45250" }, "primaryId" : "GEO:GSE45250", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45250" } ] }, "title" : "Expression data from cultured rat right ventricular papillary muscles", "dateAssigned" : "2013-03-18T00:00:00.000-05:00", "summary" : "Following a 12 hour culture period under prescribed mechanics, we used microarrays to identify genes that are up- or down-regulated in response to different amounts of mean stretch and cyclic shortening.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24302644" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45307" }, "primaryId" : "GEO:GSE45307", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45307" } ] }, "title" : "Antitumor Activity of (R,R’)-4-methoxy-1-naphthylfenoterol in a rat C6 glioma xenograft model in the mouse", "dateAssigned" : "2013-03-19T00:00:00.000-05:00", "summary" : "Keywords: fenoterol derivative; C6 glioma; tumor xenografts; microarray analysis;", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25505565" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45308" }, "primaryId" : "GEO:GSE45308", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45308" } ] }, "title" : "Profiling of copy-number variation between DNA isolation from different tissues of BN and ACI rats", "dateAssigned" : "2013-03-19T00:00:00.000-05:00", "summary" : "We used Nimblegen HD aCGH to detect DNA recovery from different tissue samples", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23618369" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45433" }, "primaryId" : "GEO:GSE45433", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45433" } ] }, "title" : "miRNA expression profile in rat carotid artery balloon injury model", "dateAssigned" : "2013-03-22T00:00:00.000-05:00", "summary" : "The proliferation and remodeling of vascular smooth muscle cells (VSMCs) is an important pathological event in atherosclerosis and restenosis. Here we report that microRNA-132 (miR-132) blocks vascular smooth muscle cells (VSMC) proliferation by inhibiting the expression of LRRFIP1 [leucine-rich repeat (in Flightless 1) interacting protein-1]. MicroRNA microarray revealed that miR-132 was upregulated in the rat carotid artery after catheter injury, which was further confirmed by quantitative real-time RT-PCR. Transfection of an miR-132 mimic significantly inhibited the proliferation of VSMCs, whereas transfection of an miR-132 antagomir increased it. Bioinformatics showed that LRRFIP1 is a target candidate of miR-132. miR-132 down-regulated luciferase activity driven by a vector containing the 3’-untranslated region of Lrrfip1 in a sequence-specific manner. LRRFIP1 induced VSMC proliferation. Immunohistochemical analysis revealed that Lrrfip1 was clearly expressed along with the basal laminar area of smooth muscle, and its expression pattern was disrupted 7 days after arterial injury LRRFIP1 mRNA was decreased 14 days after injury. Delivery of miR-132 to rat carotid artery attenuated neointimal proliferation in carotid artery injury models. Our results suggest that miR-132 is a novel regulator of VSMC proliferation that represses neointimal formation by inhibiting LRRFIP1 expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25683915" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45550" }, "primaryId" : "GEO:GSE45550", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45550" } ] }, "title" : "Molecular responses in skeletal muscles following spinal cord injury and the effect of locomotor training", "dateAssigned" : "2013-03-27T00:00:00.000-05:00", "summary" : "The overall objective of this study is to implement genome wide expression profiling of skeletal muscle to define the molecular pathways associated with muscle remodeling after SCI and during locomotor training (TM).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26380273" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45560" }, "primaryId" : "GEO:GSE45560", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45560" } ] }, "title" : "Analysis of gene expression during glucocorticoid-induced apoptosis of rat primary thymocytes", "dateAssigned" : "2013-03-27T00:00:00.000-05:00", "summary" : "Glucocorticoids induce rapid apoptosis of rat primary thymocytes through mechanisms requiring altered gene expression. The determination of genes regulating glucocorticoid-induced apoptosis of lymphocytes has received considerable attention. However, the role of specific non-coding microRNAs in the regulation of glucocorticoid-induced apoptosis of lymphocytes is poorly defined. Using deep sequencing analysis, we have identified microRNAs differentially expressed during glucocorticoid-induced apoptosis of rat primary thymocytes. We have also identified numerous loci that harbor probable novel microRNAs. Furthermore, we have validated the glucocorticoid-responsive expression of 2 novel microRNAs in the apoptotic rat primary thymocyte. These 2 novel microRNAs are predicted to target numerous messenger RNAs throughout the genome. Using whole genome expression analysis, we now seek to correlate the altered expression of these novel microRNAs with the expression of their predicted target mRNAs during glucocorticoid-induced apoptosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24250753" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45650" }, "primaryId" : "GEO:GSE45650", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45650" } ] }, "title" : "Gene expression profiles in liver of F344 rat treated with chemical", "dateAssigned" : "2013-03-30T00:00:00.000-05:00", "summary" : "The rodent carcinogenicity test requires extremely long test term and large examination cost. Therefore, now we need to develop a short term and low cost screening method. We already developed a chemical carcinogenicity short term screening method CARCINOscreen®. This study was performed to validate this screening method. We conducted 28 days-repeated dose experiments in male F344 rats with 4 carcinogens and 2 non-carcinogens, and the gene expression profiles in liver were measureed by custom oligo microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45654" }, "primaryId" : "GEO:GSE45654", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45654" } ] }, "title" : "Rat pineal gland RNA-Seq PolyA project", "dateAssigned" : "2013-03-31T00:00:00.000-05:00", "summary" : "The rat pineal gland is a highly dynamic tissue with many hundreds of genes changing more than two-fold in a 24-hr daily rhythm as measured by Affymetrix GeneChip analysis. We sought to more completely understand this dynamic transcriptome using RNA-Seq in order to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs, etc. We also wished to identify transcripts that were selectively expressed in the pineal glands relative to other tissues. Toward this end we performed RNA-Seq on three types of samples; 1) a pool of pineal glands sampled at mid-day (ZT7); 2) a pool of pineal glands sampled at mid-night (ZT19); and a pool of 15 different tissues collected from 3 animals at mid-day (ZT7). Animals were housed in a 14:10 light:dark lighting cycle. PolyA-selected RNA was fragmented and sequenced on an Illumina GAII machine, yielding paired-end 51-mer reads.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45813" }, "primaryId" : "GEO:GSE45813", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45813" } ] }, "title" : "Transcriptomic profile of mild exercise-enhanced adult hippocampal neurogenesis: Comparison with the effects of intense exercise", "dateAssigned" : "2013-04-05T00:00:00.000-05:00", "summary" : "Mild exercise (ME) with an intensity below the lactate threshold (LT) is sufficient to enhance hippocampal function, while intense exercise (IE) above the LT negates such benefits. However, the question as to why ME more effectively enhances hippocampal function than does IE remains to be clarified. Here, we investigated adult hippocampal neurogenesis (AHN) as a mechanism of ME-induced cognitive improvement, and comprehensively delineated the transcriptomic profile of the hippocampus, using a rat whole-genome microarray approach through comparison with IE. Immunohistochemical results showed that less intense exercise (ME) is better suited to improve AHN, especially in regards to the survival and maturation of newborn neurons. DNA microarray analysis revealed that ME regulated more genes than did IE (ME: 604 genes, IE: 415 genes), and only 44 genes were modified with both exercise intensities. The identified molecular components did not comprise well-known factors related to exercise-induced AHN, such as brain-derived neurotrophic factor (BDNF) and insulin-like growth factor 1 (IGF1), probably due to the timing of hippocampal tissue collection after the last training session and the technical feature of microarray. Rather, network analysis of the microarray data using Ingenuity Pathway Analysis algorithms revealed that the ME-influenced genes were principally related to lipid metabolism, protein synthesis and inflammatory response, which are recognized as associated with hippocampal neuroadaptations including AHN. In contrast, IE-influenced genes linked to immune response, a negative regulatory system of AHN and hippocampal function, were identified. Collectively, these results support our hypothesis that AHN could explain why ME enhances hippocampal function, and provide the ME-specific gene list that contain some potential regulators of this positive regulation. The list will become a foundation to elucidate the molecular pathway involving the ME-induced cognitive gain. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26061528" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45892" }, "primaryId" : "GEO:GSE45892", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45892" } ] }, "title" : "Temporal Concordance between Apical and Transcriptional Points-of-Departure for Chemical Risk Assessment", "dateAssigned" : "2013-04-09T00:00:00.000-05:00", "summary" : "The number of legacy chemicals without toxicity reference values combined with the rate of new chemical development are overwhelming the capacity of the traditional risk assessment paradigm. More efficient approaches are needed to quantitatively estimate chemical risks. In this study, rats were dosed orally with multiple doses of six chemicals for 5 days, 2, 4, and 13 weeks. Target organs were analyzed for traditional histological and organ weight changes and transcriptional changes using microarrays. Histological and organ weight changes in this study and the tumor incidences in the original cancer bioassays were analyzed using benchmark dose (BMD) methods to identify noncancer and cancer points-of-departure. The dose-response changes in gene expression were also analyzed using BMD methods and the responses grouped based on signaling pathways. A comparison of transcriptional BMD values for the most sensitive pathway with BMD values for the noncancer and cancer apical endpoints showed a high degree of correlation at all time points. When the analysis included data from an earlier study with 8 additional chemicals, transcriptional BMD values for the most sensitive pathway were significantly correlated with noncancer (r = 0.827, p = 0.0031) and cancer-related (r = 0.940, p = 0.0002) BMD values at 13 weeks. The average ratio of apical-to-transcriptional BMD values was less than two suggesting that for the current chemicals, transcriptional perturbation did not occur at significantly lower doses than apical responses. Based on our results, we propose a practical framework for application of transcriptomic data to chemical risk assessment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24194394" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45953" }, "primaryId" : "GEO:GSE45953", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45953" } ] }, "title" : "PHF6 knockdown in rat cortical neurons", "dateAssigned" : "2013-04-10T00:00:00.000-05:00", "summary" : "E18 embryonic rat cortical neurons cultured in vitro are infected with lentivirus expressing control or PHF6shRNA-2, and harvested 5 days after infection", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45997" }, "primaryId" : "GEO:GSE45997", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE45997" } ] }, "title" : "Gene expression patterns following unilateral traumatic brain injury reveals a local pro-inflammatory and remote anti-inflammatory response", "dateAssigned" : "2013-04-11T00:00:00.000-05:00", "summary" : "Abstract Background Traumatic brain injury (TBI) results in irreversible damage at the site of impact and initiates cellular and molecular processes that lead to secondary neural injury in the surrounding tissue. We used microarray analysis to determine which genes, pathways and networks were significantly altered using a rat model of TBI. Adult rats received a unilateral controlled cortical impact (CCI) and were sacrificed 24h post-injury. The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue were used for microarray analysis. Ingenuity Pathway Analysis (IPA) software was used to identify molecular pathways and networks that were associated with the altered gene expression in brain tissues following TBI. Results Inspection of the top fifteen biological functions in IPA associated with TBI in the ipsilateral tissues revealed that all had an inflammatory component. IPA analysis also indicated that inflammatory genes were altered on the contralateral side, but many of the genes were inversely expressed compared to the ipsilateral side. The contralateral gene expression pattern suggests a remote anti-inflammatory molecular response. We created a network of the inversely expressed common (i.e., same gene changed on both sides of the brain) inflammatory response (IR) genes and those IR genes included in pathways and networks identified by IPA that changed on only one side. We ranked the genes by the number of direct connections each had in the network, creating a gene interaction hierarchy (GIH). Two well characterized signaling pathways, toll-like receptor/NF-kappaB signaling and JAK/STAT signaling, were prominent in our GIH. Conclusions Bioinformatic analysis of microarray data following TBI identified key molecular pathways and networks associated with neural injury following TBI. The GIH created here provides a starting point for investigating therapeutic targets in a ranked order that is somewhat different than what has been presented previously. In addition to being a vehicle for identifying potential targets for post-TBI therapeutic strategies, our findings can also provide a context for evaluating the potential of therapeutic agents currently in development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23617241" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46069" }, "primaryId" : "GEO:GSE46069", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46069" } ] }, "title" : "Whole transcriptome profiling of rat pineal glands and retinas collected throughout a 24-hour cycle", "dateAssigned" : "2013-04-15T00:00:00.000-05:00", "summary" : "The rat pineal transcriptome is highly dynamic, with many hundreds of transcripts changing more than two-fold on a 24-hr basis, as revealed earlier using Affymetrix GeneChip analysis. The retina is evolutionally related to the pineal gland so these two tissues share many gene expression patterns. This study more completely characterizes the temporally dynamic transcriptomes of these tissues using RNA-Seq to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs, and coding transcripts not represented on the Affymetrix chips. We also identified transcripts that were selectively expressed in the pineal gland relative to other tissues by comparing pineal samples to a sample of pooled non-pineal tissues.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24351931" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46126" }, "primaryId" : "GEO:GSE46126", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46126" } ] }, "title" : "Transcriptome characterization of venous endothelium during the formation of neointimal hyperplasia and stenosis in a rat arteriovenous fistula model for kidney dialysis", "dateAssigned" : "2013-04-16T00:00:00.000-05:00", "summary" : "In patients with severe kidney disease AVF are surgically placed in order to create good access for hemodialysis. In these dialysis patients the failure rates of AVF can be as high as 24% within 6 months after surgery, causing ineffective dialysis and necessitating additional clinical interventions. The pathological processes known to lead to AVF failure are beginning to be unravelled include the formation of venous neointimal hyperplasia (VNIH), thrombosis (Chang et al. PMID 16105066), and venous stenosis (Kanterman et al. PMID7892454, Tang et al. 1998), resulting in a reduced blood flow through the fistula. We established a rat model for AVF failure in human kidney dialysis patients. The characterization of this model has been previously described (Globerman et al. 2011, PubmedID:22002501). In this model the AVFs are surgically constructed in the right leg by connecting the superficial epigastric vein SEV to the common femoral artery (CFA), resulting in exposure of the SEV to arterial pressure with pulsatile and low resistant flow patterns (Globerman et al. 2011, PMID22002501). In the present study we utilized this AVF model in order to assess the effects of arterialized flow, with consequent pathological changes of the vessel wall due to surgical AVF instalment, on the transcriptome of endothelium from the SEV. Within the SEV these pathologies of the vessel wall include the formation of NIH in the main branch, and stenosis in the side branches. By employing this rat model we assessed the changes of the endothelial transcriptome in relation to these pathologies in order to gain mechanistic understanding of the potential roles of venous endothelium in AVF failure, as well as to identify potential biomarkers preceding AVF failure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46127" }, "primaryId" : "GEO:GSE46127", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46127" } ] }, "title" : "Whole transcriptome profiling of the rat pineal gland during development from embryonic day 21 to adult", "dateAssigned" : "2013-04-16T00:00:00.000-05:00", "summary" : "The transcriptome of the rat pineal gland is highly dynamic, with many hundreds of genes changing more than two-fold on a 24-hr daily rhythm, as revealed earlier using Affymetrix GeneChip analysis. Several key transcription factors and enzymes are known to change dramatically during development of the pineal gland. Studies on a small number of genes indicate that the onset of rhythmic expression generally occurs later in development. This study characterizes this temporally dynamic transcriptome using RNA-Seq to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs and coding transcripts not represented on the Affymetrix chips.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24647753" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46221" }, "primaryId" : "GEO:GSE46221", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46221" } ] }, "title" : "Increase in membrane cholesterol of neurons in culture recapitulates Alzheimer’s disease early phenotypes.", "dateAssigned" : "2013-04-19T00:00:00.000-05:00", "summary" : "Levels of membrane-associated cholesterol were shown to be increased in the brain of individuals with sporadic Alzheimer’s disease (AD) and correlated with the severity of the disease. We previously found that heavy membrane cholesterol burden promotes amyloid precursor protein (APP) endocytosis and processing, leading to increased amyloid-¿¿¿A¿) secretion. We hypothesized that such an increase of cholesterol could trigger sporadic AD. We thus acutely loaded the plasma membrane of neurons in culture with cholesterol to reach the 30 % increase observed in AD brains. We showed by multiplex electro-chemiluminescence immuno-assay that transient membrane cholesterol loading produced a significant increase of A¿42 secretion. We also found that early endosomes were enlarged and more prone to aggregation using confocal and electron microscopy and that APP vesicular transport in neuronal processes was slowed down using fluorescence live-imaging. In addition, treatment of neurons with cholesterol induced changes in gene expression profile that are reminiscent of early AD. This model of membrane cholesterol increase in cultured neurons reproduces most of early AD changes and could thus be relevant for deciphering early mechanisms and design new targets for sporadic AD. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25524049" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46266" }, "primaryId" : "GEO:GSE46266", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46266" } ] }, "title" : "microRNAs involved in regulating embolic stroke recovery following spontaneous reperfusion [miRNA]", "dateAssigned" : "2013-04-22T00:00:00.000-05:00", "summary" : "To date, miRNA expression studies on cerebral ischemia in both human and animal models have focused mainly on acute phase of ischemic stroke. In this study, we present the roles played by microRNAs in the spontaneous recovery phases in cerebral ischemia using rodent stroke models.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23823624" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46267" }, "primaryId" : "GEO:GSE46267", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46267" } ] }, "title" : "microRNAs involved in regulating embolic stroke recovery following spontaneous reperfusion [mRNA]", "dateAssigned" : "2013-04-22T00:00:00.000-05:00", "summary" : "To date, miRNA and mRNA expression studies on cerebral ischemia in both human and animal models have focused mainly on acute phase of ischemic stroke. In this study, we present the roles played by microRNAs in the spontaneous recovery phases in cerebral ischemia using rodent stroke models.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23823624" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46295" }, "primaryId" : "GEO:GSE46295", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46295" } ] }, "title" : "Effects of a Tricaprylin Emulsion on Anti-glomerular Basement Membrane Glomerulonephritis in Rats", "dateAssigned" : "2013-04-23T00:00:00.000-05:00", "summary" : "Expression data from rat with anti-glomerular basement membrane nephritis (anti-GBM). We used microarrays to analyze the transcriptome of kidney from anti-GBM model rat with or without drug treatment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26235580" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46301" }, "primaryId" : "GEO:GSE46301", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46301" } ] }, "title" : "A conserved microRNA signature related to cellular transformation by the RAS oncogene (Affymetrix mRNA)", "dateAssigned" : "2013-04-23T00:00:00.000-05:00", "summary" : "The differential expression of microRNAs in Ras transformed epithelial cells of human and rat origin was investigated. Here we describe the group of miRNAs differentially expressed in two Ras transformed cell lines and defined it as a miRNA Ras signatures. We show that expression of these miRNAs are also affected in different primary tumors with high frequency of Ras mutation. We demonstate that introduction of different miRNAs lost during Ras transformation have big influence on cellular phenotype and mRNA expression. Importance of Ras pathway dependent transcription factors for miRNA regulation was shown as well. The complexity of miRNA – signal transduction pathways interactions and importance of miRNA regulation in Ras dependent malignant tumor formation is discussed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46373" }, "primaryId" : "GEO:GSE46373", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46373" } ] }, "title" : "Change of fate comitment in adult neural progenitor cells subjected to chronic inflammation", "dateAssigned" : "2013-04-25T00:00:00.000-05:00", "summary" : "In NPCs isolated from healthy rats, transcriptional and functional analyses revealed a higher neurogenic potential in SVZ-derived NPCs compared to spinal cord NPCs. The neurogenicity of spinal cord NPCs was increased by exposure to the inflammatory environment. Concurrently, their gliogenicity was decreased which was supported by a decreased expression of glial differentiation signature genes and related signaling pathways. Differentiation analyses showed that spinal cord NPCs from EAE rats generated fewer oligodendrocytes and astrocytes than NPCs isolated from healthy controls.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25164655" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46436" }, "primaryId" : "GEO:GSE46436", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46436" } ] }, "title" : "Expression data from neonatal rat ovaries following LPS exposure", "dateAssigned" : "2013-04-26T00:00:00.000-05:00", "summary" : "Inflammatory processes play an important role in regulation of ovarian development, in particularly early in life. Neonatal immune challenge by administration of lipopolysaccharide (LPS) has been previously demonstrated to result in diminished ovarian reserve and altered reproductive lifespan. In this study we aimed to characterise the cellular mechanisms that may underpin impaired ovulatory capacity and reduced oocyte development, induced by LPS treatment. Rat pups were administered with LPS or saline on postnatal days 3 and 5. Ovaries were obtained on postnatal day 7 to examine the effect of LPS administration on the ovarian transcriptome.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23781169" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46557" }, "primaryId" : "GEO:GSE46557", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46557" } ] }, "title" : "Interactions of wheat aleurine and plant omega-3 fatty acids on the rat gut microbiota", "dateAssigned" : "2013-05-01T00:00:00.000-05:00", "summary" : "In this study we investigated how an AX-rich WA and ALA from linseed oil (LO) modulate the gut microbiota of rats. Wistar rats were fed a standard diet and received either an iso-energetic control oil (PO), control oil + aleurone (A+PO), linseed oil (LO) or linseed oil + aleurone (A+LO) during 12 weeks. Feacal samples were recovered after the 12 week treatments. DNA extractions were performed using using the Qiagen's DNA Stool Kit (Qiagen, West Sussex, UK). 10ng of DNA template were amplified by PCR (16S gene) and purified using Qiagen's Qiaquick PCR purification kit (Qiagen, West Sussex, UK). 1ug of purified PCR product were labelled with either Cy3 or Cy5 using Genomic DNA ULS Labelling kit (Agilent Technologies, Palo Alto, CA). 250ng of labelled DNA were hybridized on the microarray for 24h at 65°C. Washings were performed as recommended by the manufacturer. Microarray scanning was performed on a Surescan Microarray scanner (Agilent Technologies, Palo Alto, CA). Data were extracted using the Feature extraction software (Agilent Technologies, Palo Alto, CA). The retained intensity value for each probe was the ratio between the spot’s median intensity signals and the median of background signals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46610" }, "primaryId" : "GEO:GSE46610", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46610" } ] }, "title" : "Effect of Mucuna pruriens against Naja sputatrix envenomation", "dateAssigned" : "2013-05-03T00:00:00.000-05:00", "summary" : "The direct protective effect probably involves functional changes to the cardiac tissue that enable the heart to resist the reduction of contractility and rate induced by the cobra venom.To explore the possibility of the direct action of MPE pretreatment on heart and to understand the molecular events involved in the protection of MPE pretreatment against the lethal action of Naja sputatrix venom, gene expression studies were carried out using microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25241584" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46669" }, "primaryId" : "GEO:GSE46669", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46669" } ] }, "title" : "A Snapshot of the Hepatic Transcriptome: Ad Libitum Alcohol Intake Suppresses Expression of Cholesterol Synthesis Genes in Alcohol-Preferring (P) Rats", "dateAssigned" : "2013-05-06T00:00:00.000-05:00", "summary" : "Conclusion: Voluntary consumption in the iP10a animals models moderate consumption in humans, does not produce intrahepatic fat accumulation, and causes down-regulation of a majority of cholesterol synthesis genes. Moderate alcohol also results in a tightly-regulated demethylation effect. Our results explain, at least in part, the J- or U-shaped relationship between level of alcohol intake and cardiovascular disease risk.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25542004" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46696" }, "primaryId" : "GEO:GSE46696", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46696" } ] }, "title" : "Gene expression profiling in subarachnoid haemorrhage", "dateAssigned" : "2013-05-07T00:00:00.000-05:00", "summary" : "We used microarrays to profile the changes in gene signatures after 6 hours of subarachnoid haemorrhage in the rat cerebral arteries .", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46702" }, "primaryId" : "GEO:GSE46702", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46702" } ] }, "title" : "Common Handling Procedures Conducted in Preclinical Safety Studies Results in Minimal Hepatic Gene Expression Changes in Sprague-Dawley Rats", "dateAssigned" : "2013-05-07T00:00:00.000-05:00", "summary" : "Gene expression profiling has been used as a tool to gain mechanistic understanding of adverse effects in response to compound exposure. However, little is known about how the common handling procedures of experimental animals during a preclinical study alter their baseline gene expression. We report on gene expression changes in the livers of female Sprague-Dawley rats following common handling procedures. Insight on baseline gene expression changes obtained in this study will allow us to evaluate how these changes may affect interpretation of gene expression profiles following compound exposure. Rats were divided into three groups (n = 10 per group): one group was not subjected to handling procedures, euthanized on day 2, and served as controls for both handled groups. Animals in the other two groups were weighed, subjected to restraint in Broome restrainers, and administered water via oral gavage daily for 1 or 4 days with tail vein blood collections at 1, 2, 4, and 8 hours postdose on days 1 and 4 followed by euthanasia on day 2 or 5. Significantly altered genes were identified in livers of animals following 1 or 4 days of handling when compared to the unhandled animals. Gene changes in animals handled for 4 days were similar to those handled for 1 day, suggesting a lack of habituation. The altered genes were primarily immune function related genes. These findings, along with a correlating increase in corticosterone levels suggest that common handling procedures may cause a minor immune system perturbance.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46717" }, "primaryId" : "GEO:GSE46717", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46717" } ] }, "title" : "Enhanced upregulation of CRH mRNA expression in the rat nucleus accumbens after a delayed second injection of methamphetamine", "dateAssigned" : "2013-05-07T00:00:00.000-05:00", "summary" : "Methamphetamine (METH) is a widely abused illicit amphetamine that causes acute biochemical and molecular changes in the brain. However, there are very few studies that have investigated the long-term effects of a single METH exposure in adult animals. The purpose of this study was thus to determine the consequences of a single injection of METH (10) mg/kg) on the biochemical and transcriptional effects of a second challenge injection of the drug (2.5 mg/kg) given one month later. Towards that end, we measured monoamine levels and gene expression by microarray and quantitative PCR analyses in the nucleus accumbens (NAc) of 4 groups of rats: saline-pretreated and saline-challenged (SS); saline-pretreated and METH-challenged (SM); METH-pretreated and saline-challenged (MS); and METH-pretreated and METH-challenged (MM). The rats were euthanized 2 hours after the acute challenge injection and NAc samples were harvested. The acute METH challenge caused increases in NAc DA and HVA levels in both the SM and MM groups. Microarray analyses revealed that an injection of METH (2.5 mg/kg) produced acute changes (1.8-fold; p < 0.01) in the expression of 418 (358 up-, 60 downregulated) genes including several immediate early genes (IEGs) such as Arc, c-fos, and fosB in the SM group. Several neuropeptides including Cart, Crf (Crh), and vasopressin were upregulated in that group. Injection of the higher dose of METH (10 mg/kg) did not influence monoamine levels but caused changes in 510 (345 up-, 165 downregulated) transcripts measured one month later (MS group). This list included Cart and Crf but not any IEGs. The MM group showed changes in 774 (572 up-, 202 downregulated) genes that also included vasopressin, Cart, and Crf whose expression was enhanced by the second METH injection. Quantitative PCR confirmed the METH-induced changes in the expression of the neuropeptides. We also confirmed the METH-induced potentiation of Crf expression in the METH-pretreated group. These observations suggest that a single injection of a moderate dose of METH can produce long-lasting changes in gene expression in the rodent NAc. The long-term increases in Crf expression also suggest that a single injection of a moderate METH dose can cause prolonged dysregulation in the endogenous stress system in the rat brain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46794" }, "primaryId" : "GEO:GSE46794", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46794" } ] }, "title" : "A conserved microRNA signature related to cellular transformation by the RAS oncogene (miRNA)", "dateAssigned" : "2013-05-09T00:00:00.000-05:00", "summary" : "The differential expression of microRNAs in Ras transformed epithelial cells of human and rat origin was investigated. Here we describe the group of miRNAs differentially expressed in two Ras transformed cell lines and defined it as a miRNA Ras signatures. We show that expression of these miRNAs are also affected in different primary tumors with high frequency of Ras mutation. We demonstate that introduction of different miRNAs lost during Ras transformation have big influence on cellular phenotype and mRNA expression. Importance of Ras pathway dependent transcription factors for miRNA regulation was shown as well. The complexity of miRNA – signal transduction pathways interactions and importance of miRNA regulation in Ras dependent malignant tumor formation is discussed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46820" }, "primaryId" : "GEO:GSE46820", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46820" } ] }, "title" : "Genome wide maps of H3K4me3 and H3ac histone modifications in C6 rat glioma cells [Illumina]", "dateAssigned" : "2013-05-10T00:00:00.000-05:00", "summary" : "We report maps of H3K4me3 and H3ac - activiting expression histone modifications in C6 rat glioma cells. The data was obtained using whole genome high throughput technology. The sequencing was performed on HiSeq Ilumina platform.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25111868" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46822" }, "primaryId" : "GEO:GSE46822", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46822" } ] }, "title" : "Genome wide map of H3K4me3 histone modification in C6 rat glioma cells [SOLiD]", "dateAssigned" : "2013-05-10T00:00:00.000-05:00", "summary" : "We report a map of H3K4me3 - an activiting expression histone modification in C6 rat glioma cells. The data was obtained using whole genome high throughput technology. The sequencing was performed on Solid 5500xl platform.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25111868" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46827" }, "primaryId" : "GEO:GSE46827", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46827" } ] }, "title" : "miRNA expression profile in PC12 cells under NGF treatment and deprivation", "dateAssigned" : "2013-05-10T00:00:00.000-05:00", "summary" : "miRNA profiling of PC12 rat pheochromocytoma cells during NGF-induced differentiation and apoptosis of differentiated cells after 24h of NGF deprivation. miRNA expression in differentiating and deprivated cells was compared to untreated and terminally differentiated PC12 cells respectivelly.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24492999" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46852" }, "primaryId" : "GEO:GSE46852", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46852" } ] }, "title" : "Expression data from NRK-52E cells treated with chlorothalonil for 6h, 24h and 72h.", "dateAssigned" : "2013-05-13T00:00:00.000-05:00", "summary" : "We used microarrays to detail the mechanism of toxicity and possibly carcinogenicity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46863" }, "primaryId" : "GEO:GSE46863", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46863" } ] }, "title" : "Clinical symptoms of right ventricular failure in experimental chronic pressure load are associated with progressive diastolic dysfunction", "dateAssigned" : "2013-05-13T00:00:00.000-05:00", "summary" : "Chronic pulmonary artery banding invariably leads to RV failure in rats, and a subset transitions to advanced clinical RVF. RVF is characterized by enhanced contractility, progressive diastolic dysfunction and derangement of energy metabolism, thus improving diastolic function and targeting RV metabolism may be the keys to treating RVF.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25486580" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46864" }, "primaryId" : "GEO:GSE46864", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46864" } ] }, "title" : "Gabazine treatment of hippocampal organotypic cultures", "dateAssigned" : "2013-05-13T00:00:00.000-05:00", "summary" : "The blockage of GABA-A ionotropic channels by means of gabazine is a widespread model of plasticity where the increased synaptic activity triggered by Gabazine leads to the up-regulation of a plethora of activity-dependent genes. Here, we sought to characterize the overall transcriptional response of GABA-A blocking of rat hippocampal organotypic cultures.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23935853" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46910" }, "primaryId" : "GEO:GSE46910", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46910" } ] }, "title" : "Gene Expression Analysis of Postnatal Day 6 Testes Sired by Paternally Exposed Males to Saline or BEP", "dateAssigned" : "2013-05-14T00:00:00.000-05:00", "summary" : "To determine the changes in gene expression of testes from postnatal day 6 pups, a window in development where spermatogonial stem cells is predominant, following paternal exposure to saline or BEP, a chemotherapeutic coktail used to treat testicular cancer", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23986570" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46988" }, "primaryId" : "GEO:GSE46988", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46988" } ] }, "title" : "Expression data from rat spinal cord injury and mesenchymal stromal cells (MSC) or olfactory ensheathing cells (OEC) transplantation", "dateAssigned" : "2013-05-15T00:00:00.000-05:00", "summary" : "We analyzed the changes in the spinal cord transcriptome after a spinal cord contusion injury and MSC or OEC transplantation. The cells were injected immediately or 7 days after the injury. The mRNA of the spinal cord injured segment was extracted and analyzed by microarray at 2 and 7 days after cell grafting.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24146830" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46997" }, "primaryId" : "GEO:GSE46997", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE46997" } ] }, "title" : "Differentially expressed genes analysis by cDNA microarray during liver regenration after partial hepatectomy and different stages of liver development in rats.", "dateAssigned" : "2013-05-16T00:00:00.000-05:00", "summary" : "In our study, the transcriptional profile of developing liver (2wks and 4 wks), regenerating liver and adult liver based on microarray data has been systematically compared. Also the biological relevance of differentially expressed genes were also analysed through gene ontology (GO) and pathway analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47020" }, "primaryId" : "GEO:GSE47020", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47020" } ] }, "title" : "Genome wide map of Stat3 binding sites in C6 rat glioma cells [NimbleGen]", "dateAssigned" : "2013-05-16T00:00:00.000-05:00", "summary" : "We report a map of Stat3 binding sites in C6 rat glioma cells. The data was obtained using whole genome technology using NimbleGen microarrays.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25111868" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47068" }, "primaryId" : "GEO:GSE47068", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47068" } ] }, "title" : "Rat Life Cycle Kidney Male Gene Expression Data", "dateAssigned" : "2013-05-17T00:00:00.000-05:00", "summary" : "The kidney is important for a number of physiological processes including blood filtering, blood pressure regulation and proper excretion of many drugs and xenobiotics. Age is a predisposing condition for susceptibility to chronic kidney disease and progression as well as acute kidney injury that may arise due to the adverse effects of some drugs. Age-related differences in kidney biology, therefore, are a key concern in understanding drug safety and disease progression. We hypothesize that the underlying suite of genes expressed in the kidney at various life cycle stages will impact susceptibility to adverse drug reactions. Therefore, establishing changes in baseline expression data between these life stages is the first and necessary step in evaluating this hypothesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23902594" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47069" }, "primaryId" : "GEO:GSE47069", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47069" } ] }, "title" : "Rat Life Cycle Kidney Female Gene Expression Data", "dateAssigned" : "2013-05-17T00:00:00.000-05:00", "summary" : "The kidney functions in key physiological processes to filter blood and regulate blood pressure via key molecular transporters and ion channels. Sex-specific differences have been observed in renal disease incidence and progression as well as acute kidney injury in response to certain drugs. Although advances have been made in characterizing the molecular components involved in various kidney functions, the molecular mechanisms responsible for sex differences are not well understood. We hypothesized that the basal expression levels of genes involved in various kidney functions throughout the life cycle will influence sex-specific susceptibilities to adverse renal events.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23902594" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47080" }, "primaryId" : "GEO:GSE47080", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47080" } ] }, "title" : "Partial urethra obstruction in rat", "dateAssigned" : "2013-05-19T00:00:00.000-05:00", "summary" : "Urethra was partially ligated and the urinary bladder was removed 10 days or 6 weeks after obstruction. Sham operated rats were used as controls. An addtitonal group of rats were repoerated 6 weeks after surgery and the obstruction was removed. These rats were then sacrificed 10 days after deobstruction. The bladder (including the urothelium) was frozen and used for RNA extraction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24340017" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47131" }, "primaryId" : "GEO:GSE47131", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47131" } ] }, "title" : "Hormonal Regulation of MicroRNA Expression in Rat Adrenal Gland", "dateAssigned" : "2013-05-21T00:00:00.000-05:00", "summary" : "To determine miRNA profiles in rat adrenals from animals treated with vehicle, ACTH, 17a-ethinyl estradiol (17a-E2) or dexamethasone (DEX). miRNA expression profiling was performed using Affymetrix® GeneChip® miRNA 2.0 Arrays. Together with qRT-PCR, several adrenal miRNAs have been identified, whose expression is subject to regulation by one or more than one hormone.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47174" }, "primaryId" : "GEO:GSE47174", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47174" } ] }, "title" : "Genome-wide mRNA expression profiles of FACS-enriched rat beta cells freshly isolated from neonatal (postnatal day 2-3) and adult (10 weeks-old) Wistar rats", "dateAssigned" : "2013-05-22T00:00:00.000-05:00", "summary" : "A genome-wide view on postnatal maturation/differentiation of the rat beta cells", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24049066" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47200" }, "primaryId" : "GEO:GSE47200", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47200" } ] }, "title" : "Ventral prostate in TRAP rats: Control vs. apocyin treatment", "dateAssigned" : "2013-05-22T00:00:00.000-05:00", "summary" : "The gene expression profling between Control and apocynin 500 mg/L treatment in ventral prostate lobe of Transgenic Rat for Adenocarcinoma of Prostate (TRAP) rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24118288" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47474" }, "primaryId" : "GEO:GSE47474", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47474" } ] }, "title" : "Transcriptome Sequencing of Gene Expression in the brain of HIV transgenic transgenic rat", "dateAssigned" : "2013-05-29T00:00:00.000-05:00", "summary" : "Conclusions: The abnormal gene expression pattern discovered in HIV-1Tg rats suggest mechanisms underlying the deficits in learning and memory and vulnerability to drug addiction and other psychiatric disorders observed in HIV positive patients. The gene expression pattern in the HIV-1Tg rats after nicotine exposure indicate that cholinergic modulators such as nicotine may have beneficial effects on HIV-1-induced neurologic deficits.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23874651" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47495" }, "primaryId" : "GEO:GSE47495", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47495" } ] }, "title" : "Transcriptional profiling of left ventricle and peripheral blood cells in rats with post-myocardial infarction", "dateAssigned" : "2013-05-29T00:00:00.000-05:00", "summary" : "We used microarrays to investigate gene expression in the left ventricle (LV) accompanying myocardial infarction and concomitant heart failure (HF) in a well validated model of post-infarcted heart failure and to evaluate their reflection in peripheral blood mononuclear cells (PBMCs)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24206753" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47529" }, "primaryId" : "GEO:GSE47529", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47529" } ] }, "title" : "Transcriptional network analysis reveals that AT1 and AT2 Angiotensin II receptors are both involved in the regulation of genes essential for glioma progression ", "dateAssigned" : "2013-05-30T00:00:00.000-05:00", "summary" : "Gliomas are aggressive primary brain tumors, presenting surgery limitations due to their highly infiltrative potential. The expression of Angiotensin II (Ang II) receptors in human astrocytomas was previously associated with a poor prognosis. Accordingly, this study was undertaken to reveal the molecular mechanisms underlying Ang II actions in gliomas through the transcriptomic analysis of glioma cells exposed to Ang II. C6 glioma cells were treated with Ang II and specific antagonists of AT1 and AT2. Total RNA was isolated at three and six hours intervals and submitted to oligonucleotide microarray protocol. The differentially expressed genes were obtained by paired t-tests with p<0.05 and interpreted using Venn diagrams, functional enrichment and protein interaction network analyses. Validation of microarray results was carried out through qPCR experiments of selected genes. We found a high number of significant genes with low fold changes in gene expression at the time intervals studied. These genes were regulated in a time dependent-manner, with most gene expression changes being exclusive to one of the time intervals evaluated. Our results indicated that blocking AT1 or AT2 changed the expression of genes involved in regulation of transcription, cell cycle, cell proliferation, differentiation, apoptosis, cell adhesion, cell migration, regulation of actin cytoskeleton, protein transport and protein ubiquitination. Additionally, the signaling pathways over-represented by the significant genes were ErbB, mTOR, MAPK, neurotrophin, insulin and Wnt. Finally, interactome analyses revealed hub genes associated with cell proliferation, survival, migration, transport, structural support, neurotrophin pathway, MAPK signaling and Wnt signaling. Taken together, our findings implicate Ang II-transcriptional regulation in glioma progression by means of the modulation of genes participating in protumoral functions. This transcriptome pattern is observed upon Ang II activation of either AT1 or AT2 receptors, thereby highlighting the relevance of both receptor subtypes in glioma progression. Interactome analyses disclosed hub genes regulated by Ang II which may present higher control over their networks. These genes participate in biological functions that could enhance the degree of malignancy in gliomas and thus should be further explored.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25365520" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47541" }, "primaryId" : "GEO:GSE47541", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47541" } ] }, "title" : "Effects of MDMA and Venlafaxine treatment in Dark Agouti rats", "dateAssigned" : "2013-05-30T00:00:00.000-05:00", "summary" : "The aim of this study was to examine the hippocampus, frontal cortex and dorsal raphe of Dark Agouti rats with gene expression arrays (Illumina RatRef bead arrays) looking for possible mechanisms and new candidates contributing to the effects of a single dose of MDMA (15 mg/kg) 3 weeks earlier or venlafaxine (40 mg/kg) administration for 3 weeks continously. We also examined the possible interaction between the single dose MDMA treatment and the continous venlafaxine treatment described above.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25423262" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47543" }, "primaryId" : "GEO:GSE47543", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47543" } ] }, "title" : "The physicochemistry of capped nanosilver predicts it biological activity in brain endothelial (RBEC4) cells", "dateAssigned" : "2013-05-30T00:00:00.000-05:00", "summary" : "This study uses the RBEC4 cell model to examine if nanosilver of different sizes (10nm and 75nm) and cappings (citrate and polyvinylpyrrolidone(PVP)) affect its cellular permeability and genomic response.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47570" }, "primaryId" : "GEO:GSE47570", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47570" } ] }, "title" : "High dietary protein decreases fat deposition induced by high-fat and high-sucrose diet in rats", "dateAssigned" : "2013-05-31T00:00:00.000-05:00", "summary" : "High-protein diets are known to reduce adiposity in the context of high carbohydrate and Western diets. However, few studies have investigated the specific high-protein effect on lipogenesis induced by a high-sucrose (HS) diet or fat deposition induced by high-fat feeding. We aimed to determine the effects of high protein intake on the development of fat deposition and partitioning in response to high-fat and/or HS feeding. A total of thirty adult male Wistar rats were assigned to one of the six dietary regimens with low and high protein, sucrose and fat contents for 5 weeks. Body weight (BW) and food intake were measured weekly. Oral glucose tolerance tests and meal tolerance tests were performed after 4th and 5th weeks of the regimen, respectively. At the end of the study, the rats were killed 2 h after ingestion of a calibrated meal. Blood, tissues and organs were collected for analysis of circulating metabolites and hormones, body composition and mRNA expression in the liver and adipose tissues. No changes were observed in cumulative energy intake and BW gain after 5 weeks of dietary treatment. However, high-protein diets reduced by 20 % the adiposity gain induced by HS and high-sucrose high-fat (HS-HF) diets. Gene expression and transcriptomic analysis suggested that high protein intake reduced liver capacity for lipogenesis by reducing mRNA expressions of fatty acid synthase (fasn), acetyl-CoA carboxylase a and b (Acaca and Acacb) and sterol regulatory element binding transcription factor 1c (Srebf-1c). Moreover, ketogenesis, as indicated by plasma ß-hydroxybutyrate levels, was higher in HS-HF-fed mice that were also fed high protein levels. Taken together, these results suggest that high-protein diets may reduce adiposity by inhibiting lipogenesis and stimulating ketogenesis in the liver.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26285832" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47581" }, "primaryId" : "GEO:GSE47581", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47581" } ] }, "title" : "Global gene expression profiling of mesotheliomas from vehicle control and VDC-exposed male F344N rats", "dateAssigned" : "2013-05-31T00:00:00.000-05:00", "summary" : "A recent two-year NTP cancer bioassay showed a marked increase in the incidence of malignant mesothelioma arising from the tunica vaginalis in male Fischer 344/N rats exposed to Vinylidene chloride (VDC). Aged male F344/N rats are prone to developing spontaneous peritoneal mesotheliomas, which also arise predominantly from the tunica vaginalis of the testes. A definitive mechanism for the observed increased incidence in VDC-exposed rats is unknown. Investigation of the molecular alterations that occur in mesotheliomas from vehicle control and VDC-exposed rats may provide insight into their pathogenesis, as well enable a better understanding regarding the mechanisms underlying chemically induced mesothelioma in rodents. Mesothelial cell function represents a complex interplay of pathways related to host defense mechanisms and maintenance of cellular homeostasis. Global gene expression profiles of spontaneous mesotheliomas from vehicle control male F344/N rats from various two-year National Toxicology Program carcinogenicity bioassays were compared to mesotheliomas from VDC-exposed rats to characterize the molecular features that are present in mesotheliomas from VDC-exposed animals, and to elucidate tumor-specific gene expression profiles. The resulting gene expression pattern showed that mesotheliomas from VDC-exposed animals are genomically very different from spontaneous tumors; while both tumor types are characterized by alterations in gene expression associated with carcinogenic pathways (oncogenes, tumor suppressor genes, growth factors, etc.), mesotheliomas from VDC-exposed animals are associated with increased dysreguation of immune pathways and inflammatory mediators. Alterations in these pathways may suggest a pro-inflammatory and immune dysfunction signature as one mechanism in the observed increased incidence of these tumors in VDC-exposed animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24958746" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47618" }, "primaryId" : "GEO:GSE47618", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47618" } ] }, "title" : "Identification of Rat foreskin biomarkers of in utero dibutyl phthalate exposure [Affymetrix]", "dateAssigned" : "2013-06-03T00:00:00.000-05:00", "summary" : "Dibutyl phthalate was administered to pregnant Sprague Dawley rats from gestational days 16-20 at either a 100 mg/kg/day or 500 mg/kg/day dose level. This timeframe covers the reproductive masculinization window which corresponds to increased androgen signalling. Dibutyl phthalate has been shown to disrupt testosterone production leading to male reproductive abnormalities. As such, we selected this exposure window for our study and examined gene expression changes in the male rat foreskin, which expresses the androgen receptor. We collected tissue samples at both gestational day 20 to identify gene expression changes immediately after exposure, and postnatal day 5 to identify gene expression changes persisting after birth using microarray analysis (Illumina RatRef 12 Bead Chips). To determine whether gene expression changes were brought on by decreased androgen signalling or additional effects of dibutyl phthalate exposure, we exposed rats to the potent androgen receptor antagonist flutamide (5 mg/kg/day) during the same period of development. Gene expression changes were compared to determine which were brought on by disruption of androgen signalling and which were the result of other aspects of chemical exposure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47676" }, "primaryId" : "GEO:GSE47676", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47676" } ] }, "title" : "Gene profiling of the early healing rat medial collateral ligament", "dateAssigned" : "2013-06-05T00:00:00.000-05:00", "summary" : "The objective of the study was to better understand the mechanism behind scar formation by identifying ECM factors and other unique genes differentially expressed during rat ligament healing via microarray. Rat medial collateral ligaments (MCL) were surgically transected or left intact. MCLs were collected at day 3 or 7 post-injury and used for microarray analysis. Results were compared to the normal intact ligaments.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21596919" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47695" }, "primaryId" : "GEO:GSE47695", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47695" } ] }, "title" : "Cross-species gene expression analysis of species-specific differences in preclinical assessment of pharmaceutical compounds (rat)", "dateAssigned" : "2013-06-06T00:00:00.000-05:00", "summary" : "Significant qualitative and quantitative differences exist between humans and the animal models used in research. However, significant quantitative and qualitative differences exist between humans and the animal models used in research. This is as a result of genetic variation between human and the laboratory animal. Therefore the development of a system that would allow the assessment of all molecular differences between species after drug exposure would have a significant impact on drug evaluation for toxicity and efficacy. Here we describe a cross-species microarray methodology that identifies and selects orthologous probes after cross-species sequence comparison to develop an orthologous cross-species gene expression analysis tool. The assumptions made by the use of this orthologous gene expression strategy for cross-species extrapolation is that; conserved changes in gene expression equate to conserved pharmacodynamic endpoints. This assumption is supported by the fact that evolution and selection have maintained the structure and function of many biochemical pathways over time, resulting in the conservation of many important processes. We demonstrate this difference using a cross-species methodology by investigating species specific differences of the peroxisome proliferator activator receptor (PPAR) alpha in rat and human.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24823806" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47752" }, "primaryId" : "GEO:GSE47752", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47752" } ] }, "title" : "Transcriptional profiling of dentate granule cells in 4 rat epilepsy models", "dateAssigned" : "2013-06-07T00:00:00.000-05:00", "summary" : "Global expression profiling of epileptogenesis has been confounded by variability across laboratories, epilepsy models, tissue sampled and experimental platforms, with the result that very few genes demonstrate consistent expression changes. The present study minimizes these confounds by combining Affymetrix microarray datasets from seven laboratories, using three status epilepticus (SE) models of epilepsy in rats (pilocarpine, kainate, self-sustained SE or SSSE) and the rat kindling model. Total RNA was harvested from laser-captured dentate granule cells from 6 rats at three times during the early-to-mid latent phase that precedes epilepsy symptoms in the SE models (1, 3 and 10 days after SE), or 24 hr after the first stage 2, stage 4 and stage 5 seizure in the kindling model. Each epilepsy model was studied in two independent laboratories except SSSE. The initial goals of this study were to a) identify model-independent transcriptional changes in dentate granule cells that could point to novel intervention targets for epileptogenesis, b) characterize the basal transcriptional profile of dentate granule cells, and c) identify genes that have highly variable expression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47754" }, "primaryId" : "GEO:GSE47754", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47754" } ] }, "title" : "Chronic Psychological Stress regulates Visceral Adipocyte-mediated Glucose Metabolism and Inflammatory Circuits in male Rats", "dateAssigned" : "2013-06-07T00:00:00.000-05:00", "summary" : "In this study we employed the chronic unpredictable stress (CUS) rat model that leads to anxiety features comparable to humans and validated in several published reports as a well-characterized model of depression symptoms with high predictive validity. Cytokines and activated intracellular kinase levels were determined using high throughput multiplex assays. RNA from freshly isolated adipocytes was used to run whole genome expression microarray profiling in control and stressed rats. Adipocyte function was assessed via tritiated glucose uptake assay. The expression of four cytokines (TNFa, IL-1ß, IL-6 and MCP-1) was validated via real-time PCR and the all showed increased expression levels with chronic unpredictable stress.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24819750" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47867" }, "primaryId" : "GEO:GSE47867", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47867" } ] }, "title" : "Behaviorally activated mRNA expression profiles produce signatures of learning and enhanced inhibition in aged rats with preserved memory", "dateAssigned" : "2013-06-12T00:00:00.000-05:00", "summary" : "Aging is often associated with cognitive decline, but many elderly individuals maintain a high level of function throughout life. Here we studied outbred rats, which also exhibit individual differences across a spectrum of outcomes that includes both preserved and impaired spatial memory. Previous work in this model identified the CA3 subfield of the hippocampus as a region critically affected by age and integral to differing cognitive outcomes. Earlier microarray profiling revealed distinct gene expression profiles in the CA3 region, under basal conditions, for aged rats with intact memory and those with impairment. Because prominent age-related deficits within the CA3 occur during neural encoding of new information, here we used microarray analysis to gain a broad perspective of the aged CA3 transcriptome under activated conditions. Behaviorally induced CA3 expression profiles differentiated aged rats with intact memory from those with impaired memory. In the activated profile, we observed substantial numbers of genes (greater than 1000) exhibiting increased expression in aged unimpaired rats relative to aged impaired, including many involved in synaptic plasticity and memory mechanisms. This unimpaired aged profile also overlapped significantly with a learning induced gene profile previously acquired in young adults. Alongside the increased transcripts common to both young learning and aged rats with preserved memory, many transcripts behaviorally-activated in the current study had previously been identified as repressed in the aged unimpaired phenotype in basal expression. A further distinct feature of the activated profile of aged rats with intact memory is the increased expression of an ensemble of genes involved in inhibitory synapse function, which could control the phenotype of neural hyperexcitability found in the CA3 region of aged impaired rats. These data support the conclusion that aged subjects with preserved memory recruit adaptive mechanisms to retain tight control over excitability under both basal and activated conditions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24349543" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47875" }, "primaryId" : "GEO:GSE47875", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47875" } ] }, "title" : "SEQC Toxicogenomics Study: microarray data set", "dateAssigned" : "2013-06-12T00:00:00.000-05:00", "summary" : "contributor: DrugMatrix, National Toxicology program (NTP)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25150839" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47943" }, "primaryId" : "GEO:GSE47943", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE47943" } ] }, "title" : "The effect of alcohol on the expression of miroRNAs in rat nucleus accumbens", "dateAssigned" : "2013-06-14T00:00:00.000-05:00", "summary" : "The results demonstrated, among the 300 detected miRNAs in NAc, multiple miRNAs were aberrantly expressed after treatment with alcohol.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48011" }, "primaryId" : "GEO:GSE48011", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48011" } ] }, "title" : "Mesenchymal stem cells gene expression on liver after ischemia-reperfusion injury.", "dateAssigned" : "2013-06-17T00:00:00.000-05:00", "summary" : "Analysis of topically applied adipose tissue deirved mesenchymal stem cells (ATSC) on the surface of liver with ischemia-reperfusion injury (IRI). Histology showed that topically applied ATSC on IRI liver surface gave a faster healing process and regeneration rate. Resutls provides insight of the expression pattern between ATSC topically applied on IRI and non-IRI liver with reference of basal expression of the ATSC in in-vitro culture", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48025" }, "primaryId" : "GEO:GSE48025", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48025" } ] }, "title" : "Affymetrix Chip Data of the Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture (Affymetrix, mRNA, batch1)", "dateAssigned" : "2013-06-17T00:00:00.000-05:00", "summary" : "We report the application of Affymetrix technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA), with acupuncture, Methotrexate, Isofluorane anesthetic and placebo treatments, as well as the healthy control.\t\t\t\t\t\t\t\t\t\t", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28008941" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48087" }, "primaryId" : "GEO:GSE48087", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48087" } ] }, "title" : "The Cellular and Genomic Response of  Dopaminergic Neurons (N27) to Commericial “Capped” Nanosilver", "dateAssigned" : "2013-06-19T00:00:00.000-05:00", "summary" : "Global gene expression indicated that N27 neurons exposed to each nanoAg material (1.0 ppm, 18 hr) responded primarily toPVP coated nanoAg of both sizes with affected pathwayslargely associated with mitochondrial dysfunction (PVP 75 nm nanoAg) and Nrf-2 mediated oxidative stress (PVP 10 nm nanoAg) pathways.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48100" }, "primaryId" : "GEO:GSE48100", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48100" } ] }, "title" : "Effect of maternal exposure to dioxin on the pituitary and hypothalamic expression of genes in PND70 male pups", "dateAssigned" : "2013-06-19T00:00:00.000-05:00", "summary" : "Our previous studies have revealed that treatment of pregnant rats with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, 1 µg/kg) at gestational day (GD) 15 reduces the pituitary synthesis of luteinizing hormone (LH) during late fetal and early postnatal period, leading to imprinting of defects in sexual behaviors at adulthood. However, it remains obscure how the attenuation of pituitary LH links to sexual immaturity. To address this issue, we firstly performed a DNA microarray analysis to identify the gene(s) responsible for dioxin-induced sexual immaturity, using the pituitary and hypothalamus of male pups, at the age of postnatal day (PND)70, born from TCDD-treated dams. Among the reduced genes, we focused on gonadotropin-releasing hormone (GnRH) in the hypothalamus, because of its role in sexual behaviors suggested so far. The present study strongly suggests that maternal exposure to TCDD fixes the status of the lowered expression of GnRH in the offspring by reducing steroidogenesis at perinatal stage, and this is the mechanism for the imprinting of defects in sexual behaviors at adulthood.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24132183" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48111" }, "primaryId" : "GEO:GSE48111", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48111" } ] }, "title" : "BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure [NRVM Expression]", "dateAssigned" : "2013-06-19T00:00:00.000-05:00", "summary" : "Heart failure (HF) is driven via interplay between master regulatory transcription factors and dynamic alterations in chromatin structure. While pathologic gene transactivation in this context is known to be associated with recruitment of histone acetyl-transferases and local chromatin hyperacetylation, the role of epigenetic reader proteins in cardiac biology is unknown. We therefore undertook a first study of acetyl-lysine reader proteins, or bromodomains, in HF. Using a chemical genetic approach, we establish a central role for BET-family bromodomain proteins in gene control during HF pathogenesis. BET inhibition potently suppresses cardiomyocyte hypertrophy in vitro and pathologic cardiac remodeling in vivo. Integrative transcriptional and epigenomic analyses reveal that BET proteins function mechanistically as pause-release factors critical to activation of canonical master regulators and effectors that are central to HF pathogenesis and relevant to the pathobiology of failing human hearts. This study implicates epigenetic readers in cardiac biology and identifies BET co-activator proteins as therapeutic targets in HF.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23911322" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48236" }, "primaryId" : "GEO:GSE48236", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48236" } ] }, "title" : "Genome-wide analysis of rats' mRNA profile after knocking down PIWIL1 in embryonic cultured neurons.", "dateAssigned" : "2013-06-24T00:00:00.000-05:00", "summary" : "We have demonstrated that PIWIL1 can regulate neuronal radial migration during corticogenesis. In order to explore the mechanism, we carried out high-throughtput sequencing (mRNA profile) to define downstream target of PIWIL during the process of neuronal migration. And we found the expression level of several microtubule-associated proteins decreased after downregulation of PIWIL1. Therefore, PIWIL1 plays an important role in neuronal migration by regulating the expression microtubule-associated proteins (such as Map1B, Map2, Tau) .", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26104391" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48266" }, "primaryId" : "GEO:GSE48266", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48266" } ] }, "title" : "Expression data from the rat knee articular cartilage at different developmental stages", "dateAssigned" : "2013-06-25T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying the rat knee cartilage and identified distinct classes of age-related miRNAs during this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48279" }, "primaryId" : "GEO:GSE48279", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48279" } ] }, "title" : "Balloon injury-induced gene expression in common carotid arteries of wistar rat", "dateAssigned" : "2013-06-25T00:00:00.000-05:00", "summary" : "The whole rat genome microarray expression profiling of carotid artery specimen was emplyed to identify the gene expression profile before and after balloon injury. In our study, the neointimal formation of carotid arteries was apparent at day 7 and markedly increased at day 21 after balloon injury. In order to investigate the underlying mechanism of neointimal formationin in injured carotid arteries, all genes involved in signaling pathways whose expression was altered 2-fold in injured carotid arteries at day 7 and day 21 as compared to uninjured arteries were filtered out. Expression of four genes (TLR4, IRAK1, I¿Ba, IL-1ß) from TLR signaling pathway was quantified in the same RNA samples by quantitative real-time PCR, conforming that TLR signaling pathway participated in neointimal formation of carotid arteries after balloon injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48298" }, "primaryId" : "GEO:GSE48298", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48298" } ] }, "title" : "Transcriptome analysis of mesothelioma induced by intraperitoneal injections of asbestos in rats", "dateAssigned" : "2013-06-26T00:00:00.000-05:00", "summary" : "Human malignant mesothelioma (MM) is an aggressive tumor strongly associated with asbestos exposure. SM patients generally have poorer prognosis compared to EM patients. To identify potential genes accounting for the differential prognosis between these two subtypes, we compared the microarray gene expression profiles of rat SM and EM tissues induced by intraperitoneal injections of 3 types of asbestos (chrysotile,crocidolite and amosite).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24839947" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48321" }, "primaryId" : "GEO:GSE48321", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48321" } ] }, "title" : "High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis", "dateAssigned" : "2013-06-26T00:00:00.000-05:00", "summary" : "Mammalian spermatogenesis is a complex and highly orchestrated combination of processes in which male germline proliferation and differentiation result in the production of mature spermatozoa. If recent genome-wide studies have contributed to the in-depth analysis of the male germline protein-coding transcriptome, little effort has yet been devoted to the systematic identification of novel unannotated transcribed regions expressed during mammalian spermatogenesis. We report high-resolution expression profiling of male germ cells in the rat using Illumina next-generation sequencing technology and highly enriched testicular cell populations. Among 20,424 high-confidence transcripts reconstructed, we defined a stringent set of 1,419 long multi-exonic unannotated transcripts expressed in the testis, named TUTs. These were classified into seven groups with different expression patterns. The vast majority of TUTs share many of the characteristics of vertebrate long non-coding RNAs (lncRNAs). We also markedly reinforced the finding that TUTs and known lncRNAs accumulate during the meiotic and postmeiotic stages of spermatogenesis in mammals, and that X-linked meiotic TUTs do not escape the silencing effects of meiotic sex chromosome inactivation. Importantly, we discovered that TUTs and known lncRNAs with a peak expression during meiosis define a distinct class of non-coding transcripts that exhibit exons twice as long as those of other transcripts. Our study provides new insights in transcriptional profiling of the male germline and represents a high-quality resource of novel loci expressed during spermatogenesis that significantly contributes to the rat genome annotation. A graphical display of the data is conveniently accessible through the ReproGenomics Viewer (RGV) at http://rgv.genouest.org.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25210130" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48342" }, "primaryId" : "GEO:GSE48342", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48342" } ] }, "title" : "Gene Expression Profiles in Engineered Cardiac Tissues Respond to Mechanical Loading and Inhibition of Tyrosine Kinase", "dateAssigned" : "2013-06-26T00:00:00.000-05:00", "summary" : "We tested the hypothesis that global ECT gene expression patterns are sensitive to mechanical loading conditions and tyrosine kinase inhibitors, similar to the maturing myocardium. We generated 3D ECTs from day 14.5 rat embryo ventricular cells, as previously published, and then treated constructs after 5 days in culture for 48 hours with mechanical stretch (5%, 0.5 Hz) and/or the p38MAPK (p38 mitogen-activated protein kinase) selective inhibitor BIRB796. RNA was isolated from 3 sets of experiments and assayed using a standard Agilent rat 4x44k V3 microarray and Pathway Analysis software for transcript expression fold changes and changes in regulatory molecules and networks. At the threshold of a 1.5 fold change in expression, mechanical stretch altered 1,559 transcripts, versus 1,411 for BIRB796, and 1,846 for stretch plus BIRB796. As anticipated, top pathways altered in response to these stimuli include Cellular Development, Cellular Growth and Proliferation; Tissue Development; Cell Death, Cell Signaling, and Small Molecule Biochemistry as well as numerous other pathways. Changes in transcript expression were confirmed by quantitative-PCR for selected regulatory molecules. Thus, ECTs display a broad spectrum of altered gene expression in response to mechanical load and/or tyrosine kinase inhibition, reflecting the complex regulation of proliferation, differentiation, and architectural alignment that occurs during ECT maturation and adaptation. This approach can now be used to test the role of individual molecules and pathways on the regulation of ECT maturation and remodeling.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48357" }, "primaryId" : "GEO:GSE48357", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48357" } ] }, "title" : "MALDI imaging MS reveals candidate lipid markers of polycystic kidney disease", "dateAssigned" : "2013-06-27T00:00:00.000-05:00", "summary" : "Genome-scale gene expression profiling of PCK and SD livers as control was performed to attempt elucidation of some of the underlying mechanisms leading to increases of cholesterol and taurine-conjugated bile acids in the PCK rat. Several pathways were found to be changed in cystic livers with up regulation or down regulation of important gene sets. Enhanced expression of steroid biosynthesis genes might result in the observed increased levels of cholesterol. In contrast, primary bile acid biosynthesis was found to be down regulated in diseased livers. These findings might be explained by compensatory mechanisms of liver metabolism to reduce toxic levels of accumulated bile acids.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23852700" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48373" }, "primaryId" : "GEO:GSE48373", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48373" } ] }, "title" : "Comparative transcriptomic profiling of liver tissue from lean (fa/+) female Zucker rats (~15 weeks old) fed a standard diet supplemented (0.5% w/w) with a rosemary extract enriched in carnosic acid (40% CA)", "dateAssigned" : "2013-06-27T00:00:00.000-05:00", "summary" : "We used Affymetrix microarrays to investigate gene expression changes in the liver of lean female Zucker rats exposed to a normal diet supplemented with a rosemary extract rich in the diterpenic compound, carnosic acid (CA).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24550204" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48407" }, "primaryId" : "GEO:GSE48407", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48407" } ] }, "title" : "Effect of wood block enrichment on gene expression data in rat liver and spleen following treatment with cyclophosphamide for 5 days", "dateAssigned" : "2013-06-28T00:00:00.000-05:00", "summary" : "We used microarrays to determine if transcriptomically, rats treated with cyclophosphamide and administered wood blocks were different from those treated with cyclophosphamide and not allowed access to wood blocks", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48455" }, "primaryId" : "GEO:GSE48455", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48455" } ] }, "title" : "Translation value of the bleomycin rat model for the treatment of patients with Idiopathic Pulmonary Fibrosis (IPF)", "dateAssigned" : "2013-07-01T00:00:00.000-05:00", "summary" : "Intratracheal application of bleomycin is known to induce inflammatory and fibrotic reactions in the lung within a short period of time and histological features include infiltration of inflammatory cells, collagen deposition and obliteration of alveolar spaces. Because some of these features are found in patients with idiopathic pulmonary fibrosis (IPF), the bleomycin-induced lung fibrosis animal model is commonly used. However, exploratory treatments that were successfully used in this animal model and progressed to clinical trials lacked significant efficacy in humans. Here, the bleomycin-induced rat lung fibrosis model was studied using whole genome expression data that was collected at various time points and the relevance to human disease was evaluated through comparison with whole genome expression data from IPF patient-derived lung biopsies. The highest gene expression correlation between both species was observed in animals 7 days after bleomycin instillation. These gene expression signatures helped to identify a set of twelve novel disease-relevant translational gene markers that were able to separate IPF patients from controls. Furthermore, three Wnt/¿-catenin pathway-related genes that belong to this translational gene marker set showed, together with clinical diffusing capacity of the lung for carbon monoxide (DLCO) measurements, the potential to stratify IPF patients according to disease severity. Pirfenidone attenuated a subset of the translational gene markers in the bleomycin-induced fibrosis model, in particular those related to Wnt/¿-catenin-signaling. This novel translational gene marker panel offers improved possibilities to evaluate disease-modifying efficacy of novel therapeutic concepts in the bleomycin-induced rat lung fibrosis model and could be applied as a diagnostic and prognostic tool for IPF patient care.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25029475" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48489" }, "primaryId" : "GEO:GSE48489", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48489" } ] }, "title" : "Dose and temporal effects of Phenobarbital on the liver miRNAome of male Fischer rats", "dateAssigned" : "2013-07-02T00:00:00.000-05:00", "summary" : "Male Fischer rats were fed a control diet or a diet supplemented with 50, 500 or 1000 ppm Phenobarbital. The 500 and 1000 ppm PB doses induced a transient hyperplasia and a sustained hepatomegaly in treated animals. The animals were sacrificed and liver miRNAome was profiled in three animals per group after 1, 3, 7, and 14 days of treatment. The aim was to investigate the time and dose dependent effects of phenobarbital treatment on the liver miRNAome", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24157574" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48492" }, "primaryId" : "GEO:GSE48492", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48492" } ] }, "title" : "Effect of treatment for three months with chemical carcinogen and non-carcinogens on liver miRNAome", "dateAssigned" : "2013-07-02T00:00:00.000-05:00", "summary" : "Here, we examined the liver microRNA profile of male Fischer rats exposed through their diet to genotoxic (2-acetylaminofluorene) and epigenetic (phenobarbital, diethylhexylphthalate, methapyrilene HCL, monuron, and chlorendic acid) chemical hepatocarcinogens, as well as to non-hepatocarcinogenic treatments (benzophenone, and diethylthiourea) for three months. The aim of the study was to investigate how liver miRNA profiles relate to mode of action and carcinogenic potential of chemicals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22584684" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48623" }, "primaryId" : "GEO:GSE48623", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48623" } ] }, "title" : "Analyzing the hippocampal gene network to determine the effects of coral calcium hydride on antioxidant ability in rat brain", "dateAssigned" : "2013-07-09T00:00:00.000-05:00", "summary" : "In our previous study, we reported that a diet rich in antioxidants such as coral calcium hydride (CCH) increased the endogenous antioxidant ability in the hippocampus of rats. We conducted this study to test the hypothesis that diet supplementation with CCH would change the gene expression in rats and to understand how CCH enhances antioxidant ability. We used a DNA array to compare the expression levels in the hippocampus of rats fed with CCH for 2 weeks with those of rats fed a normal diet. Immune response-related genes were down-regulated, while nuclear respiratory factor 2 and aldehyde dehydrogenase 3A were up-regulated. Our findings about the changes in the mRNA levels of these genes well explain the physiological finding of enhanced antioxidant ability in rat brain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48648" }, "primaryId" : "GEO:GSE48648", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48648" } ] }, "title" : "Extrauterine growth restriction on pulmonary vascular endothelial dysfunction in adult male rats: the role of epigenetic mechanisms", "dateAssigned" : "2013-07-09T00:00:00.000-05:00", "summary" : "MeDIP together with microarray analysis demonstrated that significant differences in cytosine methylation between EUGR and control rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48655" }, "primaryId" : "GEO:GSE48655", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48655" } ] }, "title" : "Expression data from growth restricted fetal rat pancreatic islets", "dateAssigned" : "2013-07-09T00:00:00.000-05:00", "summary" : "This mimics placental insufficiency. This array experiment compares gene expression changes in isolated pancreatic islets from e19, 24 hours post-surgery , or sham operated animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24408314" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48794" }, "primaryId" : "GEO:GSE48794", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48794" } ] }, "title" : "Identification of factors associated with high fat diet induced insulin resistance", "dateAssigned" : "2013-07-11T00:00:00.000-05:00", "summary" : "Whole genome expression profilling were undertaken in high fat diet (HFD)-fed obese rats to identify the genetic factors associated with metabolic dysfunction, insulin resistance and obesity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48795" }, "primaryId" : "GEO:GSE48795", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48795" } ] }, "title" : "Differential transcrpitome analysis of Sertoli cells during their phases of postnatal maturation in rat testes", "dateAssigned" : "2013-07-11T00:00:00.000-05:00", "summary" : "Spermatogenesis is a complex process involving multiple cells and cellular signals. Among all other cells, Sertoli cells (Sc) are absolutely indispensable for sperm production because they provide biochemical signal and physical support to developing germ cells in the testis. Sc drastically transform during the process of attainment of reproductive maturity. Stage specific gene expression by Sc, supplement for the changing need of developing germ cells. A conspicuous absence of comprehensive gene expression data from various stages of developing Sertoli cells hinders our knowledge of regulating inputs necessary for the process of spermatogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28065881" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48802" }, "primaryId" : "GEO:GSE48802", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48802" } ] }, "title" : "Identification of Rat foreskin biomarkers of in utero dibutyl phthalate exposure [Illumina]", "dateAssigned" : "2013-07-11T00:00:00.000-05:00", "summary" : "Dibutyl phthalate was administered to pregnant Sprague Dawley rats from gestational days 16-20 at either a 100 mg/kg/day or 500 mg/kg/day dose level. This timeframe covers the reproductive masculinization window which corresponds to increased androgen signalling. Dibutyl phthalate has been shown to disrupt testosterone production leading to male reproductive abnormalities. As such, we selected this exposure window for our study and examined gene expression changes in the male rat foreskin, which expresses the androgen receptor. We collected tissue samples at both gestational day 20 to identify gene expression changes immediately after exposure, and postnatal day 5 to identify gene expression changes persisting after birth using microarray analysis (Illumina RatRef 12 Bead Chips). To determine whether gene expression changes were brought on by decreased androgen signalling or additional effects of dibutyl phthalate exposure, we exposed rats to the potent androgen receptor antagonist flutamide (5 mg/kg/day) during the same period of development. Gene expression changes were compared to determine which were brought on by disruption of androgen signalling and which were the result of other aspects of chemical exposure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48822" }, "primaryId" : "GEO:GSE48822", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48822" } ] }, "title" : "Effect of IUGR on postnatal day 14 pancreatic islets", "dateAssigned" : "2013-07-12T00:00:00.000-05:00", "summary" : "At postnatal day 14, we isolate pancreatic islets and have compared their gene expression with that of control (sham) surgery animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24408314" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48825" }, "primaryId" : "GEO:GSE48825", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48825" } ] }, "title" : "CGH array: Sprague-Dawley rat (SDR) vs Hirosaki hairless rat (HHR)", "dateAssigned" : "2013-07-12T00:00:00.000-05:00", "summary" : "Profiling of gain and loss of DNA fragments in HHR comparing control SDR.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23997226" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48961" }, "primaryId" : "GEO:GSE48961", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE48961" } ] }, "title" : "The effect of vitamin D supplementation on tumorigenesis in a thioacetamide (TAA)-induced rat intrahepatic cholangiocarcinoma model", "dateAssigned" : "2013-07-17T00:00:00.000-05:00", "summary" : "In this study, we investigated the effect of vitamin D supplementation on tumorigenesis in a thioacetamide (TAA)-induced rat intrahepatic cholangiocarcinoma model as vitamin D is known to have a spectrum of anticancer activities. Using PET, we found that tumor formation and progression were suppressed in rats fed a diet supplemented with 6 IU/g vitamin D3(+6D) as compared to the group fed a 2 IU/g vitamin D3 diet (+2D) or controls. Microarray analysis of the tumors that arose revealed that vitamin D supplementation caused significant up- and down regulation in 21 and 16 genes, respectively.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24939880" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49040" }, "primaryId" : "GEO:GSE49040", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49040" } ] }, "title" : "Gene expression data from brain central nucleus of amygdala (CeA) following binge-like alcohol drinking by adolescent alcohol-preferring rats", "dateAssigned" : "2013-07-19T00:00:00.000-05:00", "summary" : "The objective of this study was to determine changes in gene expression within the extended amygdala following binge-like alcohol drinking by adolescent alcohol-preferring (P) rats. Starting at 28 days of age, P rats were given concurrent access to 15 and 30 % ethanol for 3 one-h sessions for 5 consecutive days each week until they were 49 days old. Rats were killed by decapitation 3 h after the first ethanol access session on the 15th day of drinking. RNA was prepared from micropunch samples of the nucleus accumbens shell (Acb-sh) and central nucleus of the amygdala (CeA). Ethanol intakes were 2.5 – 3.0 g/kg/session. There were 154 and 182 unique named genes that significantly differed (FDR = 0.2) between the water and ethanol group in the Acb-sh and CeA, respectively. Gene Ontology (GO) analyses indicated that adolescent binge drinking produced changes in the in biological processes involved in cell proliferation and regulation of cellular structure in the Acb-sh, and in neuron projection and positive regulation of cellular organization in the CeA. Ingenuity Pathway Analysis indicated that, in the Acb-sh, there were several major intracellular signaling pathways (e.g., cAMP-mediated and protein kinase A signaling pathways) altered by adolescent drinking, with 3-fold more genes up-regulated than down-regulated in the alcohol group. The cAMP-mediated signaling system was also up-regulated in the CeA of the alcohol group. Weighted gene co-expression network analysis (WGCNA) indicated significant G-protein coupled receptor signaling and transmembrane receptor protein kinase signaling categories in the Acb-sh and CeA, respectively. Overall, the results of this study indicated that binge-like alcohol drinking by adolescent P rats is differentially altering the expression of genes in the Acb-sh and CeA, some of which are involved in intracellular signaling pathways and may produce long-term changes in neuronal function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24355552" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49041" }, "primaryId" : "GEO:GSE49041", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49041" } ] }, "title" : "Gene expression data from brain nucleus accumbens shell (Acb-sh) following binge-like alcohol drinking by adolescent alcohol-preferring rats", "dateAssigned" : "2013-07-19T00:00:00.000-05:00", "summary" : "The objective of this study was to determine changes in gene expression within the extended amygdala following binge-like alcohol drinking by adolescent alcohol-preferring (P) rats. Starting at 28 days of age, P rats were given concurrent access to 15 and 30 % ethanol for 3 one-h sessions for 5 consecutive days each week until they were 49 days old. Rats were killed by decapitation 3 h after the first ethanol access session on the 15th day of drinking. RNA was prepared from micropunch samples of the nucleus accumbens shell (Acb-sh) and central nucleus of the amygdala (CeA). Ethanol intakes were 2.5 – 3.0 g/kg/session. There were 154 and 182 unique named genes that significantly differed (FDR = 0.2) between the water and ethanol group in the Acb-sh and CeA, respectively. Gene Ontology (GO) analyses indicated that adolescent binge drinking produced changes in the in biological processes involved in cell proliferation and regulation of cellular structure in the Acb-sh, and in neuron projection and positive regulation of cellular organization in the CeA. Ingenuity Pathway Analysis indicated that, in the Acb-sh, there were several major intracellular signaling pathways (e.g., cAMP-mediated and protein kinase A signaling pathways) altered by adolescent drinking, with 3-fold more genes up-regulated than down-regulated in the alcohol group. The cAMP-mediated signaling system was also up-regulated in the CeA of the alcohol group. Weighted gene co-expression network analysis (WGCNA) indicated significant G-protein coupled receptor signaling and transmembrane receptor protein kinase signaling categories in the Acb-sh and CeA, respectively. Overall, the results of this study indicated that binge-like alcohol drinking by adolescent P rats is differentially altering the expression of genes in the Acb-sh and CeA, some of which are involved in intracellular signaling pathways and may produce long-term changes in neuronal function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24355552" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49080" }, "primaryId" : "GEO:GSE49080", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49080" } ] }, "title" : "Profiling of circadian genes expressed in the uterus endometrial stromal cells of pregnant rats as revealed by DNA microarray coupled with RNA interference", "dateAssigned" : "2013-07-22T00:00:00.000-05:00", "summary" : "The circadian clock positively or negatively regulates the expression of clock-controlled genes, including growth factors and apoptosis-related factors.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23847593" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49144" }, "primaryId" : "GEO:GSE49144", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49144" } ] }, "title" : "Pulmonary toxicity and global gene expression changes in response to sub-chronic inhalation exposure to crystalline silica in rats", "dateAssigned" : "2013-07-23T00:00:00.000-05:00", "summary" : "Occupational exposure to crystalline silica results in serious health effects, most notably, silicosis and cancer. A proper understanding of the mechanism(s) underlying the initiation and progression of silica-induced pulmonary toxicity is critical for the intervention and/or prevention of the adverse health effects associated with crystalline silica exposure. Rats were exposed to crystalline silica by inhalation at a concentration of 15 mg/m3, 6 hours/day, 5 days/week for 3, 6 or 12 weeks. At the end of each exposure time point, toxicity and global gene expression changes were determined in the lungs. In general, silica exposure resulted in pulmonary toxicity that was dependent on the duration of silica exposure. A significant and silica exposure time-dependent increase in lactate dehydrogenase activity and accumulation of alveolar macrophages and infiltrating neutrophils in the bronchoalveolar lavage fluid suggested crystalline silica-induced pulmonary toxicity in the rats. Histological changes indicative of pulmonary toxicity were detectable only in the lungs of rats that were exposed to silica for 6- or 12-weeks. Minimal, sub-acute pulmonary inflammation consisting mainly of macrophage accumulation and infiltration of neutrophils was seen in 2 out of 8 rats in the 6-week silica exposure group. Chronic active inflammation, type II pneumocyte hyperplasia, and fibrosis were detected following 12-weeks of silica exposure in all rat lungs. In addition, crystalline silica was visible in the lungs of the rats belonging to the 12-week exposure group. A significant increase in the number of neutrophils seen in the blood indicated silica-induced systemic inflammation in the rats. Microarray analysis of the global gene expression profiles of the rat lungs detected significant differential expression (FDR p <0.05 and fold change >1.5) of 38, 77 and 99 genes in the rats exposed to silica for 3-, 6- and 12-weeks, respectively, compared to the time-matched controls. Bioinformatics analysis of the differentially expressed genes identified significant enrichment of functions, networks and pathways related to inflammation, cancer, oxidative stress, fibrosis and tissue remodeling in the lungs of the silica exposed rats. Collectively, the results of our study provided insights into the molecular mechanisms underlying pulmonary toxicity following sub-chronic exposure to silica in rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49303" }, "primaryId" : "GEO:GSE49303", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49303" } ] }, "title" : "Cerebellar Gene Expression Profile Analysis in a Rat Model of Acute Alcohol Intoxication", "dateAssigned" : "2013-07-29T00:00:00.000-05:00", "summary" : "We first established a model of acute alcohol intoxication in SD rats, and then used rat cDNA microarray to profile mRNA expression in the cerebella of alcohol-intoxicated rats (experimental group) and saline-treated rats (control group).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49352" }, "primaryId" : "GEO:GSE49352", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49352" } ] }, "title" : "Comparison of gene expression profiles in blood, hippocampus and prefrontal cortex in rats", "dateAssigned" : "2013-07-30T00:00:00.000-05:00", "summary" : "This study provides a baseline analysis of absolute gene expression and its differences in blood, PFC and HC brain tissue in genetically identical rats. Our data might be used for first information on gene expression levels of genes of interest in blood and brain under baseline conditions.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49389" }, "primaryId" : "GEO:GSE49389", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49389" } ] }, "title" : "Genome-wide analysis of the rat colon reveals site-specific differences in histone modifications and proto-oncogene expression", "dateAssigned" : "2013-07-31T00:00:00.000-05:00", "summary" : "Results/Conclusion: Globally, RNA-Seq results indicated that 9,866 genes were actively expressed, of which 540 genes were differentially expressed between the proximal and distal colon. With regard to differentially expressed genes, a high correlation was observed between H3K4me3-Seq and RNA-Seq data, with 96% of the canonical pathways being similarly affected in the H3K4me3-Seq and RNA-Seq data sets. Gene ontology analysis indicated that colonic crypt location significantly impacted both chromatin and transcriptional regulation of genes involved in cell transformation, lipid metabolism, lymphatic development and immune cell trafficking. Gene function analysis indicated that the PI3-Kinase signaling pathway was regulated in a site-specific manner, e.g., pathway proto-oncogenes, c-Jun, c-Fos and ATF, were up-regulated in the distal colon. Middle and long non-coding RNAs (lncRNAs) were also detected in the colon, including select lncRNAs formerly only detected in the rat nervous system. In summary, distinct combinatorial patterns of histone modifications exist in the proximal versus distal colon. These site-specific differences may explain the differential effects of chemoprotective agents on cell transformation in the ascending (proximal) and descending (distal) colon.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24151245" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49392" }, "primaryId" : "GEO:GSE49392", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49392" } ] }, "title" : "Gene expression data from HD mutant and wild type ST14A cells, differentiated for 24 hours and treated with vehicle (DMSO) or with 5µM MIND4", "dateAssigned" : "2013-07-31T00:00:00.000-05:00", "summary" : "MIND4 treatment significantly reduced levels of TNF-alpha in the cortex of symptomatic HD mice, demonstrating the neuroprotective anti-inflammatory potential of NRF2 activator in the CNS. A high affinity reversible binding of MIND4 ligands to the NRF2 inhibitor, KEAP1, was identified by a docking model and confirmed by mechanistic studies, suggesting a novel approach to activating the NRF2 pathway. The results offer a new therapeutic path for HD and other human diseases.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49473" }, "primaryId" : "GEO:GSE49473", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49473" } ] }, "title" : "A Genomics-Based Analysis of Relative Potencies of Dioxin-Like Compounds in Primary Rat Hepatocytes", "dateAssigned" : "2013-08-01T00:00:00.000-05:00", "summary" : "A toxicogenomics approach was used to qualitatively and quantitatively compare gene expression changes in rat primary hepatocytes exposed to 2,3,4,7,8-pentachlorodibenzofuran (4-PeCDF) or 2,3,7,8-tetrachlorodibenzofuran (TCDF). Hepatocytes from five individual rats were exposed for 24 hours to 11 concentrations of each chemical ranging from 0.00001 nM to 100 nM and a vehicle control.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24046277" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49485" }, "primaryId" : "GEO:GSE49485", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49485" } ] }, "title" : "Hypoxia transcriptome sequencing of blind mole rat (BMR, Spalax galili) and rat (Rattus norvegicus)", "dateAssigned" : "2013-08-02T00:00:00.000-05:00", "summary" : "Deep sequencing of mRNA from Spalax galili and Rattus norvegicus", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24892994" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49486" }, "primaryId" : "GEO:GSE49486", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49486" } ] }, "title" : "Effect of ingested whey protein hydrolysate on gene expression profiles compared to an identical composition of amino acid mixture in rat skeletal muscle", "dateAssigned" : "2013-08-02T00:00:00.000-05:00", "summary" : "We have previously showed that whey protein hydrolysate (WPH) causes a greater increase in muscle protein synthesis than an identical composition of amino acids mixture does. The present study was conducted to investigate a comparative effect of WPH on gene expression. Male Sprague-Dawley rats subjected to a 2-h swimming exercise were administered either a carbohydrate-amino acid diet or a carbohydrate-WPH diet immediately after exercise. One hour after exercise, epitrochlearis muscle mRNA was sampled and subjected to DNA microarray analysis. As a result, ingestion of WPH altered 189 genes in considering the false discovery rate. Among the upregulated genes, 8 Gene Ontology (GO) terms were enriched, which included key elements in muscle repair after exercise such as Cd24, Ccl2, Ccl7 and Cxcl1. On the other hand, 9 GO terms were enriched in the gene sets downregulated by ingestion of WPH and these GO terms fell into 2 clusters, ‘regulation of ATPase activity’, and ‘immune response’. Furthermore, we found that WPH activate the 2 upstream proteins, extracellular signal-regulated kinase 1/2 (ERK1/2) and hypoxia-inducible factor-1a (HIF-1a), which may act as key factors for regulation of gene expression. These results suggest that ingestion of WPH, compared to an identical composition of amino acid mixture, induces greater changes in the after-exercise gene expression profile via activation of the proteins, ERK1/2 and HIF-1a.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24598469" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49510" }, "primaryId" : "GEO:GSE49510", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49510" } ] }, "title" : "Global gene expression pattern difference between the high density and the regular density cultured rat bone marrow cells", "dateAssigned" : "2013-08-02T00:00:00.000-05:00", "summary" : "In vitro expansion of endothelial progenitor cells (EPCs) remains a challenge in stem cell research and its application. We hypothesize that high density culture is able to expansion EPCs from bone marrow by mimicking cell-cell interactions of the bone marrow niche. To test the hypothesis, rat bone marrow cells were either cultured in high density by seeding or cultured in regular density. Flow cytometric analyses of the cells cultured for 15 days showed that high density cells exhibited smaller cell size and higher levels of marker expression related to EPCs when compared to regular density cultured cells. Global gene expression pattern difference between the high density and the regular density cultured cells was analyzed by a microarray assay.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49548" }, "primaryId" : "GEO:GSE49548", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49548" } ] }, "title" : "Association of Cellular and Molecular Responses in the Rat Mammary Gland to 17beta-Estradiol with Susceptibility to Mammary Cancer", "dateAssigned" : "2013-08-05T00:00:00.000-05:00", "summary" : "We are using ACI and BN rats, which differ markedly in their susceptibility to 17beta-Estradiol (E2)-induced mammary cancer, to identify genetic variants and environmental factors that determine mammary cancer susceptibility. The objective of this study was to characterize the cellular and molecular responses to E2 in the mammary glands of ACI and BN rats to identify qualitative and quantitative phenotypes that associate with and/or may confer differences in susceptibility to mammary cancer. Female ACI and BN rats were treated with E2 for 1, 3 or 12 weeks and cell proliferation, apoptosis, differentiation and gene expression were evaluated. The luminal epithelium of ACI rats exhibited a rapid and sustained proliferative response to E2. By contrast, the proliferative response exhibited by the mammary epithelium of BN rats was restrained and transitory. Moreover, the epithelium of BN rats appeared to undergo differentiation in response to E2, as evidenced by production of milk proteins as well as luminal ectasia and associated changes in the extracellular matrix (ECM). Marked differences in expression of genes that encode proteins with well-defined roles in mammary gland development (Pgr, Wnt4, Tnfsf11, Prlr, Stat5a, Areg, Gata3), differentiation and milk production (Lcn2, Spp1), regulation of extracellular environment (Mmp7, Mmp9), and cell-cell or cell-ECM interactions (Cd44, Cd24, Cd52) were observed. We propose that these cellular and molecular phenotypes are heritable and may underlie, at least in part, the differences in mammary cancer susceptibility exhibited by ACI and BN rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49560" }, "primaryId" : "GEO:GSE49560", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49560" } ] }, "title" : "Rat intervertebral disc cell was stimulated by NGF", "dateAssigned" : "2013-08-05T00:00:00.000-05:00", "summary" : "The rat-tail intervertbral disc cells was incubated with NGF at a concentration of 100 ng/ml/day for a total of five days.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49592" }, "primaryId" : "GEO:GSE49592", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49592" } ] }, "title" : "Subcellular RNA Sequencing Reveals Broad Presence of Cytoplasmic Intron-sequence Retaining Transcripts in Mouse and Rat Neurons.", "dateAssigned" : "2013-08-06T00:00:00.000-05:00", "summary" : "The analysis for CIRTs was also carried out by sequencing single cells from mouse brown adipose tissue and mouse cardiomyocytes. There was widespread prevalence of CIRTs in all of the cell types.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24098440" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49599" }, "primaryId" : "GEO:GSE49599", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49599" } ] }, "title" : "Expression profiles of globular bushy cells (GBCs) during maturation", "dateAssigned" : "2013-08-06T00:00:00.000-05:00", "summary" : "We performed cell type-specific gene expression profiling of globular bushy cells (GBCs), the neurons giving rise to the calyx of Held, at different maturational stages (P3, P8 and P21).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24995587" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49631" }, "primaryId" : "GEO:GSE49631", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49631" } ] }, "title" : "Characteristic molecular and proteomic signatures of drug-induced liver injury in a rat model", "dateAssigned" : "2013-08-07T00:00:00.000-05:00", "summary" : "we assessed characteristic molecular and proteomic signatures in rat liver treated with drugs (pyrazinamide, ranitidine, enalapril, carbamazepine, and chlorpromazine) that are known to cause DILI in humans.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49786" }, "primaryId" : "GEO:GSE49786", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49786" } ] }, "title" : "Pdx-1 activates islet a- and ß-cell proliferation via a TRPC3/6- and ERK 1/2-regulated mechanism", "dateAssigned" : "2013-08-12T00:00:00.000-05:00", "summary" : "We identified genes that were upregulated or downregulated at 48 h with Pdx-1 overexpression as compared to untreated and ßgal controls.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23938296" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49797" }, "primaryId" : "GEO:GSE49797", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49797" } ] }, "title" : "Maternal overnutrition causes insulin resistance and alters skeletal muscle oxidative phosphorylation in adult rat offspring", "dateAssigned" : "2013-08-12T00:00:00.000-05:00", "summary" : "Maternal obesity can program metabolic syndrome in offspring but the mechanisms are not well characterized. Moreover, the consequences of maternal overnutrition in the absence of frank obesity remain poorly understood. This study aimed to determine the effects of maternal consumption of a high fat-sucrose diet on the skeletal muscle metabolic and transcriptional profiles of adult offspring. Female Sprague Dawley rats were fed either a diet rich in saturated fat and sucrose (HFD, 23.5% fat, 20% sucrose wt/wt) or a standard chow diet (NFD, 7% fat, 10% sucrose w/w) for the 3 weeks prior to mating and throughout pregnancy and lactation. Although maternal weights were not different between groups at conception or weaning, HFD dams were ~22% heavier than chow fed dams from mid-pregnancy until 4 days post-partum. Adult male offspring of HFD dams were not heavier than controls but demonstrated features of insulin resistance including elevated plasma insulin concentration (+40%, P<0.05). Next Generation mRNA Sequencing was used to identify differentially expressed genes in the soleus muscle of offspring, and Gene Set Enrichment Analysis (GSEA) to detect coordinated changes that are characteristic of a biological function. GSEA identified 15 pathways enriched for up-regulated genes, including cytokine signaling (P<0.005), starch and sucrose metabolism (P<0.017), and inflammatory response (P<0.024). A further 8 pathways were significantly enriched for down-regulated genes including oxidative phosphorylation (P<0.004) and electron transport (P<0.022). Western blots confirmed a ~60% reduction in the phosphorylation of the insulin signaling protein Akt (P<0.05) and ~70% reduction in mitochondrial complexes II (P<0.05) and V expression (P<0.05). On a normal diet, offspring of HFD dams developed an insulin resistant phenotype, with transcriptional evidence of muscle cytokine activation, inflammation and mitochondrial dysfunction. These data indicate that maternal overnutrition, even in the absence of pre-pregnancy obesity can promote metabolic dysregulation and predispose offspring to type 2 diabetes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24381224" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49849" }, "primaryId" : "GEO:GSE49849", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49849" } ] }, "title" : "Alterations in mRNA levels in the dentate gyrus in epileptic rats", "dateAssigned" : "2013-08-13T00:00:00.000-05:00", "summary" : "Analysis of the dentate gyrus of amygdala electrical stimulation model of temporal lobe epilepsy. Results provide insight into the molecular mechanism underlying epileptogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24146813" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49850" }, "primaryId" : "GEO:GSE49850", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49850" } ] }, "title" : "Alterations in miRNA levels in the dentate gyrus in epileptic rats", "dateAssigned" : "2013-08-13T00:00:00.000-05:00", "summary" : "Analysis of the dentate gyrus of amygdala electrical stimulation model of temporal lobe epilepsy. Results provide insight into the molecular mechanism underlying epileptogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24146813" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49980" }, "primaryId" : "GEO:GSE49980", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE49980" } ] }, "title" : "The transcriptomic response of rat hepatic stellate cells to endotoxin: implications for hepatic inflammation and immune regulation", "dateAssigned" : "2013-08-19T00:00:00.000-05:00", "summary" : "Located in the perisinusoidal space of Disse, hepatic stellate cells (HSCs) communicate with all other liver cell types by physical association and / or by producing cytokines and chemokines. In liver disease and folllowing liver transplantation, elevated levels of endotoxin (bacterial lipopolysaccharide: LPS) stimulate HSCs to produce increased amounts of cytokines and chemokines. Transcriptomic analysis of cultured HSCs stimulated with LPS yields a survey of expression changes which potentially modulate the hepatic inflammatory and immune responses.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24349206" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50014" }, "primaryId" : "GEO:GSE50014", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50014" } ] }, "title" : "Effects of estradiol and growth hormone on liver transcriptome in hypothyroid-orquiectomized rats", "dateAssigned" : "2013-08-20T00:00:00.000-05:00", "summary" : "E2 and GH are critical regulators of growth and intermediate metabolism in mammals. Hypothyroidism causes endocrine and metabolic disturbances in the liver with features that mimic deficiencies of E2 or GH signalling. In this work, we used the hypothyroid-orchiectomized (TXOX) adult rat model to evaluate the influence of E2 and GH on the liver in terms of global changes in gene expression. This study shows the changes in hepatic transcriptome that were provoked by E2 benzoate (50 ug/kg; sc; 5 days per week x 27 days), intermittent GH administration (0.3 mg/kg/day;sc injection divided into two daily injections x 7 days) or the combination of E2 plus GH in TXOX rats. E2 influenced the liver transcriptome, particularly genes involved in metabolism of lipids and endo-xenobiotics, and the GH-regulated endocrine, metabolic, gender, and immune responses. E2 did not prevent the inhibitory effects of GH on urea and amino acid metabolism-related genes. Notably, the combination of E2 and GH caused deleterious effects on transcriptional immune response. These results highlight the role of E2 as a critical regulator of liver metabolism in mammals and provide insights into the functional interplay between E2 and GH in the liver.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24816529" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50027" }, "primaryId" : "GEO:GSE50027", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50027" } ] }, "title" : "Systems biology with high-throughput sequencing revealed genetic mechanisms underlying the Metabolic Syndrome in the Lyon Hypertensive Rat", "dateAssigned" : "2013-08-20T00:00:00.000-05:00", "summary" : "The metabolic syndrome (MetS) is a collection of co-occurring complex disorders including obesity, hypertension, dyslipidemia, and insulin resistance. The Lyon Hypertensive (LH) and Lyon Normotensive (LN) rats are models of MetS sensitivity and resistance, respectively. To identify genetic determinants and mechanisms underlying MetS, 169 rats from an F2 intercross between LH and LN were studied. Multi-dimensional data were obtained including genotypes of 1536 SNPs, 23 physiological traits including blood pressure, plasma lipid and leptin levels, and body weight/adiposity, and more than 150 billion nucleotides of RNA-seq reads from the livers of 36 F2 individuals, 6 LH and 6 LN individuals. We identified 17 pQTLs (physiological quantitative trait loci) and 1200 eQTLs (gene expression quantitative trait loci). Systems biology methods were applied to identify 18 candidate MetS genes, including genes (Prcp and Aqp11) previously shown to be MetS-related. We found an eQTL hotspot on RNO17, which was also located within pQTLs for MetS-related traits. The genes regulated by this eQTL hotspot were mainly in two co-expression network modules (a mitochondria related module and a gene regulation related module) and were predicted to causally affect many MetS-related traits. Multiple evidences strongly and consistently support RGD1562963, a gene regulated in cis by this eQTL hotspot and possibly related to RNA stability, as the eQTL driver gene directly affected by genetic variation between LH and LN rats; the expression of this gene is also correlated with MetS-related traits. Our study sheds light on the intricate pathogenesis of MetS and proved that systems biology with high-throughput sequencing is a powerful method to study the etiology of complicated diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25573024" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50042" }, "primaryId" : "GEO:GSE50042", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50042" } ] }, "title" : "Inhibition of phosphodiesterase-4 promotes oligodendrocyte precursor cell differentiation and enhances CNS remyelination", "dateAssigned" : "2013-08-20T00:00:00.000-05:00", "summary" : "We used transcription-profiling to identify mitogen-activated protein kinase (Mapk) signaling as an important regulator involved in the differentiation of oligodendrocyte progenitor cells (OPCs) into oligodendrocytes. We show in tissue culture that activation of Mapk signaling by elevation of intracellular levels of cAMP using administration of either dibutyryl-cAMP or inhibitors of the cAMP-hydrolyzing enzyme phosphodiesterase-4 (Pde4) enhances OPC differentiation. Finally, we demonstrate that systemic delivery of a Pde4 inhibitor leads to enhanced differentiation of OPCs within focal areas of toxin-induced demyelination and a consequent acceleration of remyelination.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21131950" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50056" }, "primaryId" : "GEO:GSE50056", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50056" } ] }, "title" : "Comparison of gene expression between SDR and HHR mammary glands tissue", "dateAssigned" : "2013-08-21T00:00:00.000-05:00", "summary" : "To examine whether factors responsible for early involution of HHR mammary gland are different from those involved in physiologic involution of the SDR tissue, gene expression profiles of HHR tissue at lactation day 1 and SDR tissue at involution day 1 were evaluated by microarray analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50077" }, "primaryId" : "GEO:GSE50077", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50077" } ] }, "title" : "Deep sequencing reveals increased DNA methylation in chronic rat epilepsy (MBD-seq)", "dateAssigned" : "2013-08-21T00:00:00.000-05:00", "summary" : "Explore DNA methylation in chronic epilepsy and its relationship to gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24005891" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50079" }, "primaryId" : "GEO:GSE50079", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50079" } ] }, "title" : "Deep sequencing reveals increased DNA methylation in chronic rat epilepsy (mRNA-seq)", "dateAssigned" : "2013-08-21T00:00:00.000-05:00", "summary" : "Explore DNA methylation in chronic epilepsy and its relationship to gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24005891" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50143" }, "primaryId" : "GEO:GSE50143", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50143" } ] }, "title" : "Expression data of CD9 positive germ cells from young and aged Sprague Dawley germ cell specific GFP rats", "dateAssigned" : "2013-08-23T00:00:00.000-05:00", "summary" : "A full genome microarray was used to determine if distinct pathways of genes were altered in expression in CD9-positive germ cells with age", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24227752" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50151" }, "primaryId" : "GEO:GSE50151", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50151" } ] }, "title" : "Expression data from 15 month old rat brain subjected to fructose fetal programming", "dateAssigned" : "2013-08-23T00:00:00.000-05:00", "summary" : "We used microarrays to detail changes in global programme of gene expression in offspring brains from rats subjected to either a control diet or a high fructose diet during gestation and lactation", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50254" }, "primaryId" : "GEO:GSE50254", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50254" } ] }, "title" : "Integration of toxicological end points with molecular measurements in a 28-day rat repeated dose inhalation study with cigarette smoke provides mechanistic understanding of smoke impact", "dateAssigned" : "2013-08-27T00:00:00.000-05:00", "summary" : "In conclusion, a correlative evaluation of classical histopathology together with gene expression?based computational network models may facilitate a systems toxicology-based risk assessment as shown for a pMRTP.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24632068" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50381" }, "primaryId" : "GEO:GSE50381", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50381" } ] }, "title" : "Expression data in KSHV-infected primary rat mesenchymal precursor (MM) cells", "dateAssigned" : "2013-08-27T00:00:00.000-05:00", "summary" : "Kaposi's sarcoma-associated herpesvirus (KSHV) can efficiently infect and transform primary rat mesenchymal precursor (MM) cells. Regulation of cell cycle progression and apoptosis by KSHV-encoded microRNAs is required for KSHV-induced cellular transformation and tumorigenesis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50383" }, "primaryId" : "GEO:GSE50383", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50383" } ] }, "title" : "AR function is altered by polyglutamine expansion and by SUMO", "dateAssigned" : "2013-08-27T00:00:00.000-05:00", "summary" : "We used microarrays to confirm and demonstrate loss of AR function from polyQ expansion and to test the degree to which AR function is altered by preventing polyQ AR SUMOylation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25607844" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50424" }, "primaryId" : "GEO:GSE50424", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50424" } ] }, "title" : "Characterization of genome-wide transcriptional changes in liver and adipose tissues of ZDF (fa/fa) rats fed R-a-lipoic acid by next-generation sequencing", "dateAssigned" : "2013-08-28T00:00:00.000-05:00", "summary" : "We report on the characterization of lipogenic tissue transcriptional networks that support physiological responses of obese rats to a lipid-lowering bioactive food compound, R-a-lipoic acid (LA). Nine-week old male ZDF (fa/fa) rats were fed a chow diet supplemented with 3 g LA per kg diet or pair fed for two weeks. At the end of the trial, high-quality RNA was extracted from the liver and epididymal fat and subjected to transcriptome analysis using RNA-Seq technology. Results showed a substantially higher number of differentially expressed genes (DEG, q = 0.05 and absolute log2(fold change) = 1) in liver (110 genes) vs. epididymal fat (10 genes). Most epididymal fat DEG were also differentially expressed in liver and shared directionality of change. Gene Ontology (GO) analysis of these transcripts revealed significant enrichment of GO categories related to immune response, stress response, lipid metabolism, and carboxylic acid metabolic processes. Of interest interferon-related genes involved in defense against microorganism and innate immune response were induced by LA. Lipid metabolism-related transcript changes observed in LA-fed animals included downregulation of lipogenic genes (Pnpla3, Pnpla5, Elov6, Acly, Gpam, and Aacs) and concomitant upregulation of short-, medium- and long-chain fatty acid metabolic processes (Acot1, Acot2, Acsf2, and Crat). Transcriptional changes were accompanied by the lowering of abdominal adiposity and blood triacylglycerol levels. We conclude that LA dietary supplementation induces prominent gene expression changes in liver in support of significant improvement of whole-body lipid status", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24104204" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50478" }, "primaryId" : "GEO:GSE50478", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50478" } ] }, "title" : "Transcriptomic analysis of early response of rat brain orthotopic tumors after synchrotron microbeam irradiation (MRT)", "dateAssigned" : "2013-08-30T00:00:00.000-05:00", "summary" : "The aim of this study was to identify the transcriptomic response 6 hours after the MRT irradiation, in normal brain tissue (11 samples) and in glioma tissue (11 samples), in rat.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24391709" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50533" }, "primaryId" : "GEO:GSE50533", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50533" } ] }, "title" : "Aldosterone regulated genes in distal colon surface cells", "dateAssigned" : "2013-09-03T00:00:00.000-05:00", "summary" : "Effects of aldosterone on the transcriptome in distal colon.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50596" }, "primaryId" : "GEO:GSE50596", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50596" } ] }, "title" : "Placental ischemia induces changes in gene expression in chorionic tissue", "dateAssigned" : "2013-09-04T00:00:00.000-05:00", "summary" : "Placental ischemia is believed to be an important contributor to human preeclampsia, though the targets induced by the ischemia remain unclear.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50604" }, "primaryId" : "GEO:GSE50604", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50604" } ] }, "title" : "Identification and characterization of FGF2-dependent mRNA:microRNA networks during lens fiber cell differentiation", "dateAssigned" : "2013-09-05T00:00:00.000-05:00", "summary" : "Differential gene expression of FGF2-treated lens cell cultures was analyzed at 0, 2, 4, 12 and 24 hours following the treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24142921" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50607" }, "primaryId" : "GEO:GSE50607", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50607" } ] }, "title" : "Gestational food-restriction but not nicotine exposure regulates gene expression in the striatum of adolescent rats", "dateAssigned" : "2013-09-05T00:00:00.000-05:00", "summary" : "We used microarrays to determine the effect of prenatal nicotine exposure on gene expression profiles in the striatum of adolescent rats. We found a number of immediate early genes to be differentially expressed due to food-restriction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24586432" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50664" }, "primaryId" : "GEO:GSE50664", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50664" } ] }, "title" : "Gene expression profiles in rat lung following intratracheal instillation with single-wall carbon nanotubes", "dateAssigned" : "2013-09-06T00:00:00.000-05:00", "summary" : "Gene expression profiling of the rat lung following intratracheal instillation with single-wall carbon nanotubes (SWCNTs) was employed to gain insights into these molecular events. We attempted to characterize time-dependent changes in the gene expression until 754 days after intratracheal instillation with SWCNTs suspensions at 0.2 mg (L-SWCNT) and 0.4 mg (H-SWCNT) injected dose per rat, and to identify the shift from the acute-phase to the chronic-phase phase on the basis of evaluation at the molecular level.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24911292" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50707" }, "primaryId" : "GEO:GSE50707", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50707" } ] }, "title" : "Mechanical loading and gene expression - Microarray study", "dateAssigned" : "2013-09-09T00:00:00.000-05:00", "summary" : "Skeletal integrity in humans and animals is maintained by daily mechanical loading. It has been widely accepted that osteocytes function as mechanosensors. Many biochemical signaling molecules are involved in the response of osteocytes to mechanical stimulation. The aim of this study was to identify genes involved in the translation of mechanical stimuli into bone formation. The four-point bending model was used to induce a single period of mechanical loading (comprising 300 cycles (2 Hz) using a peak magnitude of 60 N) on the right tibia, while the contra lateral left tibia served as control. Six hours after loading, the effects of mechanical loading on gene-expression were determined with microarray analysis. Protein expression of differentially regulated genes was evaluated with immunohistochemistry. Nine genes were found to exhibit a significant differential gene expression in LOAD compared to control. MEPE, Garnl1, V2R2B, and QFG TN1 olfactory receptor were up-regulated, and creatine kinase (muscle form), fibrinogen-B beta-polypeptide, monoamine oxidase A, troponin-C and kinesin light chain-C were down-regulated. Validation with real-time RT-PCR analysis confirmed the up regulation of MEPE and the down-regulation of creatine kinase (muscle form) and troponin-C in the loaded tibia. Immunohistochemistry showed that the increase of MEPE protein expression was already detectable six hours after mechanical loading. In conclusion, these genes probably play a role during translation of mechanical stimuli six hours after mechanical loading. The modulation of MEPE expression may indicate a connection between bone mineralization and bone formation after mechanical stimulation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24255709" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50747" }, "primaryId" : "GEO:GSE50747", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50747" } ] }, "title" : "Origins and functional evolution of Y chromosome gene repertoires across the class Mammalia", "dateAssigned" : "2013-09-10T00:00:00.000-05:00", "summary" : "For marmoset samples, we added Y coding genes and noncoding sequences to the reference genomes in order to assess their expression levels. We then mapped all RNA-seq reads with TopHat 1.4.0 and used Cufflinks 2.0.0 (all mapped reads, embedded multi-read and fragment bias correction) to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for all genes in the genomes with our refined annotations.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24759410" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50799" }, "primaryId" : "GEO:GSE50799", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50799" } ] }, "title" : "Genome-wide effects of maternal undernutrition", "dateAssigned" : "2013-09-11T00:00:00.000-05:00", "summary" : "A comparison of the liver transcriptomes of 1 day old rats that are born to mothers fed with three different diets during gestation. The first animal group was fed with a normal diet (control); second group received much less protein than normal and slightly more carbs (low protein); third group diet was same as low protein but with an extra dosage of folic acid (lowp.+f). All diets were matched for energy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24391732" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50804" }, "primaryId" : "GEO:GSE50804", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50804" } ] }, "title" : "Effects of gentamycin on gene expression of kidney in SD rats", "dateAssigned" : "2013-09-12T00:00:00.000-05:00", "summary" : "To investigate the gene expression profile of genamycin induced nephrotoxicity in a time-series aspect, SD rats were administrated once daily with saline, genamycin 80 mgkg for 28 consecutive days by intramuscular injection folled by 28 days recovery. Kidney samples were collected for microarray analysis and histological examination. There were 4360 and 4323 regulated genes for females and males, respectively, however, the overlapping expression genes coregluated at each time point were few, with 2 for females and 12 for males. By Principle Component Analysis and Hierarchical Cluster, the gene expression patterns were apparently associated with the disease stage of the nephrotoxicity,while GO Annotation showed the biological processes were specific to each course of this nephrotoxicity.Our studymapped the different gene expression patterns at the initiation, development and recovery stage of gentamycin-induced nephrotoxicity", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50815" }, "primaryId" : "GEO:GSE50815", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50815" } ] }, "title" : "Hepatocyte Nuclear Factors 4a and 1a (Hnf4a and Hnf1a) Regulate Kidney Developmental Expression of Drug-Metabolizing Enzymes and Drug Transporters", "dateAssigned" : "2013-09-12T00:00:00.000-05:00", "summary" : "The transcriptional regulation of drug-metabolizing enzymes and transporters (here collectively referred to as DMEs) in the developing proximal tubule is not well understood. As in the liver, DME regulation in the PT may be mediated through nuclear receptors which are thought to “sense” deviations from homeostasis by being activated by ligands, some of which are handled by DMEs, including drug transporters. Systems analysis of transcriptomic data during kidney development predicted a set of upstream transcription factors, including Hnf4a and Hnf1a, as well as Nr3c1 (Gr), Nfe2l2 (Nrf2), Ppara, and Tp53. Motif analysis of cis-regulatory further suggested that Hnf4a and Hnf1a are the main transcriptional regulators in the PT. Available expression data from tissue-specific Hnf4a KO tissues revealed that distinct subsets of DMEs were regulated by Hnf4a in a tissue-specific manner. ChIP-seq was performed to characterize the PT-specific binding sites of Hnf4a in rat kidneys at three developmental stages (prenatal, immature, adult), which further supported a major role for Hnf4a in regulating PT gene expression, including DMEs. In ex vivo kidney organ culture, an antagonist of Hnf4a (but not a similar inactive compound) led to predicted changes in DME expression, including among others Fmo1, Cyp2d2, Cyp2d4, Nqo2, as well as organic cation transporters and organic anion transporters Slc22a1(Oct1), Slc22a2 (Oct2), Slc22a6 (Oat1), Slc22a8(Oat3), and Slc47a1(Mate1). Conversely, overexpression of Hnf1a and Hnf4a in primary mouse embryonic fibroblasts (MEFs), sometimes considered a surrogate for mesenchymal stem cells, induced expression of several of these proximal tubule DMEs, as well as epithelial markers and a PT-specific brush border marker Ggt1. These cells had organic anion transporter function. Taken together, the data strongly supports a critical role for HNF4a and Hnf1a in the tissue-specific regulation of drug handling and differentiation toward a PT cellular identity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24038112" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50935" }, "primaryId" : "GEO:GSE50935", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50935" } ] }, "title" : "Genome wide effects of maternal undernutrition", "dateAssigned" : "2013-09-17T00:00:00.000-05:00", "summary" : "DNA methylation profiles of the livers of 1 day old rats from mothers fed with three different diets during gestation. The first animal group was fed with a normal diet (c=control); second group received much less protein than normal and slighlty more carbs (p=low protein, or programmed); third group diet was same as low protein but with extra folic acid (f=low protein+folate). All diets were matched for energy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24391732" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50940" }, "primaryId" : "GEO:GSE50940", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50940" } ] }, "title" : "MicroRNA profiling of rat hippocampus after status epilepticus induced by amygdala stimulation", "dateAssigned" : "2013-09-17T00:00:00.000-05:00", "summary" : "MicroRNAs (miRNAs) are small and endogenously expressed non-coding RNAs that negatively regulate the expression of protein-coding genes at the translational level. Emerging evidence suggests that miRNAs play critical roles in central nervous system under physiological and pathological conditions. However, their expression and functions in status epilepticus (SE) have not been well characterized thus far. Here, we characterized miRNA expression profile in rat hippocampus at 24 hours following SE induced by amygdala stimulation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24205215" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50941" }, "primaryId" : "GEO:GSE50941", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50941" } ] }, "title" : "Opposing Effects of HIF1a and HIF2a on Chromaffin Cell Phenotypic Features and Tumor Cell Proliferation: Insights from MAX [rat]", "dateAssigned" : "2013-09-17T00:00:00.000-05:00", "summary" : "Pheochromocytomas and paragangliomas (PPGLs) are catecholamine-producing tumors with diverse phenotypic features reflecting mutations in numerous genes, including MYC-associated factor X (MAX). To establish whether PPGL phenotypic differences reflect a MAX-mediated mechanism and opposing influences of HIF2a and HIF1a, we combined observational investigations in PPGLs and gene-manipulation studies in two pheochromocytoma cell lines. In cell lines lacking Max, re-expression of the gene resulted in maturation of phenotypic features and decreased cell cycle progression. In cell lines lacking Hif2a, overexpression of the gene led to immature phenotypic features, failure of dexamethasone to induce differentiation and increased proliferation. HIF1a has opposing actions to HIF2a. These model systems explain the features observed in PPGLs due to mutations of MAX and other PPGL susceptibility genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24676840" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50946" }, "primaryId" : "GEO:GSE50946", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE50946" } ] }, "title" : "Tissue-specific response of microRNAs to carcinogenicity and mutagenicity of aristolochic acid in rats", "dateAssigned" : "2013-09-17T00:00:00.000-05:00", "summary" : "Aristolochic acid (AA) is an active component of herbal drugs derived from the Aristolochia species that have been used for medicinal purposes since antiquity. However, AA is genotoxic and induces tumors in animals and humans. AA induces mutations and tumors in the kidney but solely mutations in the liver. To evaluate whether miRNAs could indicate AA’s tissue-specific carcinogenicity and mutagenicity, we first conducted microarray analysis of miRNA expression in kidneys and livers of rats treated with a carcinogenic dose of AA. Then, miR-21, a biomarker for carcinogenicity, and miR-34a, a biomarker for mutagenicity, the two miRNAs whose expressions were most altered, were evaluated for their expression in the kidney (the AA’s mutagenic and carcinogenic target tissue), liver (the AA’s mutagenic target tissue), and testis, the non-target tissue where neither tumors nor mutation induction was found in previous studies and in this study. Genomic analysis of miRNA expression for kidney and liver samples showed that miRNA expression was globally changed by the treatment. Nineteen miRNAs were significantly dysregulated by the treatment in the kidney. Most of these miRNAs are related to carcinogenesis. Only one miRNA, miR-34a, was differentially expressed in the liver. Expression of miR-21 was induced in the kidney by AA treatment in a dose-dependent manner while no changes occurred in the liver or testis, indicating that the kidney is the carcinogenic target. miR-34a was dose-dependently up-regulated in the kidneys and livers of rats treated with AA, but not in the testis, suggesting that the kidney and liver are mutagenic target tissues, but the testis is not. Our results demonstrate that miRNA profiles can reflect the AA’s carcinogenicity in a tissue-specific manner while specific miRNAs can signify the target tissues for carcinogenicity or mutagenicity of AA.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51125" }, "primaryId" : "GEO:GSE51125", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51125" } ] }, "title" : "Molecular characterization of 4-NQO induced F344 rat tongue carcinogenesis: alteration of multiple gene expression and hypomethylation of PTGS2 proximal promoter", "dateAssigned" : "2013-09-24T00:00:00.000-05:00", "summary" : "The 4-NQO induced rat tongue carcinogenesis model presenting considerable histologic and molecular similarity to oral cancers commonly seen in humans is very useful for investigating oral carcinogenesis. In order to understand the molecular basis of oral carcinogenesis and identify gene biomarkers and potential chemopreventive targets for future studies, we characterized the molecular changes in oral squamous cell carcinoma (SCC) samples generated from this model system using F344 rats by performing gene expression microarray and methylation analysis of selected genes. Microarray studies identified 1735 genes to be upregulated by at least 2 fold (p<0.05, n=11) and 1803 genes to be downregulated by at least 50% (p<0.05, n=11) in SCC in comparison to the adjacent normal tissues and 28 KEGG pathways to be altered in SCC (p<0.01). Among the altered genes, keratins and keratin associated proteins were found to be differentially regulated and the keratin profile appeared to an important biomarker for oral SCC. PTGS2 and PTGS2 relevant genes, which are potential targets of chemoprevention and therapy, were also found to be upregulated in SCC and confirmed by qRT-PCR. The upregulation of PTGS2 appeared to correlate with hypomethylation of its proximal promoter. Methylation analysis of other selected genes showed that the first exon of APC2 was methylated in normal tissues, and the methylation level increased moderately in SCC samples (p<0.01, n=8). These results demonstrate that 4-NQO induced tongue carcinogenesis in F344 rats is accompanied by alteration of multiple gene expression, hypomethylation of PTGS2 and increased methylation of APC2.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25635769" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51147" }, "primaryId" : "GEO:GSE51147", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51147" } ] }, "title" : "Expression data from rat tumors formed by 9L.EV or 9L.EGFRvIII cells", "dateAssigned" : "2013-09-24T00:00:00.000-05:00", "summary" : "Analysis of rat tumor xenografts revealed genes that are upregulated in tumors expressing EGFRvIII", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25934697" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51163" }, "primaryId" : "GEO:GSE51163", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51163" } ] }, "title" : "Expression data from NRK-52E cells treated with monuron for 6h, 24h and 72h and rats exposed to monuron for 72h.", "dateAssigned" : "2013-09-25T00:00:00.000-05:00", "summary" : "We used microarrays to detail the mechanism of toxicity and possibly carcinogenicity of monuron.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51207" }, "primaryId" : "GEO:GSE51207", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51207" } ] }, "title" : "Exposure to Cobalt Causes Transcriptomic and Proteomic Changes in Two Rat Liver Derived Cell Lines", "dateAssigned" : "2013-09-26T00:00:00.000-05:00", "summary" : "Cobalt is a transition group metal present in trace amounts in the human diet, but in larger doses it can be acutely toxic or cause adverse health effects in chronic, long term exposures. Its use in many industrial processes and alloys worldwide presents opportunities for occupational exposures, as well as exposures to military personnel. While the toxic effects of cobalt have been widely studied, the exact mechanisms of toxicity remain unclear. In order to further elucidate these mechanisms and identify potential biomarkers of exposure or effect, we exposed two rat liver-derived cell lines, H4-II-E-C3 and MH1C1, to two concentrations of cobalt chloride. We examined changes in gene expression using DNA microarrays in both cell lines and examined changes in cytoplasmic protein abundance in MH1C1 cells using mass spectrometry. We chose to closely examine differentially expressed genes and proteins changing in abundance in both cells lines in order to remove cell line specific effects. We identified enriched pathways, networks, and biological functions using commercial bioinformatic tools and manual annotation. Many of the genes, proteins, and pathways modulated by exposure to cobalt appear to be due to an induction of a hypoxic-like response and oxidative stress. Genes that may be differentially expressed due to a hypoxic-like response are involved in Hif-1a signaling, glycolysis, gluconeogenesis, and other energy metabolism related processes. Gene expression changes linked to oxidative stress are also known to be involved in the NRF2-mediated response, protein degradation, and glutathione production. Using microarray and mass spectrometry analysis, we were able to identify modulated genes and proteins, further elucidate the mechanisms of toxicity of cobalt, and identify biomarkers of exposure and effect in vitro, providing targets for focused in vitro studies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24386269" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51248" }, "primaryId" : "GEO:GSE51248", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51248" } ] }, "title" : "Dlx1 and Rgs5 in the Ductus Arteriosus: Vessel-specific Genes Identified by Transcriptional Profiling of Laser-capture Microdissected Endothelial and Smooth Muscle Cells", "dateAssigned" : "2013-09-27T00:00:00.000-05:00", "summary" : "Gene expression profiling of laser-captured microdissected cells offers the opportunity to study gene expression profiles in cells of different embryonic origin", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24489801" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51267" }, "primaryId" : "GEO:GSE51267", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51267" } ] }, "title" : "Temporal Transcriptomic Signatures Associated with Post-viral Bronchiolitis Sequelae in Rats", "dateAssigned" : "2013-09-30T00:00:00.000-05:00", "summary" : "Early life respiratory viral infections and atopic characteristics are significant risk factors for the development of childhood asthma. It is hypothesized that repeated respiratory viral infections might induce structural remodeling by interfering with the normal process of lung maturation; however, the specific molecular processes that mediate these developments are not understood. To define relevant molecular pathways, we used a well-established Sendai virus infection model in weanling rats to compare transcriptome signatures between a post-infection asthma prone susceptible strain (BN) and a post-infection asthma resistant strain (F344). Specific to this weanling model and not described in adult models, Sendai virus infection in the susceptible strain resulted in morphological abnormalities in distal airways that persist into adulthood, suggesting a disruption of normal lung growth. Gene expression data from infected and control lungs across five time points indicated that specific features of the immune response following viral infection were heightened and prolonged in lungs from BN compared with F344 rats. These features included an increase in macrophage cell number and related gene expression, which then transitioned to an increase in mast cell number and related gene expression. In contrast to the heightened immune response in infected BN lungs, infected F344 lungs displayed more efficient re-epithelialization. We conclude that the structural defects that developed and persisted in infected BN but not F344 lungs were preceded by a pronounced macrophage and mast cell response to viral infection acting in parallel with an inadequate re-epithelialization.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51294" }, "primaryId" : "GEO:GSE51294", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51294" } ] }, "title" : "HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain [spinal cord tissue]", "dateAssigned" : "2013-09-30T00:00:00.000-05:00", "summary" : "Histone deacetylase inhibitors (HDACIs) interfere with the epigenetic process of histone acetylation and are known to have analgesic properties in models of chronic inflammatory pain. The aim of this study was to determine whether these compounds could also affect neuropathic pain. Different class I HDACIs were delivered intrathecally into rat spinal cord in models of traumatic nerve injury and antiretroviral drug-induced peripheral neuropathy (stavudine, d4T). Mechanical and thermal hypersensitivity was attenuated by 40% to 50% as a result of HDACI treatment, but only if started before any insult. The drugs globally increased histone acetylation in the spinal cord, but appeared to have no measurable effects in relevant dorsal root ganglia in this treatment paradigm, suggesting that any potential mechanism should be sought in the central nervous system. Microarray analysis of dorsal cord RNA revealed the signature of the specific compound used (MS-275) and suggested that its main effect was mediated through HDAC1. Taken together, these data support a role for histone acetylation in the emergence of neuropathic pain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23693161" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51295" }, "primaryId" : "GEO:GSE51295", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51295" } ] }, "title" : "HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain [DRG tissue]", "dateAssigned" : "2013-09-30T00:00:00.000-05:00", "summary" : "Histone deacetylase inhibitors (HDACIs) interfere with the epigenetic process of histone acetylation and are known to have analgesic properties in models of chronic inflammatory pain. The aim of this study was to determine whether these compounds could also affect neuropathic pain. Different class I HDACIs were delivered intrathecally into rat spinal cord in models of traumatic nerve injury and antiretroviral drug-induced peripheral neuropathy (stavudine, d4T). Mechanical and thermal hypersensitivity was attenuated by 40% to 50% as a result of HDACI treatment, but only if started before any insult. The drugs globally increased histone acetylation in the spinal cord, but appeared to have no measurable effects in relevant dorsal root ganglia in this treatment paradigm, suggesting that any potential mechanism should be sought in the central nervous system. Microarray analysis of dorsal cord RNA revealed the signature of the specific compound used (MS-275) and suggested that its main effect was mediated through HDAC1. Taken together, these data support a role for histone acetylation in the emergence of neuropathic pain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23693161" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51380" }, "primaryId" : "GEO:GSE51380", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51380" } ] }, "title" : "Gene expression data from 16-month and 3-month old male rats, with three different levels of activity over the life span: sedentary, twice weekly physical activity, regular running wheel exercise.", "dateAssigned" : "2013-10-17T00:00:00.000-05:00", "summary" : "We used microarrays to detail global gene expression underlying select health-related phenotypes and identified differentially expressed genes among the three groups.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51381" }, "primaryId" : "GEO:GSE51381", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51381" } ] }, "title" : "The ability of VSL#3 to restore the age-related deficit in LTP is associated with changes in brain genes expression", "dateAssigned" : "2013-10-17T00:00:00.000-05:00", "summary" : "A deficit in synaptic plasticity is one of the many changes that occurs with age. Specifically the archetypal model of plasticity, long-term potentiation (LTP), is reduced in hippocampus of middle-aged and aged animals. Several factors are likely to contribute to this deficit including morphological changes like a net loss of neurons and loss of synapses with the consequent changes in receptor signalling. However it is also clear that ageing is associated with development of oxidative stress, and also inflammatory stress which is typified by increased activation of microglia. Recent evidence has indicated that probiotics exert anti-inflammatory in the gut. Specifically VSL#3, a proprietary probiotic comprising 8 Gram-positive bacterial strains, decreased markers of inflammation in the colon in an animal model of colitis. We considered that its anti-inflammatory effects might extend to brain and therefore that treatment of aged rats with VSL#3 might attenuate the age-related deficit in LTP. The evidence indicates that LTP was impaired in control-treated aged rats but sustained in aged rats which received VSL#3. This was accompanied by a modest decrease in markers of microglial activation and an increase in BDNF and synapsin . The microarray analysis demonstrated that VSL#3 treatment induces changes also in the expression of some brain genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25202975" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51467" }, "primaryId" : "GEO:GSE51467", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51467" } ] }, "title" : "Expresion profile of TGR-1 (Myc+/+) and HO15.19 (Myc-/-) infected with a retrovirus expressing Hhex or GFP (controls)", "dateAssigned" : "2013-10-21T00:00:00.000-05:00", "summary" : "The aim of this experiment is to determine Hhex targets in the presence and absence of Myc.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25220416" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51586" }, "primaryId" : "GEO:GSE51586", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51586" } ] }, "title" : "miRNA profiling of control and ischemic samples in vitro and in vivo", "dateAssigned" : "2013-10-23T00:00:00.000-05:00", "summary" : "miRNA microarray profiling of primary cortical neurons exposed to 4h oxygen and glucose deprivation (OGD) in vitro. RNA samples collected at 8h post-OGD terminaion. miRNAs were also profiled in mice exposed to 3- vessel occlusion model of stroke. RNA samples collected from contralateral (control) and ipsilateral (infarct) sides of the brain following 24h of reperfusion.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51593" }, "primaryId" : "GEO:GSE51593", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51593" } ] }, "title" : "Bone marrow-derived stromal cells from double transgenic rats (of Sprague-Dawley origin) harboring the human angiotensinogen and human renin genes, and control rats", "dateAssigned" : "2013-10-23T00:00:00.000-05:00", "summary" : "Hypertension and persistent activation of the renin-angiotensin system (RAS) are predisposing factors for development of acute kidney injury (AKI). Although bone marrow-derived stromal cells (BMSCs) have shown therapeutic promise in treatment of AKI, the impact of pathological RAS on BMSC functionality has remained unresolved. RAS and its local components in the bone marrow are involved in several key steps of cell maturation processes. This may also render BMSC population vulnerable to alterations even in the early phases of RAS pathology. We isolated TG-BMSCs from young, end organ disease-free rats with increased RAS activation (human angiotensinogen/renin double transgenic rats; dTGR) that eventually develop hypertension and die of end-organ damage and kidney failure at 8-weeks-of-age. Control cells were isolated from wild-type Sprague-Dawley rats (SD-BMSCs). Cell phenotype, mitochondrial reactive oxygen species (ROS) production and respiration were assessed, and gene expression profiling was carried out using microarrays. Cells’ therapeutic efficacy was evaluated in a rat model of acute ischemia-reperfusion-induced AKI. Serum urea and creatinine were measured at 24h and 48h. Acute tubular damage was scored and immunohistochemistry was used for evaluation for markers of inflammation (MCP-1, ED-1), and kidney injury (KIM-1, NGAL). TG-BMSCs showed distinct mitochondrial morphology, decreased cell respiration, and increased production of ROS. Gene expression profiling revealed a pronounced pro-inflammatory phenotype. In contrast to the therapeutic effect of SD-BMSCs, administration of TG-BMSCs in the AKI model resulted in exacerbation of kidney injury and high mortality. Our results demonstrate that early persistent RAS activation can dramatically compromise therapeutic potential of BMSCs by shift into a pro-inflammatory phenotype with mitochondrial dysfunction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25534858" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51657" }, "primaryId" : "GEO:GSE51657", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51657" } ] }, "title" : "The influence of long-term use of diet enriched with biologically active substances on transcirptomic profile in rats liver", "dateAssigned" : "2013-10-24T00:00:00.000-05:00", "summary" : "The aim of the study was to identify genes which are differentially expressed in the liver from rat fed with control diet and rat fed with diet enriched with biologicaly active compounds after 3 and 14 months of experiment", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51708" }, "primaryId" : "GEO:GSE51708", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51708" } ] }, "title" : "Effects of CREB3L1 on gene expression", "dateAssigned" : "2013-10-25T00:00:00.000-05:00", "summary" : "CREB3L1 is a member of the unfolded protein response family of proteins. CREB3L1 expression is lost from metastatic breast cancer cells. We wanted to determine the effctes CREB3L1 expression had on gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24126059" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51781" }, "primaryId" : "GEO:GSE51781", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51781" } ] }, "title" : "Expression data from oligodendroglial cell line", "dateAssigned" : "2013-10-28T00:00:00.000-05:00", "summary" : "We used microarray analysis to detail the changes in gene expression caused by alpha-synuclein aggregation followed by cellular degeneration", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24361600" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51797" }, "primaryId" : "GEO:GSE51797", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51797" } ] }, "title" : "Hepatic expression data from 2-stage carcinogenesis study in rats", "dateAssigned" : "2013-10-28T00:00:00.000-05:00", "summary" : "We used microarrays to obtain the global gene expression profile of livers to understand the mechanism of carcinogenesis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51802" }, "primaryId" : "GEO:GSE51802", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51802" } ] }, "title" : "Association of CREB3L1 with promoters in LN4D6 CREB3L1 cells", "dateAssigned" : "2013-10-28T00:00:00.000-05:00", "summary" : "CREB3L1 is a member of the unfolded protein response family of proteins. CREB3L1 expression is lost from metastatic breast cancer cells. We wanted to determine the promoters of genes that CREB3L1 bound to.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24126059" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51806" }, "primaryId" : "GEO:GSE51806", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51806" } ] }, "title" : "Expression data from rat androgenetic embryonic stem cells", "dateAssigned" : "2013-10-28T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global gene expression profile of RahES cells and identified distinct classes of up-regulated and down-regulated genes compared with the expression of normal diploid rat ES cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51824" }, "primaryId" : "GEO:GSE51824", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE51824" } ] }, "title" : "Reversible and irreversible differentiation of cardiac fibroblasts", "dateAssigned" : "2013-10-29T00:00:00.000-05:00", "summary" : "Aim: Differentiation of cardiac fibroblasts (Fb) into myofibroblasts (MyoFb) is responsible for connective tissue buildup in myocardial remodeling. We examined reversibility of MyoFb differentiation. Methods and Results: Adult rat cardiac Fb were cultured on a plastic substratum providing mechanical stress, with conditions to obtain different Fb phenotypes. Fb spontaneously differentiated to proliferating MyoFb (p-MyoFb) with stress fiber formation decorated with alpha-smooth muscle actin (a-SMA). Transforming growth factor-ß1 (TGF-ß1) promoted terminal differentiation into a-SMA positive MyoFb showing near absence of proliferation i.e. non-p-MyoFb (2-fold increase in cell number after 12 days vs 11-fold for p-MyoFb). SD-208, a TGF-ß-receptor-I kinase blocker, inhibited p-MyoFb differentiation as shown by stress fiber absence, low levels of a-SMA protein expression, and high levels of proliferation (32-fold increase after 12 days). Fb seeded in collagen matrices induced no contraction, whereas p-MyoFb and non-p-MyoFb induced 2.5- and 4-fold contraction. Fb produced low levels of collagen and secreted high levels of IL-10. Non-p-MyoFb showed high collagen production and high MCP-1 and TIMP-1 secretion. Transcriptome analysis indicated differential gene expression between all phenotypes. Dedifferentiation of p-MyoFb, but not of non-p-MyoFb, was induced by SD-208 despite maintained stress, shown by stress fiber de-polymerization in 30% of p-MyoFb vs in 8% of non-p-MyoFb. Stress fiber de-polymerization could be induced by mechanical strain release in p-MyoFb and non-p-MyoFb (2 day culture in unrestrained 3-D collagen matrices). Only p-MyoFb showed true dedifferentiation after long-term 3-D culture. Conclusions: Both reduction in mechanical strain and TGF-ß-receptor-I kinase inhibition can reverse p-MyoFb differentiation but not in non-p-MyoFb.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24368833" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52001" }, "primaryId" : "GEO:GSE52001", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52001" } ] }, "title" : "Effects of Salidroside on gene expression in ischemic brain of rats", "dateAssigned" : "2013-11-01T00:00:00.000-05:00", "summary" : "We employed DNA microarray to identify genes differentially regulated by salidroside in ischemic brain of MCAO rats. With a cut of p < .01 and 2-fold change, we found that 121 genes were upregulated and 142 genes were down-regulated in the MCAO group, compared to the sham group. Administration of salidroside (1 h after reperfusion, daily for 6 d) enhanced 28 transcripts and suppressed 16 transcripts. The genes involved in neuroplasticity and oxygen carrier were further confirmed by qRT-PCR. Our data suggest that salidroside could regulate neuroplasticity in post-ischemic stroke, in addition to its neuroportective function.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52054" }, "primaryId" : "GEO:GSE52054", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52054" } ] }, "title" : "Expression data from rat livers - Naproxen and NO-Naproxen treatment", "dateAssigned" : "2013-11-04T00:00:00.000-06:00", "summary" : "In this dataset, we include the expression data obtained from liver of untreated rats and rats treated with naproxen (400mg/kg diet) or NO-naproxen (550mg/kg diet) for 7 days.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52055" }, "primaryId" : "GEO:GSE52055", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52055" } ] }, "title" : "miRNAs expression of soleus response to simulated microgravity", "dateAssigned" : "2013-11-04T00:00:00.000-06:00", "summary" : "The expression of 23 out of 174 miRNAs was found to change at least 2-fold of 7 and/or 14 days of TS. By using real-time PCR assays, we verified the microarray data using some of the expected genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52056" }, "primaryId" : "GEO:GSE52056", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52056" } ] }, "title" : "Gene expression of soleus response to simulated microgravity", "dateAssigned" : "2013-11-04T00:00:00.000-06:00", "summary" : "The expression of 787 (373 upregulated and 414 downregulated) and 923 (491 upregulated and 432 downregulated) genes out of 28000 was altered respectively at least 2-fold of 7 and 14 days TS, which represented 397 (233 upregulated and 164 downregulated) genes of common alteration. By using real-time PCR assays, we verified the microarray data using some of the expected genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52142" }, "primaryId" : "GEO:GSE52142", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52142" } ] }, "title" : "Open lung approach with low tidal volume mechanical ventilation attenuates lung injury in rats with massive brain damage", "dateAssigned" : "2013-11-06T00:00:00.000-06:00", "summary" : "Conclusions: In BD, LVT/OLPEEP minimizes lung morpho-functional changes and inflammation compared to HVT/LPEEP. LVT/OLPEEP might represent a suitable ventilatory strategy in massive brain damage.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24693992" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52204" }, "primaryId" : "GEO:GSE52204", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52204" } ] }, "title" : "A Global Approach to Dissect Palmitate-induced Impairment of Hepatic Glucose Production", "dateAssigned" : "2013-11-07T00:00:00.000-06:00", "summary" : "Obesity-induced insulin resistance of the liver is characterised by increased gluconeogenesis, which contributes to elevated blood glucose levels in individuals with type 2 diabetes. Research into how fatty acids induce insulin resistance has commonly focused on the induction of insulin resistance. We hypothesise that by shifting focus to the reversal of an insulin resistant phenotype, novel insights can be made into the mechanisms by which insulin resistance can be overcome. Using global gene and lipid expression profiling, we aimed to identify biological pathways altered in parallel with restoration of palmitate-induced deregulation of glucose production using metformin and sodium salicylate. FAO hepatoma cells were treated with palmitate (0.075mM, 48h) with or without metformin (0.25mM) and sodium salicylate (2mM) in the final 24h of palmitate treatment, and effects on glucose production were determined. Microarray followed by gene set enrichment analysis was performed to investigate pathway regulation. A lipidomic analysis (HPLC-MS/MS) and measurement of secreted bile acids and cholesterol were performed. Reversal of palmitate-induced impairment of glucose production by metformin and sodium salicylate was characterised by down-regulated expression of metabolic pathways regulating acetyl-CoA to cholesterol and bile acid biosynthesis. Total levels of intracellular and secreted cholesterol and bile acids were not different between impaired and restored glucose production. Total intracellular levels of diacylgycerol, triacylglycerol and cholesterol esters increased with palmitate (impaired glucose production), however, these were not further altered with metformin and sodium salicylate (restored glucose production). Six individual lipid species containing 18:0 and 18:1 side-chains were reduced by metformin and sodium salicylate. Widespread lipid metabolism changes induced by the reversal of palmitate-induced deregulation of glucose production with metformin and sodium salicylate were identified. While cholesterol and bile acid levels remained unchanged, the flux through these pathways may in part explain these findings. The identification of lipid species containing 18:0 and 18:1 side chains being regulated alongside changes to glucose production may indicate potential mediators of glucose production and insulin resistance.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52350" }, "primaryId" : "GEO:GSE52350", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52350" } ] }, "title" : "Systems analysis of transcriptional data provides insights into muscle's biological response to botulinum toxin-A (BoNT-A)", "dateAssigned" : "2013-11-13T00:00:00.000-06:00", "summary" : "Introduction:The purpose of this study is to provide athe first global transcriptomic profiling and systems analysis of BoNT-A treated muscle over a one year period. Microarray analysis was performed on rat TA muscle from 4 groups (n=4/group) at 1,4, 12 and 52 weeks after BoNT-A injection and saline injected rats at 12 weeks as control. Fold changes were computed at each time point with respect to control. Results: Dramatic transcriptional adaptation occurs at 1 week with a paradoxical increase in expression of slow and immature isoforms; increased expression of genes in competing pathways of repair and atrophy; impaired mitochondrial biogenesis and increased metal ion imbalance. ECM adaptations occurred at 4weeks to the basal lamina and fibrillar ECM. The muscle transcriptome returned to the unperturbed state 12 weeks post-injection. Conclusion: Transcriptional adaptations resemble denervated muscle albeit some differences. Overall gene expression, across time, correlates with the generally accepted BoNT-A time course.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24536034" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52443" }, "primaryId" : "GEO:GSE52443", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52443" } ] }, "title" : "Genome-wide microRNA expression profiles of rat hippocampus in a chronic temporal lobe epilepsy model induced by amygdala stimulation", "dateAssigned" : "2013-11-18T00:00:00.000-06:00", "summary" : "MicroRNAs (miRNAs) have been found to participate in the pathogenesis of several neurological diseases including epilepsy. To date, the expression and functions of miRNAs in chronic temporal lobe epilepsy (TLE), the most common type of refractory epilepsy in adults, have not been well characterized. Here, we adopted high-throughput sequencing to investigate miRNA expression profile in a chronic TLE model induced by amygdala stimulation", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24751812" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52481" }, "primaryId" : "GEO:GSE52481", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52481" } ] }, "title" : "Rat Astrocyte-Neuron Co-cultures versus purified co-cultured Astrocytes versus Astrocyte alone", "dateAssigned" : "2013-11-18T00:00:00.000-06:00", "summary" : "Over the last decade, the importance of astrocyte-neuron communication in neuronal development and synaptic plasticity has become increasingly clear. Since neuron-astrocyte interactions represent highly dynamic and reciprocal processes, we hypothesized that at least part of the involved astrocyte genes may be regulated as a consequence of their interactions with maturing neurons. In order to identify such neuron-induced astrocyte genes in vitro, we tested the effectiveness of the ‘cold jet’, a new method for separation of neurons from co-cultured astrocytes. The cold jet method is performed under ice-cold conditions and avoids protease-mediated isolation of astrocytes or time-consuming centrifugation, yielding intact astrocyte mRNA with approximately 90% of neuronal RNA removed. Using this method, we executed genome-wide profiling in which RNA derived from astrocyte-only cultures was compared with astrocyte RNA derived from differentiating neuron-astrocyte co-cultures. Data analysis revealed changes in expression of a large number of mRNAs and biological processes, including novel findings. Thus, cold jet is an efficient method to separate astrocytes from neurons in co-culture, and in this study reveals that neurons induce robust gene-expression changes in co-cultured astrocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24523672" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52500" }, "primaryId" : "GEO:GSE52500", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52500" } ] }, "title" : "Gene expression data from rat cochlear lateral wall after 3NP damage", "dateAssigned" : "2013-11-19T00:00:00.000-06:00", "summary" : "We used microarrays to detail the global programme of gene expression in the damaged cochlear lateral wall by 3NP and identified distinct classes of up-regulated/ down-regulated genes during the process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52516" }, "primaryId" : "GEO:GSE52516", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52516" } ] }, "title" : "Down-regulation as the dominant hippocampal gene expression profile with voluntary resistance wheel running by DNA microarray analysis", "dateAssigned" : "2013-11-19T00:00:00.000-06:00", "summary" : "Exercise improves brain function enhancing neuronal plasticity and cognitive enhancement. For voluntary resistance wheel running (RWR) exercise, with a load of 30% of body weight, we reported enhancement of neurogenesis and spatial memory associated with hippocampal brain-derived neurotrophic factor (BDNF) signaling compared to wheel running (WR) without a load (Lee et al., 2012; Lee et al., 2013). Despite these new evidences, mechanisms for RWR-induced improvement of hippocampal function remained to be clarified. In the present study, we have utilized the high-throughput DNA microarray approach to gain deep insight into molecular mechanisms underlying these changes that could be novel targets of RWR-induced hippocampal plasticity. To do so, whole genome (4x44K) high-density oligonucleotide microarrays were used to monitor the expression level of gene transcripts in the hippocampus of rats voluntary running for 4 weeks in comparison with sedentary animals. These rats showed a significant decrease in average running distance although average work levels immensely increased 12-fold in the RWR group, resulting in muscular adaptation for the fast-twitch plantaris muscle. DNA microarray analysis revealed that 122 (sedentary x WR) and 157 (sedentary x RWR) genes were up-regulated (> 1.5-fold change) as compared with 97 (sedentary x WR) and 467 (sedentary x RWR) down-regulated genes (< 0.75-fold change). Functional categorization using the Ingenuity Pathway Analysis (IPA) revealed expression pattern changes in the major categories of disease and disorders, molecular functions and physiological system development and function. Among these, RWR up-regulated genes such as NFATc1, AVPR1A and FGFR4, which are crucial role for neuronal development and its functions. The down-regulated inflammatory cytokines (IL1B, IL10, IL2RA, TNF) and chemokines (CXCL1, CXCL9, CXCL10, CCL2, CCL13, CCR4) might be important to neuronal dysfunction and vulnerability. Taken together, these gene candidates are suggested to play a critical role in hippocampal plasticity. This is a first study presenting not only new information into the voluntary RWR influenced transcriptome in the rat hippocampus, but also provides a hypothesis for the RWR influenced enhancement in brain function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25413326" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52603" }, "primaryId" : "GEO:GSE52603", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52603" } ] }, "title" : "Expression data from Control diet, Western diet and Western diet + DHA fed rats.", "dateAssigned" : "2013-11-21T00:00:00.000-06:00", "summary" : "Array results from two pooled samples (5 rats in each pool) for n=10 per treatment group were used for comparisons. Comparisons between Western vs. Control, Western + DHA vs. Control and Western + DHA vs. Western diets was subjected to analysis to generate log fold changes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52615" }, "primaryId" : "GEO:GSE52615", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52615" } ] }, "title" : "Effects of an antipsychotic (Olanzapine) involves alterations in gene specific DNA methylation", "dateAssigned" : "2013-11-21T00:00:00.000-06:00", "summary" : "The results suggest that these downstream effects, aside from D2 blockade, may play a critical role in the biological actions of antipsychotics. These include altered expressions of relevant genes involved in GABAergic, glutamatergic, cholinergic, neuregulin and ErbB signaling pathways. Epigenetic mechanisms involving changes in DNA methylation could, therefore, explain the delay and individualized non-specificity of biological effects of olanzapine. The results also suggest that DNA methylation may play a role in the process of therapeutic efficacy of olanzapine by altering the transcriptome via tissue-specific methylation of genes involved in schizophrenia signaling pathways.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52753" }, "primaryId" : "GEO:GSE52753", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52753" } ] }, "title" : "Effects of fibroblast growth factors (FGF) on dissociated myelinating cultures", "dateAssigned" : "2013-11-26T00:00:00.000-06:00", "summary" : "Analysis of the effects of three members of the FGF family (FGF1, FGF2 and FGF9) and bone morphogenic protein 4 (BMP4) on myelinating cultures generated from dissociated embryonic spinal cord. The results of both immediate (24 hours, T1 (24 hrs)) and long term treatments (10days, T2) give insights into the cumulative effects of sustained FGF and BMP mediated signal transduction in the pathogenesis of demyelinating diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25907862" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52754" }, "primaryId" : "GEO:GSE52754", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52754" } ] }, "title" : "miRNA expression atlas in male rat", "dateAssigned" : "2013-11-26T00:00:00.000-06:00", "summary" : "MicroRNAs (miRNAs) are small (~22 nucleotide) noncoding RNAs that play pivotal roles in regulation of gene expression. The value of miRNAs as circulating biomarkers is now broadly recognized; such tissue-specific biomarkers can be used to monitor tissue injury and several pathophysiological conditions in organs. In addition, miRNA profiles of normal organs and tissues are important for obtaining a better understanding of the source of modulated miRNAs in blood and how those modulations reflect various physiological and toxicological conditions. This work was aimed at creating an miRNA atlas in rats, as part of a collaborative effort with the Toxicogenomics Informatics Project in Japan (TGP2). We analyzed genome-wide miRNA profiles of 55 different organs and tissues obtained from normal male rats using miRNA arrays. The work presented herein represents a comprehensive dataset derived from normal samples profiled in a single study. Here we present the whole dataset with miRNA profiles of multiple organs, as well as precise information on experimental procedures and organ-specific miRNAs identified in this dataset.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25977763" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52761" }, "primaryId" : "GEO:GSE52761", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52761" } ] }, "title" : "Gene expression in 2,3-Pentanedione Induced Bronchiolitis Oblliterans", "dateAssigned" : "2013-11-26T00:00:00.000-06:00", "summary" : "Fibrotic and nonfibrotic bronchial tissues were collected from lungs of pentandione exposed rats by laser capture microdissection. Analogous tissue was collected from air-exposed controls. Miroarray analysis revealed a number of DEGs", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25710175" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52763" }, "primaryId" : "GEO:GSE52763", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52763" } ] }, "title" : "Gene expression profiles in the spinal cord below the lesion level and influence of treadmill locomotor training", "dateAssigned" : "2013-11-26T00:00:00.000-06:00", "summary" : "Traumatic spinal cord injury (SCI) often leads to loss of locomotor function. Neuroplasticity of spinal circuitry underlies some functional recovery and therefore represents a therapeutic target to improve locomotor function following SCI. However, the cellular and molecular mechanisms mediating neuroplasticity below the lesion level are not fully understood. The present study performed a gene expression profiling in the rat lumbar spinal cord at 1 and 3 weeks after contusive SCI at T9. The below-level gene expression profiles were compared with those of animals that were subjected to treadmill locomotor training.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24520355" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52897" }, "primaryId" : "GEO:GSE52897", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52897" } ] }, "title" : "Adenine-induced chronic renal failure causes decreased aortic relaxation rate and altered expression of genes involved in excitation-contraction coupling in vascular smooth muscle cells", "dateAssigned" : "2013-12-02T00:00:00.000-06:00", "summary" : "In conclusion, rats with A-CRF show a marked reduction in the rate of relaxation of larger conduit arteries localized proximal to the common femoral artery. This abnormality may be caused by reduced cytosolic Ca2+ clearance in vascular smooth muscle cells secondary to dysregulation of genes involved in excitation-contraction coupling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27239807" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52969" }, "primaryId" : "GEO:GSE52969", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE52969" } ] }, "title" : "Expression data from Sar1 isoform overexpressing rat hepatoma cell lines", "dateAssigned" : "2013-12-04T00:00:00.000-06:00", "summary" : "We used microarrays to investigate the effect of overexpression of Sar1 isoforms and a constitutively active mutant form of Sar1B, Sar1B:H79G, on global gene expression in rat hepatoma cell line, McArdle RH7777 and identified a strong down-regulation of cholesterol biosynthetic gene mRNA expression in the Sar1B:H79G-, but not the wild-type Sar1A- or Sar1B-overexpressing cell lines.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24338480" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53028" }, "primaryId" : "GEO:GSE53028", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53028" } ] }, "title" : "Parental binge alcohol abuse alters F1 generation hypothalamic gene expression in the absence of direct fetal alcohol exposure", "dateAssigned" : "2013-12-05T00:00:00.000-06:00", "summary" : "Adolescent binge alcohol exposure has been previously shown to have long-lasting effects on the expression of hypothalamic genes that regulate the stress response, even in the absence of subsequent adult alcohol exposure. Those data suggested that alcohol can induce permanent gene expression changes, potentially through epigenetic modifications. Importantly, epigenetic modifications can be transmitted to future generations therefore, in these studies we investigated the effects of adolescent binge alcohol exposure on hypothalamic gene expression patterns in the F1 generation offspring. It has been well documented that maternal alcohol exposure during fetal development can have devastating neurological consequences. However, less is known about the consequences of maternal and/or paternal alcohol exposure outside of the gestational time frame. Here, we exposed adolescent male and female rats to a repeated binge EtOH exposure paradigm and then mated them in adulthood. Hypothalamic samples were taken from the offspring of these animals at postnatal day (PND) 7 and subjected to a genome-wide microarray analysis followed by qRT-PCR for selected genes. Importantly, the parents were not intoxicated at the time of mating and were not exposed to EtOH at any time during gestation therefore, the offspring were never directly exposed to EtOH. Our results showed that the offspring of alcohol-exposed parents had significant differences in the expression of hypothalamic genes that mediate neurogenesis and synaptic plasticity during neurodevelopment, genes important for directing chromatin remodeling, posttranslational modifications or transcription regulation, as well as genes involved in regulation of obesity and reproductive function. These data demonstrate that repeated binge alcohol exposure during pubertal development can potentially have detrimental effects on future offspring even in the absence of direct fetal alcohol exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24586686" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53082" }, "primaryId" : "GEO:GSE53082", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53082" } ] }, "title" : "Cross-platform toxicogenomics for the prediction of nongenotoxic hepatocarcinogenesis in rat (mRNA)", "dateAssigned" : "2013-12-06T00:00:00.000-06:00", "summary" : "In this study we performed microarray-based molecular profiling of liver samples from Wistar rats exposed to genotoxic carcinogens (GC), nongenotoxic carcinogens (NGC) or non-hepatocarcinogens (NC) for up to 14 days. In contrast to previous toxicogenomics studies aimed at the inference of molecular signatures for assessing the potential and mode of compound carcinogenicity, we considered multi-level omics data. Besides evaluating the predictive power of signatures observed on individual biological levels, such as mRNA, miRNA and protein expression, we also introduced novel feature representations which capture putative molecular interactions or pathway alterations by integrating expression profiles across platforms interrogating different biological levels.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24830643" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53083" }, "primaryId" : "GEO:GSE53083", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53083" } ] }, "title" : "Cross-platform toxicogenomics for the prediction of nongenotoxic hepatocarcinogenesis in rat (miRNA)", "dateAssigned" : "2013-12-06T00:00:00.000-06:00", "summary" : "In this study we performed microarray-based molecular profiling of liver samples from Wistar rats exposed to genotoxic carcinogens (GC), nongenotoxic carcinogens (NGC) or non-hepatocarcinogens (NC) for up to 14 days. In contrast to previous toxicogenomics studies aimed at the inference of molecular signatures for assessing the potential and mode of compound carcinogenicity, we considered multi-level omics data. Besides evaluating the predictive power of signatures observed on individual biological levels, such as mRNA, miRNA and protein expression, we also introduced novel feature representations which capture putative molecular interactions or pathway alterations by integrating expression profiles across platforms interrogating different biological levels.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24830643" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53084" }, "primaryId" : "GEO:GSE53084", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53084" } ] }, "title" : "Cross-platform toxicogenomics for the prediction of nongenotoxic hepatocarcinogenesis in rat (protein)", "dateAssigned" : "2013-12-06T00:00:00.000-06:00", "summary" : "In this study we performed microarray-based molecular profiling of liver samples from Wistar rats exposed to genotoxic carcinogens (GC), nongenotoxic carcinogens (NGC) or non-hepatocarcinogens (NC) for up to 14 days. In contrast to previous toxicogenomics studies aimed at the inference of molecular signatures for assessing the potential and mode of compound carcinogenicity, we considered multi-level omics data. Besides evaluating the predictive power of signatures observed on individual biological levels, such as mRNA, miRNA and protein expression, we also introduced novel feature representations which capture putative molecular interactions or pathway alterations by integrating expression profiles across platforms interrogating different biological levels.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24830643" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53256" }, "primaryId" : "GEO:GSE53256", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53256" } ] }, "title" : "Expression data from fracture hematoma tissue of young and old rats after 3days of rigid or semi-rigid fixation of an osteotomy", "dateAssigned" : "2013-12-12T00:00:00.000-06:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying the influence of fixation stability in young and old rats and identified distinct classes of regulated genes during this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53305" }, "primaryId" : "GEO:GSE53305", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53305" } ] }, "title" : "Transcriptional profiling of retinal progenitors, exposed to endothelial cells or EGF", "dateAssigned" : "2013-12-13T00:00:00.000-06:00", "summary" : "Embryonic day 18 retinal cells showed self-renewal properties such as clonal propagation without compromising multipotentiality when grown in the presence of endothelial cell conditioned medium and not EGF alone.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53361" }, "primaryId" : "GEO:GSE53361", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53361" } ] }, "title" : "Small artery remodeling depends on the genetic background in spontaneously hypertensive rats (microRNA)", "dateAssigned" : "2013-12-16T00:00:00.000-06:00", "summary" : "Spontaneously hypertensive rats (SHR) have been used frequently as a model for human essential hypertension. However, both the SHR and its normotensive control, the Wistar Kyoto rat (WKY), consist of genetically different sublines. We tested the hypothesis that discrepant data in literature regarding the pathophysiology of vascular remodeling in hypertension result from the use of different rat sublines. Using micro-arrays, we studied miRNA and mRNA expression in resistance arteries of WKY and SHR from three different sources, at 6 weeks and 5 months of age. Both WKY and SHR showed an age-related expression pattern that involved many genes related to the extracellular matrix. In SHR, this pattern was more extensive and included a specific increase in miR132-3p, and type III deiodinase. Direct comparison of WKY to SHR also yielded differences in expression, including thrombospondin 4. Heterogeneity in gene expression among sublines was associated with differences in blood pressure, body weight, vascular remodeling, endothelial function, and vessel ultrastructure. Common features in vessels from SHR were an increase in wall thickness, wall-to-lumen ratio, and internal elastic lamina thickness. These results indicate that endothelial dysfunction, vascular stiffening, and inward remodeling of small arteries are not common features of hypertension, but are subline-dependent. Relatively minor differences in genetic background associate with different types of vascular remodeling in hypertensive rats. The clinical implication of this study is that more research into personalized treatment in hypertension is warranted.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26356734" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53363" }, "primaryId" : "GEO:GSE53363", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53363" } ] }, "title" : "Small artery remodeling depends on the genetic background in spontaneously hypertensive rats (mRNA)", "dateAssigned" : "2013-12-16T00:00:00.000-06:00", "summary" : "Spontaneously hypertensive rats (SHR) have been used frequently as a model for human essential hypertension. However, both the SHR and its normotensive control, the Wistar Kyoto rat (WKY), consist of genetically different sublines. We tested the hypothesis that discrepant data in literature regarding the pathophysiology of vascular remodeling in hypertension result from the use of different rat sublines. Using micro-arrays, we studied miRNA and mRNA expression in resistance arteries of WKY and SHR from three different sources, at 6 weeks and 5 months of age. Both WKY and SHR showed an age-related expression pattern that involved many genes related to the extracellular matrix. In SHR, this pattern was more extensive and included a specific increase in miR132-3p, and type III deiodinase. Direct comparison of WKY to SHR also yielded differences in expression, including thrombospondin 4. Heterogeneity in gene expression among sublines was associated with differences in blood pressure, body weight, vascular remodeling, endothelial function, and vessel ultrastructure. Common features in vessels from SHR were an increase in wall thickness, wall-to-lumen ratio, and internal elastic lamina thickness. These results indicate that endothelial dysfunction, vascular stiffening, and inward remodeling of small arteries are not common features of hypertension, but are subline-dependent. Relatively minor differences in genetic background associate with different types of vascular remodeling in hypertensive rats. The clinical implication of this study is that more research into personalized treatment in hypertension is warranted.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26356734" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53365" }, "primaryId" : "GEO:GSE53365", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53365" } ] }, "title" : "Characterization of neuroendocrine tumors in heterozygous mutant MENX rats: a novel model of invasive medullary thyroid carcinoma [adrenal]", "dateAssigned" : "2013-12-16T00:00:00.000-06:00", "summary" : "We here show that the reduction to a single functional p27 allele predisposes MENX heterozygous rats to the development of neuroendocrine malignancies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29142006" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53390" }, "primaryId" : "GEO:GSE53390", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53390" } ] }, "title" : "Characterization of gene expression in trigeminal nerves of BDIX, BDIV, BDIX.BDIV-Mss4a and BDIX.BDIV-Mss4d rats of both sexes.", "dateAssigned" : "2013-12-17T00:00:00.000-06:00", "summary" : "Identification of genes being differentially expressed between a) female and male rats within each strain and b) tumor susceptible and tumor resistant strains using Microarray analyses.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53453" }, "primaryId" : "GEO:GSE53453", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53453" } ] }, "title" : "Rat insulin-producing INS-1E exposed to cytokines IL-1ß and IFN-¿", "dateAssigned" : "2013-12-18T00:00:00.000-06:00", "summary" : "The measurement of mRNA expression following ß-cell exposure to these cytokines gives a picture of the changes in gene expression characterizing the path to ß-cell dysfunction and death.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24462878" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53512" }, "primaryId" : "GEO:GSE53512", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53512" } ] }, "title" : "Fetal-Adult Cardiac Transcriptome Analysis in Rats with Contrasting Left Ventricular Mass Reveals New Candidates for Cardiac Hypertrophy", "dateAssigned" : "2013-12-19T00:00:00.000-06:00", "summary" : "Reactivation of fetal gene expression patterns has been demonstrated to play a crucial role in common cardiac diseases in adult life including left ventricular (LV) hypertrophy (LVH). Thus, increased wall stress and neurohumoral activation are discussed to induce the return to expression of fetal genes after birth in LVH. We therefore aimed to test whether fetal gene expression programs are linked to the genetic predisposition to LVH. We performed genome-wide gene expression analysis by microarray-technology in a genetic rat model of LVH, i.e. the stroke-prone spontaneously hypertensive rat (SHRSP), to identify differences in expression patterns between day 20 of development (E20) and week 14 in comparison to a normotensive rat strain with low LV mass, i.e. Fischer (F344). 15232 probes from LV RNA from rats at week 14 and at E20 were detected as expressed (p < 0.05) and screened for differential expression. We identified 24 genes with a SHRSP specific up-regulation and 21 genes up-regulated in F344. Further bioinformatic analysis presented Efcab6, Ephx2 and Kcne1 as candidate genes for LVH that showed only in the hypertensive SHRSP rat a differential expression pattern during development and were significantly differentially expressed in adult SHRSP rats compared with two F344 and normotensive Wistar-Kyoto rats. They represent thus interesting novel targets for further functional analyses and the elucidation of mechanisms leading to LVH. Here we report a new approach to identify candidate genes for cardiac hypertrophy by analysing both gene expression differences between strains with contrasting cardiac phenotype and additionally the gene expression program during development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25646840" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53518" }, "primaryId" : "GEO:GSE53518", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53518" } ] }, "title" : "Genome-wide DNA methylation analysis of livers obtained from 2-stage carcinogenesis model in rats", "dateAssigned" : "2013-12-19T00:00:00.000-06:00", "summary" : "Identification of epigenetic alterations in the early stage of carcinogenesis promises a great contribution for mechanism analysis and marker exploration for the drug development. For this purpose, we conducted comprehensive analyses for DNA methylation and gene expression in livers obtained from a rat 2-stage carcinogenesis study using nitrosodiethylamine, thioacetamide, methapyrilene and acetaminophen as an initiator and phenobarbital as a promoter. Here, we report the result of MeDIP-seq using methylated DNA enriched by MBD2-protein in rat livers. Comprehensive gene expression analysis was also conducted using same liver samples. The obtained tag sequences were mapped onto rat genome and arbitrary tag count values were calculated and used as each gene DNA methylation state. Using these methylation and gene expression data, pathway analyses for each treatment was performed. The data indicated that livers accompanying preneoplastic legions acquired carcinogenic character of DNA methylation and immune-response related pathways were affected.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53762" }, "primaryId" : "GEO:GSE53762", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53762" } ] }, "title" : "Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (RNA-Seq)", "dateAssigned" : "2014-01-02T00:00:00.000-06:00", "summary" : "Poly(A) enriched RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to RNA-seq analysis at different sequencing depths", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24472155" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53764" }, "primaryId" : "GEO:GSE53764", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53764" } ] }, "title" : "Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (Affymetrix transcript-level)", "dateAssigned" : "2014-01-02T00:00:00.000-06:00", "summary" : "RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to microarray analysis and expression was determined at the exon and gene level", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24472155" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53860" }, "primaryId" : "GEO:GSE53860", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53860" } ] }, "title" : "Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (Affymetrix exon-level)", "dateAssigned" : "2014-01-07T00:00:00.000-06:00", "summary" : "RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to microarray analysis and expression was determined at the exon and gene level", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24472155" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53862" }, "primaryId" : "GEO:GSE53862", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53862" } ] }, "title" : "Chromatin occupancy and target genes of TCF7L2 in hepatocytes", "dateAssigned" : "2014-01-07T00:00:00.000-06:00", "summary" : "TCF7L2 regulates multiple metabolic pathways in hepatocytes through a transcriptional network involving HNF4a", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25414334" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53897" }, "primaryId" : "GEO:GSE53897", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53897" } ] }, "title" : "Genome-wide analysis of dorsal root ganglion (DRG) gene expression after morphine or oxycodone treatment", "dateAssigned" : "2014-01-08T00:00:00.000-06:00", "summary" : "Results provide important information to understand the analgesic effects of oxycodone as compared to morphine in a neuropathic pain model", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24618941" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53937" }, "primaryId" : "GEO:GSE53937", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53937" } ] }, "title" : "Identification of genes involved in cell death induced by sodium fluoride in rat oral epithelial cells", "dateAssigned" : "2014-01-09T00:00:00.000-06:00", "summary" : "In this study, to identify genes involved in cell death induced by sodium fluoride (NaF) in rat oral epithelial ROE2 cells, global-scale gene expression analysis was carried out using a GeneChip® system.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24853129" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53953" }, "primaryId" : "GEO:GSE53953", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53953" } ] }, "title" : "Heme oxygenase-1 knocked down rat mesangial cells treated with hydrogen peroxide", "dateAssigned" : "2014-01-09T00:00:00.000-06:00", "summary" : "HO-1 cells denote the cultured rat mesangial cells with heme oxygenase-1 knocked down by RNA interference (using lentiviral vector). GFP cells denote the cultured rat mesangial cells that are transfected with empty lentiviral vector containing GFP cassette. Cells are treated with hydrogen peroxide 100 micromolar for 2 hours, or without. RNA are then harvested for array analysis. Biological replicates are performed (two independent experiment sets).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53960" }, "primaryId" : "GEO:GSE53960", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE53960" } ] }, "title" : "A rat RNA-Seq transcriptomic Bodymap across eleven organs and four developmental stages", "dateAssigned" : "2014-01-09T00:00:00.000-06:00", "summary" : "The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat transcriptomic BodyMap created by performing RNASeq on 320 samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats. We catalogue the expression profiles of 40,064 genes, 65,167 transcripts, 31,909 alternatively spliced transcript variants and 2,367 non-coding genes/non-coding RNAs (ncRNAs) annotated in AceView. We find that organ-enriched, differentially expressed genes reflect the known organ-specific biological activities. A large number of transcripts show organ-specific, age-dependent or sex-specific differential expression patterns. We create a web-based, open-access rat BodyMap database of expression profiles with crosslinks to other widely used databases, anticipating that it will serve as a primary resource for biomedical research using the rat model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24510058" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54005" }, "primaryId" : "GEO:GSE54005", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54005" } ] }, "title" : "Dextran sodium sulfate treatment of wild type and Pirc rats alters colonic normal tissue gene expression", "dateAssigned" : "2014-01-12T00:00:00.000-06:00", "summary" : "Dextran sodium sulfate (DSS) causes inflammation in the gut similar to ulcerative colitis in humans. Patients with ulcerative colitis have increased risk of developing colon cancer. We sought to determine which genes are altered in the normal colonic epithelium, and which changes depend on the Pirc mutation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54007" }, "primaryId" : "GEO:GSE54007", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54007" } ] }, "title" : "Immunoprecipitation from rat kidney with 8-oxoguanine", "dateAssigned" : "2014-01-12T00:00:00.000-06:00", "summary" : "8-oxoguanine (8-oxoG) is one of the most common DNA lesions generated by reactive oxygen species. Here we show the genome-wide distribution of 8-oxoG by coupling immunoprecipitation by antibodies specific for the DNA fragments containing 8-oxoG with microarray that covers rat genome. Genome-wide mapping of 8-oxoG in rat kidney reveals that 8-oxoG preferentially located at gene deserts and depleted in genic regions. We did not observe the difference in 8-oxoG level between highly- and lowly-expressed groups of genes, may be because of the low level of 8-oxoG in genic regions in general comparing to gene deserts. Rather, the distribution of 8-oxoG highly correlates with the distribution of lamina associated domains (LADs), suggesting that the spatial location of the genomic regions in the nucleus is the major determinant for the susceptibility to oxidative modifications. One possible explanation for the enrichment of 8-oxoG in LADs is that the nuclear periphery is more susceptible to the oxidative damage coming from outside the nucleus. Another explanation is that LADs take rather compact conformation, which might prevent the recruitment of the repairing complex to the modified bases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25008760" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54028" }, "primaryId" : "GEO:GSE54028", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54028" } ] }, "title" : "Next Generation Sequencing Facilitates Quantitative Analysis of miRNAs in hepatic fibrosis and normal tissues.", "dateAssigned" : "2014-01-13T00:00:00.000-06:00", "summary" : "Aim: Hepatic fibrosis is a major worldwide medical problem and can develop into liver cirrhosis and hepatocellular carcinoma(HCC). Until now, there are no effective drugs for liver ¿brosis because the molecular mechanism of progression of liver fibrosis is not fully understood. MicroRNAs (miRNAs) are an important class of small non-coding functional RNAs that play a key role in many biological processes. The purpose of this study was to clarify how the aberrant expression of miRNAs participates in development of the liver fibrosis in rat liver fibrosis model. Methods: Fibrotic and paired normal liver tissues were collected and assesssed by deep sequencing technology. MiRNA pro¿ling results were validated by quantitative real-time polymerase chain reaction (qRT-PCR) and bioinformatics was used to predict miRNA targets. Results: Nine deregulated miRNAs were induced in porcine serum (PS)-induced hepatic fibrosis versus normal liver. Further analysis revealed several signaling pathways (e.g., gap junction and neuroactive ligand-receptor interaction) may be associated with hepatic fibrogenesis. Conclusion: Several miRNAs are dysregulated in PS-induced hepatic fibrosis and seem to be closely associated with hepatic fibrogenesis. These results provide an experimental basis for understanding the mechanism of hepatic fibrosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24927615" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54035" }, "primaryId" : "GEO:GSE54035", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54035" } ] }, "title" : "Dextran sodium sulfate treatment of Pirc rats alters colonic and tumor gene expression", "dateAssigned" : "2014-01-13T00:00:00.000-06:00", "summary" : "Dextran sodium sulfate (DSS) causes inflammation in the gut similar to ulcerative colitis in humans. Patients with ulcerative colitis have increased risk of developing colon cancer. We sought to determine whether genes altered in the normal colonic epithelium or tumor differed between sporadic and inflammation-associated tumor development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25200834" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54037" }, "primaryId" : "GEO:GSE54037", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54037" } ] }, "title" : "In vitro ischemia triggers a transcriptional response to down-regulate synaptic proteins in hippocampal neurons.", "dateAssigned" : "2014-01-13T00:00:00.000-06:00", "summary" : "The present study has used whole-rat genome microarray expression profiling to identify genes whose expression is significantly altered in hippocampal neuronal cultures submitted to oxygen and glucose deprivation (OGD), an established in vitro model for cerebral global ischemia that is suitable for investigations at the molecular level. To do so, total RNA was extracted from hippocampal neuronal cultures at an early (7h) and delayed (24h) time point after OGD, as well as from control neurons. Analysis of gene ontology showed that OGD followed by 7h or 24h of recovery induces changes in the expression levels of genes related with inflammation, response to oxidative stress, metabolism, apoptosis, synaptic proteins and ion channels and, importantly, genes that show different expression levels are mainly specific to one of the two time points of recovery analyzed. The expression levels of several genes were confirmed by qPCR and were in good agreement with the microarray data, showing that the combined use of the OGD model and the microarray technology can be a useful tool for the study molecular mechanisms contributing to the neuronal demise after transient global ischemia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24960035" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54085" }, "primaryId" : "GEO:GSE54085", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54085" } ] }, "title" : "Gene expression analysis of rat glomerular parietal epithelial cells", "dateAssigned" : "2014-01-15T00:00:00.000-06:00", "summary" : "Very little is known about the function of glomerular parietal epithelial cells (PECs). In this study, we performed genome-wide expression analysis on PEC-enriched capsulated vs. PEC-deprived decapsulated rat glomeruli to determine the transcriptional state of PECs under normal conditions. We identified hundreds of differentially expressed genes that mapped to distinct biologic modules including development, tight junction, ion transport, and metabolic processes. Since developmental programs were highly enriched in PECs, we characterized several of their candidate members at the protein level. Collectively, our findings confirm that PECs are multifaceted cells and help define their diverse functional repertoire.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25127402" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54121" }, "primaryId" : "GEO:GSE54121", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54121" } ] }, "title" : "A rat toxicogenomics study with Calcium Sensitizer EMD 82571 reveals a pleiotropic cause in teratogenicity", "dateAssigned" : "2014-01-15T00:00:00.000-06:00", "summary" : "The aim of reprotoxicity testing is to reveal adverse effects of chemicals and drugs on reproduction and on pre and postnatal fetal development. There is very limited data available on gene expression profiling for elucidation of the teratogenic effects of nongenotoxic teratogens. Therefore, research was undertaken to obtain knowledge on the molecular effects of MSC1096199 (previously known as EMD 82571), a calcium sensitizer that was abandoned in the preclinical development phase due to its teratogenic effects in some foetuses. Pregnant wistar rats were dose daily with either MSC1096199 (50 or 150 mg/kg) or Retinoic acid (10 mg/kg) on gestational days 6-17. Microarray experiment were performed using four different tissues (maternal liver, embryo liver (GD20), embryo bone (GD20), and whole embryo (GD12)) under four different conditions (vehicle, low dose and high dose of MSC1096199 and Retinoic acid) to determine the drug regulated genes. In the high dose treatment group, approximately 58% of the fetuses showed malformations i.e. exencephaly and agnathia, and toxicogenomics evidenced that the genes critically involved in osteogenesis, odontogenesis and extra cellular matrix components to be significantly regulated by MSC1096199, therefore providing a molecular rational for the observed teratogenic effects.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24977338" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54132" }, "primaryId" : "GEO:GSE54132", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54132" } ] }, "title" : "Genome-wide profiling of gene expression under electro-acupuncture treatment on MI heart in rats", "dateAssigned" : "2014-01-16T00:00:00.000-06:00", "summary" : "Conclusions: Our results for the first time generated genome-wide gene expression profiles both in the rat MI model and in acupuncture treatment by high throughput sequencing. The optimized data analysis workflows reported here should provide a framework for acupuncture investigations of expression profiles.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24722278" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54134" }, "primaryId" : "GEO:GSE54134", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54134" } ] }, "title" : "A network pharmacology study of Chinese Medicine QSYQ to reveal its underlying multi-compound, multi-target, multi-pathway mode of action", "dateAssigned" : "2014-01-16T00:00:00.000-06:00", "summary" : "Male Sprague Dawley rat model of myocardial infarction were administered QSYQ intragastrically for 7 days while the control group was not treated. The differentially expressed genes (DEGs) were identified from myocardial infarction rat model treated with QSYQ, followed by constructing a cardiovascular disease (CVD)-related multilevel compound-target-pathway network connecting main compounds to those DEGs supported by literature evidences and the pathways that are functionally enriched.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24817581" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54216" }, "primaryId" : "GEO:GSE54216", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54216" } ] }, "title" : "Expression data of articular and growth plate cartilage zones in 10-day-old rat proximal tibial epiphysis", "dateAssigned" : "2014-01-20T00:00:00.000-06:00", "summary" : "We found that many genes that were spatially upregulated in intermediate/deep zone of articular cartilage were also spatially upregulated in resting zone of growth plate cartilage (overlap greater than expected by chance, P < 0.001). Interestingly, superficial zone of articular cartilage showed an expression profile with similarities to both proliferative and hypertrophic zones of growth plate cartilage (P < 0.001 each). Additionally, significant numbers of known proliferative zone markers (3 out of 6) and hypertrophic zone markers (27 out of 126) were spatially upregulated in superficial zone compared to intermediate/deep zone (more than expected by chance, P < 0.001 each). In conclusion, we provide evidence that intermediate/deep zone of articular cartilage has a gene expression profile more similar to resting zone of growth plate cartilage, whereas superficial zone has a gene expression profile more similar to proliferative and hypertrophic zones.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25068449" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54294" }, "primaryId" : "GEO:GSE54294", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54294" } ] }, "title" : "Gene Expression Profiling of Peri-implant Healing of PLGA-Li+ Implants Suggests an Activated Wnt Signaling Pathway in vivo", "dateAssigned" : "2014-01-22T00:00:00.000-06:00", "summary" : "Bone development and regeneration is associated with the Wnt signaling pathway that, according to literature, can be modulated by lithium ions (Li+). The aim of this study was to evaluate the gene expression profile during peri-implant healing of poly(lactic-co-glycolic acid) (PLGA) implants with incorporated Li+, while PLGA without Li+ was used as control, and a special attention was then paid to the Wnt signaling pathway. The implants were inserted in rat tibia for 7 or 28 days and the gene expression profile was investigated using a genome-wide microarray analysis. The results were verified by qPCR and immunohistochemistry. Histomorphometry was used to evaluate the possible effect of Li+ on bone regeneration. The microarray analysis revealed a large number of significantly differentially regulated genes over time within the two implant groups. The Wnt signaling pathway was significantly affected by Li+, with approximately 34% of all Wnt-related markers regulated over time, compared to 22% for non-Li+ containing (control; Ctrl) implants. Functional cluster analysis indicated skeletal system morphogenesis, cartilage development and condensation as related to Li+. The downstream Wnt target gene, FOSL1, and the extracellular protein-encoding gene, ASPN, were significantly upregulated by Li+ compared with Ctrl. The presence of ß-catenin, FOSL1 and ASPN positive cells was confirmed around implants of both groups. Interestingly, a significantly reduced bone area was observed over time around both implant groups. The presence of periostin and calcitonin receptor-positive cells was observed at both time points. This study is to the best of the authors’ knowledge the first report evaluating the effect of a local release of Li+ from PLGA at the fracture site. The present study shows that during the current time frame and with the present dose of Li+ in PLGA implants, Li+ is not an enhancer of early bone growth, although it affects the Wnt signaling pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25047349" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54338" }, "primaryId" : "GEO:GSE54338", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54338" } ] }, "title" : "Expression of microRNAs in rat kidney treated with a carcinogenic dose of Aristolochic Acid", "dateAssigned" : "2014-01-23T00:00:00.000-06:00", "summary" : "Aristolochic Acid (AA), a natural component of Aristolochia plants found in a variety of herbal remedies and health supplements, is classified as a group 1 carcinogen by the International Agency for Research on Cancer. In order to search for miRNA regulation in AA-induced carcinogenesis, we treated rats with 10 mg/kg AA and vehicle control for 12 weeks and eight kidney samples (4 for the treatment and 4 for the control) were used for examining miRNA by deep sequencing.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54356" }, "primaryId" : "GEO:GSE54356", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54356" } ] }, "title" : "Gene regulation in denervated hairy skin of the adult rat", "dateAssigned" : "2014-01-23T00:00:00.000-06:00", "summary" : "This study aimed to quantify the regulation of transcripts in the hairy skin of the back of adult rats in the condition of loss of sensory and autonomic (sympathetic) innervation (i.e., denervated). Denervated skin has reduced wound healing capacity, reduced proliferation of epidermal progenitor cells, and also expresses factors that regulate ingrowth of sensory and sympathetic axons from neighboring regions of innervated skin. It was expected that this quantification f transcript regulation would offer insight into the general and specific mechanisms that may contribute to these important biological processes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24808906" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54413" }, "primaryId" : "GEO:GSE54413", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54413" } ] }, "title" : "Genome-wide Transcriptional Profiling of Skin and Dorsal Root Ganglia after Ultraviolet-B-Induced Inflammation", "dateAssigned" : "2014-01-27T00:00:00.000-06:00", "summary" : "Ultraviolet-B (UVB) irradiation of the skin was performed on rat (skin and DRG) and human (skin) tissue. The resulting changes in gene expression were then profiled by using RNA-seq to compare gene expression between irradiated and non-irradiated samples", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54584" }, "primaryId" : "GEO:GSE54584", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54584" } ] }, "title" : "Altered Gene Expression Profile in Ovarian Follicle in Rats Treated with Indomethacin and RU486", "dateAssigned" : "2014-01-31T00:00:00.000-06:00", "summary" : "It is well-known that indomethacin (the cyclooxygenase 1 & 2 inhibitor) and RU486 (or mifepristone, the progesterone receptor antagonist) block follicular rupture in rats. To characterize genetic alterations in unruptured follicles, gene expression profiles in ovarian follicle were analyzed in indomethacin- and RU486-treated female Sprague-Dawley rats. Ovaries are collected at 22:00 on the proestrus day and 10:00 on the following estrus day after a single dose of indomethacin and RU486. Histopathologically, changes depicting responses to LH surge were observed in ovaries, uteri and vagina. Total RNA was extracted from pre-ovulatory follicles or unruptured follicles collected by laser microdissection and analyzed by GeneChip. Among genes showing statistically significant changes compared to control groups, following changes were considered relevant to induction of unruptured follicles. In indomethacin-treated rats, Wnt4 was down-regulated, suggesting effect on tissue integrity and steroid genesis. In RU486-treated rats, Adamts1, Adamts9, Edn2, Ednra, Lyve1, Plat, and Pparg were down-regulated. These changes suggest effects on proteolysis for extracellular matrix or surrounding tissue (Adamts1 & 9, and Plat), constriction of smooth muscle surrounding follicles (Edn2, Ednra, and Pparg), follicular fluid (Lyve1), and angiogenesis (Pparg). Down-regulation of angiogenesis related genes (Angpt2, Hmox1, and Vegfa) was observed in both treatment groups. Here, we clarify genetic alterations induced by the inhibition of cyclooxygenase or progesterone receptor.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25972201" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54624" }, "primaryId" : "GEO:GSE54624", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54624" } ] }, "title" : "TGF-ß/Smad3 Stimulates Stem Cell/Developmental Gene Expression and Vascular Smooth Muscle Cell De-Differentiation", "dateAssigned" : "2014-02-03T00:00:00.000-06:00", "summary" : "More than 200 genes were differentially expressed (>2.0 fold change, p<0.05) in TGF-b/Smad3 stimulated SMCs. We then performed GO term enrichment analysis using the DAVID bioinformatics database and found that TGF-b/Smad3 activated the expression of multiple genes related to either development or cell differentiation, several of which have been shown to be associated with multipotent stem or progenitor cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54673" }, "primaryId" : "GEO:GSE54673", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54673" } ] }, "title" : "Bile acid flux is necessary for normal liver regeneration", "dateAssigned" : "2014-02-04T00:00:00.000-06:00", "summary" : "Bile acid return from the intestine and attendant signaling is necessary for liver regeneration after partial hepatectomy or CCl4 injury", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54714" }, "primaryId" : "GEO:GSE54714", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54714" } ] }, "title" : "Gene Expression of Kidney from FHH and Nr4a1 Deficient Rats", "dateAssigned" : "2014-02-05T00:00:00.000-06:00", "summary" : "Nr4a1 deficient rats (Nr4a1-/-) were developed using the fawn hooded hypertensive rat (FHH), which provided a genetic background susceptible to kidney injury. Both groups of animals were evaluated for blood pressure, proteinuria, renal function, and whole transcriptome gene pathway changes. Gene expression profiling was performed at week 8, 16, and 24 using kidney from FHH and Nr4a1-/- rats. To identify differentially expressed gene between FHH and Nr4a1-/- two statistical methods were utilized: (1) FWER (family-wise error rate) procedure, p<0.05 and fold-change ±1.2 or greater; and/or (2) Benjamani and Hochberg FDR (false discovery rate) using p<0.05, and fold-change ±1.2 or greater. Two-way ANOVA using a p<0.01 or lower was performed to identify strain X time interaction effects between groups. Gene networks and functional analysis were evaluated through the use of Ingenuity Pathways Analysis .", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24722447" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54897" }, "primaryId" : "GEO:GSE54897", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54897" } ] }, "title" : "Peripheral blood mononuclear cells gene expression reflects adaptive response and metabolic damage associated to the intake of diets with an unbalanced proportion of macronutrients", "dateAssigned" : "2014-02-11T00:00:00.000-06:00", "summary" : "Gene expression studies in peripheral blood mononuclear cells (PBMC) can provide knowledge that would be difficult to obtain using other types of biological samples, as these cells can reflect overall response of the body to a specific stimulus, such as diet. Here, we aimed to study the impact of sustained intake of isocaloric diets with an unbalanced macronutrient proportion (rich in fat or protein) on PBMC gene expression in rats using transcriptomics, to better understand the effects of these diets on metabolism and health. Macronutrient diet composition (especially increased protein content) affected PBMC gene expression. An important effect was observed in immune response-related genes. High protein (HP) diet produced an activation of genes mainly related to antigen recognition/presentation, whereas the high fat (HF) diet was more related to a decreased expression of these genes. Key energy homeostasis genes (mainly involved in lipid metabolism) were also affected, reflecting a nutritional adaptive response to the diets. Decreased Dhrs3 and increased Pref-1/Dlk1 expression observed in HP-fed animals reflects a lower lipogenic capacity. In addition, HF diet affected the expression of genes related to insulin resistance/signaling (Msra/Slc9a6, Asb6), hypoxia (Akap12), cardiovascular problems (Ethe1, Lr11), cognitive impairment (Tmcc2) and tumorigenesis (Ddx17, Phb, Rnasen/Drosha, and Tsc2). HP diet also impaired the expression of genes related to glucose metabolism and insulinemia (Glut-4/Slc2a4, Sfxn5, Slc16a1), but positively affected genes involved in liver function (Clec4f and St6galnac3) and cardiovascular protection (Sort1). In conclusion, gene expression analysis in PBMC can provide information that could be useful to detect metabolic deviations and health consequences of diets with an unbalanced macronutrient composition.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25660595" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54935" }, "primaryId" : "GEO:GSE54935", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54935" } ] }, "title" : "Gene expression profiles in heterogeneous stock rats that differ in glucose tolerance", "dateAssigned" : "2014-02-12T00:00:00.000-06:00", "summary" : "Using heterogeneous stock (HS) rats, we have identified a region on rat chromosome 1 that maps multiple diabetic traits. We sought to use global expression analysis to determine if genes within this region are differentially expressed between HS rats with normal glucose tolerance and those with glucose intolerance", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25236446" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54965" }, "primaryId" : "GEO:GSE54965", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE54965" } ] }, "title" : "Early gene expression in salivary gland after isoproterenol treatment", "dateAssigned" : "2014-02-13T00:00:00.000-06:00", "summary" : "Isoproterenol, a ß-adrenergic agonist, has been shown to induce salivary gland hyperplasia. To gain a better understanding of the underlying molecular changes altered by isoproterenol, microarray-based gene expression analysis was conducted on rat parotid glands at 10, 30, and 60 minutes after isoproterenol injection. After isoproterenol treatment, the number of differentially expressed genes was increased in a time-dependent manner. The regulation of up- and down-expression of genes related to cell proliferation/survival provides a better understanding of the mechanism of isoproterenol-induced parotid gland enlargement.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25336019" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55077" }, "primaryId" : "GEO:GSE55077", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55077" } ] }, "title" : "Nkx6.1 regulates islet ß-cell proliferation via Nr4a1 and Nr4a3 nuclear receptors", "dateAssigned" : "2014-02-17T00:00:00.000-06:00", "summary" : "Loss of functional ß-cell mass is a hallmark of Type 1 and Type 2 diabetes, and methods for restoring these cells are needed. We have previously reported that overexpression of the homeodomain transcription factor Nkx6.1 in rat pancreatic islets induces ß-cell proliferation and enhances glucose-stimulated insulin secretion, but the pathway by which Nkx6.1 activates ß-cell expansion has not been defined. Here we demonstrate that Nkx6.1 induces expression of the Nr4a1 and Nr4a3 orphan nuclear receptors, and that these factors are both necessary and sufficient for Nkx6.1-mediated ß-cell proliferation. Consistent with this finding, global knockout of Nr4a1 results in a decrease in ß-cell area in neonatal and young mice. Overexpression of Nkx6.1 and the Nr4a receptors results in increased expression of key cell cycle inducers E2F1 and cyclin E1. Furthermore, Nkx6.1 and Nr4a receptors induce components of the anaphase-promoting complex, including Ube2c, resulting in degradation of the cell cycle inhibitor p21CIP1. These studies identify a new bipartite pathway for activation of ß-cell proliferation, suggesting several new targets for expansion of functional ß-cell mass.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24706823" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55078" }, "primaryId" : "GEO:GSE55078", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55078" } ] }, "title" : "Nr4a1 and Nr4a3 upregulate cell cycle genes upregulated in the Nkx6.1 ß-cell proliferation pathway", "dateAssigned" : "2014-02-17T00:00:00.000-06:00", "summary" : "Loss of functional ß-cell mass is a hallmark of Type 1 and Type 2 diabetes, and methods for restoring these cells are needed. Nkx6.1 induces ß-cell proliferation, but the pathway by which Nkx6.1 activates ß-cell expansion has not been defined. Here we demonstrate that Nkx6.1 induces expression of the Nr4a1 and Nr4a3 orphan nuclear receptors, and that these factors are both necessary and sufficient for Nkx6.1-mediated ß-cell proliferation. Overexpression of the Nr4a receptors results in increased expression of key cell cycle inducers E2F1 and cyclin E1. Furthermore, Nr4a receptors induce components of the anaphase-promoting complex, including Ube2c.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24706823" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55088" }, "primaryId" : "GEO:GSE55088", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55088" } ] }, "title" : "miRNA expression data from callus in standard fracture healing models and from fibrous tissues in nonunion models in rats on post-fracture day 14", "dateAssigned" : "2014-02-18T00:00:00.000-06:00", "summary" : "Profiling of miRNA expressions comparing standard fracture healing models with nonunion models in rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26224835" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55142" }, "primaryId" : "GEO:GSE55142", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55142" } ] }, "title" : "Expression data from intestinal epithelium", "dateAssigned" : "2014-02-19T00:00:00.000-06:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying damage or protection effect and identified distinct classes of up-regulated or down-regulated genes during drinking different waters test in this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55243" }, "primaryId" : "GEO:GSE55243", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55243" } ] }, "title" : "Genomic Microarray of Rat Alveolar Type 2 cells Following Chronic Ethanol Ingestion", "dateAssigned" : "2014-02-21T00:00:00.000-06:00", "summary" : "Chronic alcohol ingestion changes the alveolar landscape. We used microarrays to characterize the change in mRNA expression following chronic alcohol ingestion in male Sprague Dawley rates (EtOH 36% of calories)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24682449" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55260" }, "primaryId" : "GEO:GSE55260", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55260" } ] }, "title" : "Identification of new therapeutic targets by genome-wide analysis of gene expression in the ipsilateral cortex of aged rats after stroke", "dateAssigned" : "2014-02-21T00:00:00.000-06:00", "summary" : "We employed the Affymetrix platform to analyze the whole-gene transcriptome following temporary ligation of the middle cerebral artery in aged and young rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23251410" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55347" }, "primaryId" : "GEO:GSE55347", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55347" } ] }, "title" : "SEQC Toxicogenomics Study: RNA-Seq data set", "dateAssigned" : "2014-02-25T00:00:00.000-06:00", "summary" : "The comparative advantages of RNA-Seq and microarrays in transcriptome profiling were evaluated in the context of a comprehensive study design. Gene expression data from Illumina RNA-Seq and Affymetrix microarrays were obtained from livers of rats exposed to 27 agents that comprised of seven modes of action (MOAs); they were split into training and test sets and verified with real time PCR.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25150839" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55352" }, "primaryId" : "GEO:GSE55352", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55352" } ] }, "title" : "Regional commonalities and specificities of age-related changes in hippocampal transcriptome.", "dateAssigned" : "2014-02-25T00:00:00.000-06:00", "summary" : "The project examined age-related change in hippocampal gene expression in Fisher 344 x Brown Norway F1 rats from the NIA aging colony (Adult = 12M, Aged = 24M). CA1, CA3, and DG specific dissections were examined from one cohort of animals and from a second cohort whole hippocampus was used.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24994846" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55369" }, "primaryId" : "GEO:GSE55369", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55369" } ] }, "title" : "Analysis of gene expression changes in amyloid-beta (ADDL) and CAT-SKL antioxidant treated primary rat neuronal cells", "dateAssigned" : "2014-02-26T00:00:00.000-06:00", "summary" : "Amyloid-beta (Aß)-induced neurotoxicity is a major contributor to the pathologies associated with Alzheimer’s disease (AD). The formation of reactive oxygen species (ROS), and early response induced by the Aß peptide, plays a significant role in effecting cellular pathogenesis. Here we apply a particularly effective form of exogenous Aß, i.e., amyloid beta-derived diffusible ligands (ADDLs), to cultured primary cortical/hippocampal neurons to elicit ROS and drive cellular dysfunction. To prevent and even reverse such effects, we employed a cell-penetrating, peroxisome-targeted, protein biologic - called CAT-SKL. We show the recombinant enzyme enters neurons, reverses Aß-induced oxidative stress, and increases cell viability. Dramatic restorative effects on damaged neuronal processes were also observed. CAT-SKL, a targeted antioxidant, may represent a new therapeutic approach for treatment disorders, like Alzheimer’s disease, where oxidative stress is manifest. Preclinical testing is warranted and ongoing", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24828380" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55378" }, "primaryId" : "GEO:GSE55378", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55378" } ] }, "title" : "A diet enriched with biologically active substances as a protecting factor against carcinogenesis process induced by 1,2-dimethylhydrazine in rat liver", "dateAssigned" : "2014-02-26T00:00:00.000-06:00", "summary" : "The aim of this study was to evaluate the ability of a diet enriched with biologically active compounds to protect against 1,2-dimethylhydrazine - induced carcinogenesis in 14-month old rats liver.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55384" }, "primaryId" : "GEO:GSE55384", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55384" } ] }, "title" : "Early Leptin Intervention Reverses Perturbed Energy Balance Regulating Hypothalamic Neuropeptides in the Pre- and Postnatal Calorie Restricted Offspring", "dateAssigned" : "2014-02-26T00:00:00.000-06:00", "summary" : "Pre- and postnatal calorie restriction is associated with postnatal growth restriction, reduced circulating leptin concentrations and perturbed energy balance. Hypothalamic regulation of energy balance demonstrates enhanced orexigenic (NPY, AgRP) and diminished anorexigenic (POMC, CART) neuropeptide expression (PN21) setting the stage for subsequent development of obesity. Leptin replenishment during the early postnatal period (PN2-PN8) led to reversing the hypothalamic orexigenic:anorexigenic neuropeptide ratio at PN21 by only reducing the orexigenic (NPY, AgRP) without affecting the anorexigenic (POMC, CART) neuropeptide expression. This hypothalamic effect was mediated via enhanced leptin receptor (ObRb) signaling that involved increased pSTAT3 but reduced PTP1B. This was further confirmed by an increase in body weight at PN21 in response to intracerebroventricular administration of antisense ObRb oligonucleotides (PN2-PN8). The change in the hypothalamic neuropeptide balance in response to leptin administration caused increased oxygen consumption, carbon dioxide production and physical activity which resulted in increased milk intake (PN14) with no change in body weight. This is in contrast to the reduction in milk intake with no effect on energy expenditure and physical activity observed in controls. We conclude that pre- and postnatal calorie restriction perturbs hypothalamic neuropeptide regulation of energy balance setting the stage for hyperphagia and reduced energy expenditure, hallmarks of obesity. Leptin in turn reverses this phenotype by increasing hypothalamic ObRb signaling (sensitivity) and affecting only the orexigenic arm of the neuropeptide balance.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55434" }, "primaryId" : "GEO:GSE55434", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55434" } ] }, "title" : "Expression data from rat hepatocyte during liver regeneration after partial hepatectomy", "dateAssigned" : "2014-02-27T00:00:00.000-06:00", "summary" : "We used microarrays to further highlight the regulatory role of hepatocyte in liver regeneration at gene transcription level.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55573" }, "primaryId" : "GEO:GSE55573", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55573" } ] }, "title" : "Using DNA microarray to screen intracellular signal pathways of hypoglycemic activity by electroacupuncture of Zusanli (ST36) acupoints in streptozotocin-induced rats with diabetes", "dateAssigned" : "2014-03-04T00:00:00.000-06:00", "summary" : "The aim of this study is to screen the possible effective intracellular signaling pathways of EA on bilateral Zusanli acupoint (ST36) by DNA microarray in rats with diabetes. Streptozotocin (STZ) rats with diabetes were randomly assigned to the experimental (EA) group or the control (non-EA) group. The exploratory methods for analysis in this study were the following points: (i) detecting plasma glucose levels (ii) pathway analysis by DNA microarray in rats' gastrocnemius muscle. The pathway analysis of DNA microarray showed that the insulin signaling pathway, PPAR signaling pathway, MAPK signaling pathway or Wnt signal pathway might be related to the hypoglycemic effect of STZ rats with diabetes induced by EA. Using DNA microarray would be helpful in screening the possible targets of signaling pathways. The hypoglycemic effect of EA was close relative to insulin and relative intracellular signal pathways. Further research will be required to determine the details of the intracellular signaling pathways of the hypoglycemic effect induced by EA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26025382" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55612" }, "primaryId" : "GEO:GSE55612", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55612" } ] }, "title" : "Differential gene expression is not correlated to age-related vascular pathology in aorta and mesenteric artery of Brown Norway and Fischer344xBrown Norway rats", "dateAssigned" : "2014-03-05T00:00:00.000-06:00", "summary" : "Customized therapies for vascular disease will require matching the vessel type and genetic background of the patient. Our previous studies showed that progressive age-related vascular pathology is strain specific in the thoracic aorta (TA) and mesenteric arteries (MA) of the Brown Norway (BN) and the Fisher344/Brown Norway F1 hybrid (F1) rats. The purpose of this study was to identify novel genetic pathways associated with successful and/or unsuccessful vascular aging. TA and MA were collected from anesthetized 6, 15 and 24 month old age-matched F1 and BN rats for total RNA isolation. The gene microarrays were generated using the Affimetrix GeneChip Rat Expression 230A Array. Gene expression data was analyzed with the Ingenuity Pathway Analysis and proprietary software. Despite more pronounced age-related vascular pathology in the F1 strain, more genes were differentially expressed in the BN strain during aging. A sample of common key genes (KLB1, TRIO, HLA-C and PCP4) showed similar expression at 6 and 15 months and downregulation at 24 months in F1 vs. upregulation in BN rats. Among the top 50 canonical pathways there was only a 10 and 30% overlap, respectively, between the F1 and BN strains in MA and TA. Most of the overexpressed molecules associated with the same vascular-related biological functions are different between strains. The data suggest that age-related vascular pathology and decrement in function is both strain and vessel-dependent and different genetic programs could be employed to accomplish both normal and pathological physiological processes in conduit and resistance arteries.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55777" }, "primaryId" : "GEO:GSE55777", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55777" } ] }, "title" : "Hippocampal neurons, nylon-1 experiments", "dateAssigned" : "2014-03-11T00:00:00.000-05:00", "summary" : "Ongoing neuronal activity during development and plasticity acts to refine synaptic connections and contributes to the induction of plasticity and ultimately long term memory storage. Activity-dependent post-transcriptional control of mRNAs occurs through transport to axonal and dendritic compartments, local translation, and mRNA stability. We have identified a mechanism that contributes to activity-dependent regulation of mRNA stability during synaptic plasticity. In this study we demonstrate rapid, post-transtriptional control over process-enriched mRNAs by neuronal activity. Systematic analysis of the 3'-UTRs of destablized transcripts, identifies enrichment in sequence motifs corresponding to miRNA binding sites. The miRNAs that were identified, miR-326-3p/miR-330-5p, miR-485-5p, miR-666-3p, and miR-761 are predicted to regulate networks of genes important in plasticity and development. We find that these miRNAs are developmentally regulated in the hippocampus, many increasing by postnatal day 14. We further show that miR-485-5p controls NGF-induced neurite outgrowth in PC12 cells, tau expression, and axonal development in hippocampal neurons. miRNAs can function at the synapse to rapidly control and affect short- and long-term changes at the synapse. These processes likely occur during refinement of synaptic connections and contribute to the induction of plasticity and learning and memory.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25135970" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55778" }, "primaryId" : "GEO:GSE55778", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55778" } ] }, "title" : "Hippocampal neurons, nylon-2 experiments", "dateAssigned" : "2014-03-11T00:00:00.000-05:00", "summary" : "Ongoing neuronal activity during development and plasticity acts to refine synaptic connections and contributes to the induction of plasticity and ultimately long term memory storage. Activity-dependent post-transcriptional control of mRNAs occurs through transport to axonal and dendritic compartments, local translation, and mRNA stability. We have identified a mechanism that contributes to activity-dependent regulation of mRNA stability during synaptic plasticity. In this study we demonstrate rapid, post-transtriptional control over process-enriched mRNAs by neuronal activity. Systematic analysis of the 3'-UTRs of destablized transcripts, identifies enrichment in sequence motifs corresponding to miRNA binding sites. The miRNAs that were identified, miR-326-3p/miR-330-5p, miR-485-5p, miR-666-3p, and miR-761 are predicted to regulate networks of genes important in plasticity and development. We find that these miRNAs are developmentally regulated in the hippocampus, many increasing by postnatal day 14. We further show that miR-485-5p controls NGF-induced neurite outgrowth in PC12 cells, tau expression, and axonal development in hippocampal neurons. miRNAs can function at the synapse to rapidly control and affect short- and long-term changes at the synapse. These processes likely occur during refinement of synaptic connections and contribute to the induction of plasticity and learning and memory.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25135970" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55780" }, "primaryId" : "GEO:GSE55780", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55780" } ] }, "title" : "Hippocampal neurons, Illumina experiments", "dateAssigned" : "2014-03-11T00:00:00.000-05:00", "summary" : "Ongoing neuronal activity during development and plasticity acts to refine synaptic connections and contributes to the induction of plasticity and ultimately long term memory storage. Activity-dependent post-transcriptional control of mRNAs occurs through transport to axonal and dendritic compartments, local translation, and mRNA stability. We have identified a mechanism that contributes to activity-dependent regulation of mRNA stability during synaptic plasticity. In this study we demonstrate rapid, post-transtriptional control over process-enriched mRNAs by neuronal activity. Systematic analysis of the 3'-UTRs of destablized transcripts, identifies enrichment in sequence motifs corresponding to miRNA binding sites. The miRNAs that were identified, miR-326-3p/miR-330-5p, miR-485-5p, miR-666-3p, and miR-761 are predicted to regulate networks of genes important in plasticity and development. We find that these miRNAs are developmentally regulated in the hippocampus, many increasing by postnatal day 14. We further show that miR-485-5p controls NGF-induced neurite outgrowth in PC12 cells, tau expression, and axonal development in hippocampal neurons. miRNAs can function at the synapse to rapidly control and affect short- and long-term changes at the synapse. These processes likely occur during refinement of synaptic connections and contribute to the induction of plasticity and learning and memory.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25135970" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55783" }, "primaryId" : "GEO:GSE55783", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55783" } ] }, "title" : "Timed regulation of Piwi-interacting RNAs expression during rat liver regeneration", "dateAssigned" : "2014-03-11T00:00:00.000-05:00", "summary" : "Small noncoding (snc) RNAs represent a growing family of transcripts that regulate key cellular processes, including mRNA degradation, translational repression and transcriptional gene silencing. Among these, the PIWI-interacting RNAs (piRNAs), a major class of sncRNAs initially identified in the germline of a variety of species, are now being found to be functionally active also in somatic cells. However, whether the Piwi/piRNA pathway is associated with fundamental biological processes, such as cell cycle progression, remains elusive. Here we investigated the possibility that piRNAs are expressed in liver and modulated during regenerative proliferation of this organ. To this aim, smallRNA-Seq was applied to identify and quantitate expression of these RNAs in rat liver before, during and after the wave of cell proliferation that follows partial hepatectomy (PH). Q-PCR analysis revealed the presence in rat liver of two PIWI (PIWI-Like) subfamily members (PIWIL2/HILI and, to a much lower level, PIWIL4/HIWI2) and other components of the piRNA biogenesis pathways, suggesting that this is present and functional in hepatocytes. Indeed, ~1400 piRNAs originally identified in rat and other mammalian germline cells are expressed in adult rat liver, including 72 that show timed changes in expression during cell cycle progression. Most piRNAs are up-regulated 24-48h after hepatectomy, a timing that corresponds to cell transition through the S phase, and return to basal levels by 168 h, when organ regeneration is completed and hepatocytes reach quiescence. These results indicate that the piRNA pathway is active in somatic cells and, more important, that it is subject to regulation during physiological processes, such as cell proliferation, when piRNAs may exert their regulatory functions on the cell genome and transcriptome.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24930433" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55803" }, "primaryId" : "GEO:GSE55803", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55803" } ] }, "title" : "Rat hypothalamus: Methimazole (MMI)-saline vs MMI-T3", "dateAssigned" : "2014-03-11T00:00:00.000-05:00", "summary" : "Sprague Dawley rats rendered hypothyroid with 22 days of MMI treatment with half the receiving T3 injection on day 21. Rats killed 24h later and hypothalamic tissue recovered.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55842" }, "primaryId" : "GEO:GSE55842", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55842" } ] }, "title" : "Gene expression analysis of eight-cell stage rat embryos sired by paternally exposed males to saline or BEP", "dateAssigned" : "2014-03-12T00:00:00.000-05:00", "summary" : "8-cell stage rat embryos were sired by males treated with saline or a chemotherapeutic cocktail, BEP, consisting of Bleomycin, Etoposide, and Cisplatin for 9 weeks. Animals were given an additional 9 weeks of recovery, without any treatment, prior to mating.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24478030" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55885" }, "primaryId" : "GEO:GSE55885", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55885" } ] }, "title" : "The identification of putative circulating miRNA biomarkers of Thioacetamide-induced hepatotoxicity.", "dateAssigned" : "2014-03-13T00:00:00.000-05:00", "summary" : "miRNA microarray profiling of RNA extracted from the plasma of rats treated with Thioacetamide revealed that a subset of miRNAs were differentially expressed following treatment. These miRNAs appeared to mediate pathways involved in hepatic fibrosis and stellate cell activation, suggesting that they might function as predictive biomarkers following compound-induced hepatotoxicity. The changes correlated well with increases in ALT levels, which are the current gold standard method for determining the extent of liver injury. Furthermore, it is hypothesised that particular aetiologies of liver damage might cause differing expression profiles of miRNAs, thus certain miRNAs could be implemented in a panel-type expression study to distinguish between different types of hepatic injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55895" }, "primaryId" : "GEO:GSE55895", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55895" } ] }, "title" : "Profiling of copy-number variation in tumors from heterozygous and homozygous Tp53C273X knockout rats", "dateAssigned" : "2014-03-13T00:00:00.000-05:00", "summary" : "We used Nimblegen HD aCGH to detect copy-number variants between tumor and ear control-DNA samples from heterozygous and homozygous Tp53C273X knockout rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25811670" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55992" }, "primaryId" : "GEO:GSE55992", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE55992" } ] }, "title" : "Gene expression of rat uterine endometrial stromal cells treated with ethanol (vehicle) or 0.1 nM progestin R5020", "dateAssigned" : "2014-03-18T00:00:00.000-05:00", "summary" : "Although non-genomic steroid receptor pathways have been studied over the past decade, little is known about the direct gene expression changes that take place as a consequence of their activation. Progesterone controls proliferation of rat endometrial stromal cells during the peri-implantation phase of pregnancy. We showed that picomolar concentration of progestin R5020 mimics this control in UIII endometrial stromal cells via ERK1-2 and AKT activation mediated by interaction of Progesterone Receptor (PR) with Estrogen Receptor beta (ERb) and without transcriptional activity of endogenous PR and ER. Here we identify early downstream targets of cytoplasmic PR signaling and their possible role in endometrial stromal cell proliferation. Microarray analysis of global gene expression changes in UIII cells treated for 45 min with progestin identified 97 up- and 341 down-regulated genes. The most over-represented molecular functions were transcription factors and regulatory factors associated with cell proliferation and cell cycle, a large fraction of which were repressors down-regulated by hormone. Further analysis verified that progestins regulate Ccnd1, JunD, Usf1, Gfi1, Cyr61, and Cdkn1b through PR-mediated activation of ligand-free ER, ERK1-2 or AKT, in the absence of genomic PR binding. ChIP experiments show that progestin promoted the interaction of USF1 with the proximal promoter of the Cdc2 gene, and Usf1 knockdown abrogated Cdc2 progestin-dependent transcriptional regulation providing a mechanism for direct regulation of its expression. Finally, Cdc2 knockdown blocked R5020 induced UIII cell proliferation. We conclude that progestin induced proliferation of endometrial stromal cells requires ERK1-2 and AKT mediated early regulation of USF1, that induces Cdc2. To our knowledge, this is the first description of early target genes of progestin-activated classical PR via crosstalk with protein kinases and independently of hormone receptor binding to the genomic targets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24859236" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56028" }, "primaryId" : "GEO:GSE56028", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56028" } ] }, "title" : "Molecular regulation in the hippocampal dentate gyrus in the onset and treatment of depression", "dateAssigned" : "2014-03-19T00:00:00.000-05:00", "summary" : "Using the unpredictable chronic mild stress (uCMS) animal model of depression, the molecular commonalities and specificities of the ADs were determined. All ADs, except agomelatine, could reverse the behavioral deficits produced by uCMS, and the neuroplastic changes in the DG; agomelatine reversed only the anhedonic profile in the sucrose consumption test. Chronic stress induced mild but relevant molecular changes that were mostly reversed by fluoxetine, imipramine and tianeptine. Fluoxetine reduced pro-inflammatory response and increased cell metabolism pathways. Its actions were mostly dependent on molecular changes occurring in neurons. Similarities were found between imipramine and tianeptine molecular actions and targets, as both activated pathways related to cellular protection. Moreover, no particular neural cell type enrichment was found with both treatments. Agomelatine presented a very dissimilar molecular pattern impacting greatly on Rho-GTPases-related pathways in oligodendrocytes and neurons. The recognition of these molecular alterations contributes to the understanding of the processes implicated in the onset and treatment of depression and may pave the way for more effective therapeutic interventions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25035085" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56071" }, "primaryId" : "GEO:GSE56071", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56071" } ] }, "title" : "Rat liver tissue: IR vs. iPoC", "dateAssigned" : "2014-03-20T00:00:00.000-05:00", "summary" : "microRNAs expression of rat liver tissue comparing ischemia-reperfusion (IR) group with ischemic postconditioning(iPoC) group", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56113" }, "primaryId" : "GEO:GSE56113", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56113" } ] }, "title" : "Superiority of spatially fractionated over broad beam synchrotron radiotherapy", "dateAssigned" : "2014-03-21T00:00:00.000-05:00", "summary" : "Transcriptomic response of tumoral and normal brain tissue, treated with the MRT irradiation or the BB irradiation, after 6 h, 48 h, 8 days, 15 days, using Affymetrix GeneChip® Rat 230_ 2.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56166" }, "primaryId" : "GEO:GSE56166", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56166" } ] }, "title" : "Expression data from liver of young and old rats fed on different dietary fat sources, namely virgin olive, sunflower or fish oils", "dateAssigned" : "2014-03-25T00:00:00.000-05:00", "summary" : "We used microarrays to detail the changes in gene expression provides by feeding lifelong on different dietary fat sources, and identified distinct classes of up and down-regulated genes during aging under different dietary conditions.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56238" }, "primaryId" : "GEO:GSE56238", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56238" } ] }, "title" : "Peri-adolescent high-fructose diet effects on hypothalamic transcriptome", "dateAssigned" : "2014-03-26T00:00:00.000-05:00", "summary" : "Fructose consumption has increased by over 25% since 1970, and excess consumption has deleterious metabolic effects. Additionally, fructose can alter hypothalamic pituitary adrenal axis function, potentially resulting in increased vulnerability to mood disorders. Adolescents are the greatest consumers of fructose and also at a critical period of development. Here, we examine the effects of consumption of a 55% fructose diet from weaning until adulthood on the hypothalamic transcriptome.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26356038" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56246" }, "primaryId" : "GEO:GSE56246", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56246" } ] }, "title" : "Dectin-1-mediated signaling leads to characteristic gene expressions in rat mast cells", "dateAssigned" : "2014-03-26T00:00:00.000-05:00", "summary" : "Dectin-1-mediated signaling stimulated characteristic gene expression, such as MCP-1, IL-4, IL-13, TNF-aand Nfkbiz.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25246527" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56263" }, "primaryId" : "GEO:GSE56263", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56263" } ] }, "title" : "Matrine derivative 1b(MASM) offers radioprotection and modulates acute lethal total-body irradiation-induced alterations of gene expression", "dateAssigned" : "2014-03-27T00:00:00.000-05:00", "summary" : "Pathway enrichment analysis indicated that these genes were mainly involved in a total of 21 pathways, such as metabolic pathways, pathways in cancer, and MAPK signaling pathway.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56289" }, "primaryId" : "GEO:GSE56289", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56289" } ] }, "title" : "Rat ventral prostate gland gene profile after androgen deprivation", "dateAssigned" : "2014-03-27T00:00:00.000-05:00", "summary" : "The microarray approach was done to figure out what genes are expressed and how the cells of ventral prostate gland responses when the androgen is not available comparing three diferent androgen deprivation methods (sirurgical castration, high dose of 17-beta estradiol and both treatment combined).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56300" }, "primaryId" : "GEO:GSE56300", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56300" } ] }, "title" : "Distinctive Profile of IsomiR Expression and Novel MicroRNAs in Rat Heart Left Ventricle", "dateAssigned" : "2014-03-27T00:00:00.000-05:00", "summary" : "MicroRNAs (miRNAs) are single-stranded non-coding RNAs that negatively regulate target gene expression through mRNA cleavage or translational repression. There is mounting evidence that they play critical roles in heart disease. The expression of known miRNAs in the heart has been studied at length by microarray and quantitative PCR but it is becoming evident that microRNA isoforms (isomiRs) are potentially physiologically important. It is well known that left ventricular (patho)physiology is influenced by transmural heterogeneity of cardiomyocyte phenotype, and this likely reflects underlying heterogeneity of gene expression. Given the significant role of miRNAs in regulating gene expression, knowledge of how the miRNA profile varies across the ventricular wall will be crucial to better understand the mechanisms governing transmural physiological heterogeneity. To determinine miRNA/isomiR expression profiles in the rat heart we investigated tissue from different locations across the left ventricular wall using deep sequencing. We detected significant quantities of 145 known rat miRNAs and 68 potential novel orthologs of known miRNAs, in mature, mature* and isomiR formation. Many isomiRs were detected at a higher frequency than their canonical sequence in miRBase and have different predicted targets. The most common miR-133a isomiR was more effective at targeting a construct containing a sequence from the gelsolin gene than was canonical miR-133a, as determined by dual-fluorescence assay. We identified a novel rat miR-1 homolog from a second miR-1 gene; and a novel rat miRNA similar to miR-676. We also cloned and sequenced the rat miR-486 gene which is not in miRBase (v18). Signalling pathways predicted to be targeted by the most highly detected miRNAs include Ubiquitin-mediated Proteolysis, Mitogen-Activated Protein Kinase, Regulation of Actin Cytoskeleton, Wnt signalling, Calcium Signalling, Gap junctions and Arrhythmogenic Right Ventricular Cardiomyopathy. Most miRNAs are not expressed in a gradient across the ventricular wall, with exceptions including miR-10b, miR-21, miR-99b and miR-486.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23799049" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56516" }, "primaryId" : "GEO:GSE56516", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56516" } ] }, "title" : "Gut microbiome metabolites alter genomic networks in PC12 cells relevant to autism spectrum diorders", "dateAssigned" : "2014-04-04T00:00:00.000-05:00", "summary" : "Alterations in the composition of the gut microbiome have an emerging role in brain function and behaviour. We have porposed that short chain fatty acids (SCFA) including propionate and butyrate which are present in the diet and are fermantation products of many gastrointestinal bacteria are contributing environmental factors in autism spectrum disorders (ASD). Here we used the microarray technology to compare global changes in gene expression profiles following exposure of PC12 cells to structurally related SCFA propionate and butyrate each in two different concentrations. Large number of affected genes, common for both SCFA were identified, including genetic networks and GO processes implicated in ASD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25170769" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56533" }, "primaryId" : "GEO:GSE56533", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56533" } ] }, "title" : "Scgb1a1, Lpo and Gbp2 is Characteristically Expressed in Rat Peri-Implant Epithelium.", "dateAssigned" : "2014-04-07T00:00:00.000-05:00", "summary" : "The peri-implant epithelium plays an important role in the prevention against initial stage of inflammation. In order to minimize the risk of peri-implantitis, it is necessary to understand the biological characteristics of the peri-implant epithelium. The aim of this study was to investigate the characteristic gene expression profile of peri-implant epithelium as compared to junctional epithelium using laser microdissection and microarray analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56638" }, "primaryId" : "GEO:GSE56638", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56638" } ] }, "title" : "Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation", "dateAssigned" : "2014-04-09T00:00:00.000-05:00", "summary" : "We present high quality deep read-depth single cell RNA sequencing for 91 cells from five mouse tissues and 18 cells from two rat tissues, along with 30 control samples of bulk RNA diluted to single-cell levels. We find that transcriptomes differ globally across tissues with regard to the number of genes expressed, the average expression patterns, and within cell-type variation patterns. We develop methods to filter genes for reliable quantification and to calibrate biological variation. All cell types include genes with high variability in expression, in a tissue-specific manner. We also find evidence that single cell variability of neuronal genes in mice is correlated with that in rats consistent with the hypothesis that levels of variation may be conserved.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26056000" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56666" }, "primaryId" : "GEO:GSE56666", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56666" } ] }, "title" : "Genetic Diversity Influences the Response of the Brain to Developmental Lead Exposure.", "dateAssigned" : "2014-04-09T00:00:00.000-05:00", "summary" : "In this study we analyzed the effects of lead-exposure up hippocampal gene expression in males and females exposed to 0ppm, 250ppm and 750ppm lead during two different developmental periods, perinatal (in utero through to weaning at PND21) and postnatal (PND0-PND45), across three strains (Fischer, Long Evans and Sprague Dawley). All tissue was taken at PND 55. We used affymetrix Rat Gene 1.0ST arrays to obtain global gene expression data from each animal, with a group size of 4 for all conditions (Total number of Arrays = 119)", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56740" }, "primaryId" : "GEO:GSE56740", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56740" } ] }, "title" : "Patterns of gene expression associated with recovery and injury in heat-stressed rats", "dateAssigned" : "2014-04-11T00:00:00.000-05:00", "summary" : "Conclusions: Global transcriptomic and proteomic analysis identified networks of genes and proteins initiating an unfolded protein response, metabolic dysfunction, and mitochondrial energy crisis in animals with histopathologic evidence of persistent heat injury, providing the basis for a systems-level physiological model of heat illness and recovery.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25471284" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56743" }, "primaryId" : "GEO:GSE56743", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56743" } ] }, "title" : "RNA-seq profiling of microdissected rat renal tubule segments", "dateAssigned" : "2014-04-11T00:00:00.000-05:00", "summary" : "We sequenced mRNAs from glomeruli and 14 different rat renal tubule segments collected by hand microdissection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25817355" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56951" }, "primaryId" : "GEO:GSE56951", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56951" } ] }, "title" : "Regulation of gene expression by Set-beta in rat retinal ganglion cells", "dateAssigned" : "2014-04-21T00:00:00.000-05:00", "summary" : "The goal of this experiment was to investigate the molecular mechanism of how Set-beta regulates neurite growth. Set-beta’s subcellular localization is regulated by posttranslational modifications. We found that Set-beta suppresses neurite growth of purified postnatal rat retinal ganglion cell (RGC) primary neurons when it is overexpressed in the nucleus, whereas recruiting Set-beta to cellular membrane by fusing myr-tag to its N-terminus promotes neurite growth. Here, we transfected purified by immunopanning postnatal rat RGC with wild-type Set-beta which localizes to the nucleus, myr-Set-beta which is recruited to cellular membranes, and mCherry control, and analyzed with microarrays Set-beta’s subcellular localization-dependent effects on gene expression. We found that wild-type Set-ß regulated expression of significantly more genes than myr-Set-ß, consistent with wild-type Set-ß’s nuclear localization and previously described roles in regulating transcription. These data reveal potential downstream gene effectors regulating neurite growth, and specific candidate genes could be validated and tested in future experiments.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24849368" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56956" }, "primaryId" : "GEO:GSE56956", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE56956" } ] }, "title" : "Expression analysis of genes in Rattus norvegicus lungs at postnatal day 4, 10 and 21 after intrauterine growth restriction induced by low protein diet", "dateAssigned" : "2014-04-22T00:00:00.000-05:00", "summary" : "We performed RNA microarray in a low protein diet (LPD) model of IUGR at three key time points of alveolarization process. IUGR and control rat pups had been studied for each time point considered: on postnatal day 4 (P4) before beginning of the alveolarization process, on P10, peak of alveolarization process and on P21 at the end of it.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25347958" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57005" }, "primaryId" : "GEO:GSE57005", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57005" } ] }, "title" : "EWAT transcriptomic analysis in male rat offspring of HF-fed dams treated with GSPE or vehicle during pregnancy and lactation", "dateAssigned" : "2014-04-23T00:00:00.000-05:00", "summary" : "Objective: Procyanidins are polyphenolic bioactive compounds that exert beneficial effects against obesity and its related diseases. The aim of this study was to evaluate whether the supplementation with low doses of a grape seed procyanidin extract (GSPE) to dams during pre and postnatal periods has biological effects on their offspring at youth. Design: The metabolic imprinting effect of GSPE was evaluated in 30 days-old male offspring of four groups of rats that were fed either a standard diet (STD) or a high-fat diet (HFD) and supplemented with either GSPE at 25 mg per kg of body weight/day or vehicle during pregnancy and lactation. Results: A significant increase in the adiposity index and in the weight of all the white adipose tissue depots studied (retroperitoneal –RWAT-, mesenteric –MWAT-, epididymal –EWAT- and inguinal –IWAT-) was observed in offspring of dams fed with a HFD and treated with GSPE (HFT group), compared to the offspring of dams fed with the same diet and that do not received procyanidins (HF group). HFT animals also showed a higher number of cells in the EWAT, a sharply decrease of the circulating levels of monocyte chemoattractant protein-1 (MCP-1) as well as a moderate, but significant, decrease of plasma glycerol levels. The transcriptomic analysis performed in the EWAT showed 238 genes differentially expressed between HF and HFT animals, covering an entire range of processes related with the immune function and the inflammatory response (the metabolic pathway mainly reflected in the EWAT), adipose tissue remodeling and function, lipid and glucose homeostasis and metabolism of methyl groups. Conclusion: GSPE treatment to dams fed a HFD during pregnancy and lactation increases adiposity, decreases the circulating levels of MCP-1 and modulates the expression of key genes involved in the adipose tissue metabolism of their offspring.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57011" }, "primaryId" : "GEO:GSE57011", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57011" } ] }, "title" : "Gene expression profiles in rat Acute Respiratory Distress Syndrome (ARDS)", "dateAssigned" : "2014-04-23T00:00:00.000-05:00", "summary" : "Rat model of ARDS was induced by saline lavage and mechanical ventilation. Total RNA from rat lungs were used for dual color DNA microarray hybridization with 3DNA 50 kit version 2.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25070658" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57066" }, "primaryId" : "GEO:GSE57066", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57066" } ] }, "title" : "Genome-wide analysis of perinatal effect of NF-kabbaB inhibition by pyrrolidine dithiocarbamate (PDTC) on the kidneys of Fawn-Hooded Hypertensive (FHH) rats at ages 2 days, 2 weeks and adult", "dateAssigned" : "2014-04-24T00:00:00.000-05:00", "summary" : "Microarray was performed on kidneys of Fawn-Hooded Hypertensive (FHH) rats in order to elucidate the so-called \"beneficial\" effect of perinatal treatment with PDTC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25958302" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57110" }, "primaryId" : "GEO:GSE57110", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57110" } ] }, "title" : "Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging ", "dateAssigned" : "2014-04-25T00:00:00.000-05:00", "summary" : "Using RNA-seq, 39 cerebral cortex RNA samples were sequenced. The study design was as follows: Ad libitum fed rats at 6 months (n=3, 6 individuals pooled), 12 months (n=3, 6 individuals pooled) and 28 months (n=3, 6 individuals pooled). Calorie restricted rats at 6 months (n=3, 6 individuals pooled), 12 months (n=3, 6 individuals pooled) and 28 months (n=3, 6 individuals pooled). Rats fed alpha lipoic acid as a supplement to ad libitum at 12 months (n=3, 6 individuals pooled) and 28 months (n=3, 6 individuals pooled). Diet switching groups, where diet was changes at 12 months; 28 month ad libitum switched to calorie restriction (n=3, 6 individuals pooled), 28 month calorie restriction switched to ad libitum (n=3, 6 individuals pooled), 28 month ad libitum plus lipoic acid switched to calorie restriction (n=3, 6 individuals pooled), 28 month calorie restriction switched to ad libitum plus lipoic acid (n=3, 6 individuals pooled).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26694192" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57117" }, "primaryId" : "GEO:GSE57117", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57117" } ] }, "title" : "Genome-wide 10K SNP profiles in heterogeneous stock rats that differ in glucose tolerance", "dateAssigned" : "2014-04-26T00:00:00.000-05:00", "summary" : "Using heterogeneous stock (HS) rats, we have identified a region on rat chromosome 1 that maps multiple diabetic traits. We sought to use global expression analysis to determine if genes within this region are differentially expressed between HS rats with normal glucose tolerance and those with glucose intolerance", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25236446" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57223" }, "primaryId" : "GEO:GSE57223", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57223" } ] }, "title" : "miRNA expression profiles in rat Acute Respiratory Distress Syndrome (ARDS)", "dateAssigned" : "2014-04-30T00:00:00.000-05:00", "summary" : "Rat model of ARDS was induced by saline lavage and mechanical ventilation. miRNA from rat lungs were used for dual color DNA microarray hybridization with 3DNA 50 kit version 2.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25070658" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57232" }, "primaryId" : "GEO:GSE57232", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57232" } ] }, "title" : "ChIP-seq experiment analyzing binding of HDAC2 and HDAC3 to genomic loci in rat Neural Stem Cells", "dateAssigned" : "2014-05-01T00:00:00.000-05:00", "summary" : "Binding of HDAC2 and HDAC3 was assayed using antibodies SC-7899x and SC-11417x", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25241747" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57377" }, "primaryId" : "GEO:GSE57377", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57377" } ] }, "title" : "mRNA-seq analysis of superficial zone (SFZ) and deeper layers (deep AC) of articular cartilage of adult rats", "dateAssigned" : "2014-05-07T00:00:00.000-05:00", "summary" : "We compared gene expression profiles of SFZ and deep AC of articular cartilage through laser microdissection (LMD) using adhesive tape, linear amplification of mRNA, and mRNA-seq analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25152035" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57505" }, "primaryId" : "GEO:GSE57505", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57505" } ] }, "title" : "Direct genesis of functional rodent and human Schwann cells from skin mesenchymal precursors (rat)", "dateAssigned" : "2014-05-09T00:00:00.000-05:00", "summary" : "Recent reports of directed reprogramming have raised questions about the stability of cell lineages. Here, we have addressed this issue, focusing upon skin-derived precursors (SKPs), a dermally-derived precursor cell. We show by lineage tracing that murine SKPs from dorsal skin originate from mesenchymal and not neural crest-derived cells. These mesenchymally-derived SKPs can, without genetic manipulation, generate functional Schwann cells, a neural crest cell type, and are highly similar at the transcriptional level to Schwann cells isolated from the peripheral nerve. This is not a mouse-specific phenomenon, since human SKPs that are highly similar at the transcriptome level can be made from facial (neural crest-derived) and foreskin (mesodermally-derived) dermis, and the mesodermally-derived SKPs can make myelinating Schwann cells. Thus, non-neural crest-derived mesenchymal precursors can differentiate into bona fide peripheral glia in the absence of genetic manipulation, suggesting that developmentally-defined lineage boundaries are more flexible than widely thought.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25068124" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57573" }, "primaryId" : "GEO:GSE57573", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57573" } ] }, "title" : "Global gene expression profile of INS1E cells, hIAPP-INS1E cells and rIAPP-INS1E cells.", "dateAssigned" : "2014-05-12T00:00:00.000-05:00", "summary" : "In this dataset, we include the expression data obtained from the rat pancreatic beta-cells INS1E stably transfected with human (hIAPP) or rat (rIAPP) IAPP, which lead to the overexpression of the different variants of IAPP protein. We also include INS1E cells with empty vector as control.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25342134" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57598" }, "primaryId" : "GEO:GSE57598", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57598" } ] }, "title" : "Next-generation sequencing facilitates quantitative analysis of hepatic sex-differences in ZSF1 rats", "dateAssigned" : "2014-05-12T00:00:00.000-05:00", "summary" : "The aim of this study was to identify sex-specific hepatic genes in Zucker spontaneously hypertensive fatty rats (ZSF1), a rat model for diabetic nephropathy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57638" }, "primaryId" : "GEO:GSE57638", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57638" } ] }, "title" : "Effects on gene expression in rat liver after administration of RXR agonists: UAB30, 4-methyl-UAB30, and Targretin", "dateAssigned" : "2014-05-13T00:00:00.000-05:00", "summary" : "Examination of three retinoid X receptor (RXR) agonists [Targretin (TRG), UAB30, and 4-methyl-UAB30 (4-Me-UAB30)] showed that all inhibited mammary cancer in rodents and two (TRG and 4-Me-UAB30) strikingly increased serum triglyceride levels. Agents were administered in diets to female Sprague-Dawley rats. Liver RNA was isolated and microarrayed on the Affymetrix GeneChip Rat Exon 1.0 ST array. Statistical tests identified genes that exhibited differential expression and fell into groups, or modules, with differential expression among agonists. Genes in specific modules were changed by one, two, or all three agonists. An interactome analysis assessed the effects on genes that heterodimerize with known nuclear receptors. For proliferator-activated receptor a/RXR-activated genes, the strongest response was TRG > 4-Me-UAB30 > UAB30. Many liver X receptor/RXR-related genes (e.g., Scd-1 and Srebf1, which are associated with increased triglycerides) were highly expressed in TRG and 4-Me-UAB30- but not UAB30-treated livers. Minimal expression changes were associated with retinoic acid receptor or vitamin D receptor heterodimers by any of the agonists. UAB30 unexpectedly and uniquely activated genes associated with the aryl hydrocarbon hydroxylase (Ah) receptor (Cyp1a1, Cyp1a2, Cyp1b1, and Nqo1). Based on the Ah receptor activation, UAB30 was tested for its ability to prevent dimethylbenzanthracene (DMBA)-induced mammary cancers, presumably by inhibiting DMBA activation, and was highly effective. Gene expression changes were determined by reverse transcriptase-polymerase chain reaction in rat livers treated with Targretin for 2.3, 7, and 21 days. These showed similar gene expression changes at all three time points, arguing some steady-state effect. Different patterns of gene expression among the agonists provided insight into molecular differences and allowed one to predict certain physiologic consequences of agonist treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23292798" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57653" }, "primaryId" : "GEO:GSE57653", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57653" } ] }, "title" : "Transfection of rat Sertoli cells with human androgen receptor leads to alternated gene expression without androgen incubation", "dateAssigned" : "2014-05-14T00:00:00.000-05:00", "summary" : "We introduced a full-length human AR into the expression vector pcDNA 6.2 C-EmGFP and transfected AR-deficient rat Sertoli cells (93RS2) by electroporation. We compared gene expression levels of AR-deficient Sertoli cell line (93RS2_noAR) and a full-length-human-AR transfected Sertoli cell line (93RS2_AR17) using microarray analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57663" }, "primaryId" : "GEO:GSE57663", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57663" } ] }, "title" : "Target mRNAs induce tailing and trimming of Ago2-loaded miRNAs in neurons", "dateAssigned" : "2014-05-14T00:00:00.000-05:00", "summary" : "We show that target mRNAs trigger the non-templated addition of nucleotides (mainly adenosines and uridines) and shortening of their cognate miRNAs in primary hippocampal neurons. The induced effect is observable both in total RNA and in Ago2-associated RNA, demonstrating that the process is initiated in Ago2 bound miRNAs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25724380" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57692" }, "primaryId" : "GEO:GSE57692", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57692" } ] }, "title" : "Hong Shan Capsule (HSC) offers radioprotection and modulates acute lethal total-body irradiation-induced alterations of gene expression in rats", "dateAssigned" : "2014-05-15T00:00:00.000-05:00", "summary" : "Pathway enrichment analysis indicated that these genes were mainly involved in a total of 32 pathways, such as olfactory transduction, uroactive ligand-receptor interaction, pathways in cancer, calcium signaling pathway, vascular smooth muscle contraction, cytokine-cytokine receptor interaction, mitogen-activated protein kinase (MAPK) signaling pathway, peroxisomal proliferator-activated receptor (PPAR)signaling pathway, gonadotropin-releasing hormone (GnRH) signaling pathway, Wnt signaling pathway, janus kinase-signal transducers and activators of transcription (Jak-STAT) signaling pathway, Notch signaling pathway.Our analysis indicated that the pretreatment of rats with HSC attenuated radiation-induced these pathways, such as multiple MAPK pathways, suggesting that the protective effect of HSC acts mainly through the attenuation of these pathways.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57693" }, "primaryId" : "GEO:GSE57693", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57693" } ] }, "title" : "Transgenerational actions of environmental compounds on reproductive disease and identification of epigenetic biomarkers of ancestral exposures.", "dateAssigned" : "2014-05-15T00:00:00.000-05:00", "summary" : "Environmental factors during fetal development can induce a permanent epigenetic change in the germ line (sperm) that then transmits epigenetic transgenerational inheritance of adult-onset disease in the absence of any subsequent exposure. The epigenetic transgenerational actions of various environmental compounds and relevant mixtures were investigated with the use of a pesticide mixture (permethrin and insect repellant DEET), a plastic mixture (bisphenol A and phthalates), dioxin (TCDD) and a hydrocarbon mixture (jet fuel, JP8). After transient exposure of F0 gestating female rats during the period of embryonic gonadal sex determination, the subsequent F1-F3 generations were obtained in the absence of any environmental exposure. The effects on the F1, F2 and F3 generations pubertal onset and gonadal function were assessed. The plastics, dioxin and jet fuel were found to promote early-onset female puberty transgenerationally (F3 generation). Spermatogenic cell apoptosis was affected transgenerationally. Ovarian primordial follicle pool size was significantly decreased with all treatments transgenerationally. Differential DNA methylation of the F3 generation sperm promoter epigenome was examined. Differential DNA methylation regions (DMR) were identified in the sperm of all exposure lineage males and found to be consistent within a specific exposure lineage, but different between the exposures. Several genomic features of the DMR, such as low density CpG content, were identified. Exposure-specific epigenetic biomarkers were identified that may allow for the assessment of ancestral environmental exposures associated with adult onset disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22389676" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57708" }, "primaryId" : "GEO:GSE57708", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57708" } ] }, "title" : "Expression data from uterus of SD rat during pre-implantation period.", "dateAssigned" : "2014-05-15T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying molecular targets and pathways identified under the influence of Ormeloxifene .", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57800" }, "primaryId" : "GEO:GSE57800", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57800" } ] }, "title" : "Exposure of rat to a variety of toxicants, heart assayed by Affymetrix microarray", "dateAssigned" : "2014-05-19T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25058030" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57805" }, "primaryId" : "GEO:GSE57805", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57805" } ] }, "title" : "In vitro exposure of rat hepatocytes to a variety of toxicants, assayed by Affymetrix microarray", "dateAssigned" : "2014-05-19T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25058030" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57811" }, "primaryId" : "GEO:GSE57811", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57811" } ] }, "title" : "Exposure of rat to a variety of toxicants, kidney assayed by Affymetrix microarray", "dateAssigned" : "2014-05-19T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26260164" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57815" }, "primaryId" : "GEO:GSE57815", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57815" } ] }, "title" : "Exposure of rat to a variety of toxicants, liver assayed by Affymetrix microarray", "dateAssigned" : "2014-05-20T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25058030" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57816" }, "primaryId" : "GEO:GSE57816", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57816" } ] }, "title" : "Exposure of rat to a variety of toxicants, thigh muscle assayed by Affymetrix microarray", "dateAssigned" : "2014-05-20T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25058030" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57858" }, "primaryId" : "GEO:GSE57858", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57858" } ] }, "title" : "Isocaloric intake of diets differing in macronutrient content (high protein or high fat) in adult rats indicate adverse effects as analysed by hepatic transcriptomics", "dateAssigned" : "2014-05-21T00:00:00.000-05:00", "summary" : "Intake of high-protein (HP) diets has increased over the last years, mainly due to their popularity for body weight control. Liver is the main organ handling ingested macronutrients and it is associated with the beginning of different pathologies. We aimed to deepen our knowledge on molecular pathways affected by long-term intake of an HP diet. We performed a transcriptome analysis on liver of rats chronically fed with a casein-rich HP diet and analyzed molecular parameters related to liver injury. Chronic increase in the dietary protein/carbohydrate ratio up-regulated processes related with amino acid uptake/metabolism and lipid synthesis, promoting a molecular environment indicative of hepatic triacylglycerol (TG) deposition. Moreover, changes in expression of genes involved in acid–base maintenance and oxidative stress indicate alterations in the pH balance due to the high acid load of the diet, which has been linked to liver/health damage. Up-regulation of immune-related genes was also observed. In concordance with changes at gene expression level, we observed increased liver TG content and increased serum markers of hepatic injury/inflammation (aspartate transaminase, C-reactive protein and TNF-alpha). Moreover, the HP diet strongly increased hepatic mRNA and protein levels of HSP90, a marker of liver injury. Thus, we show for the first time that long-term consumption of an HP diet, resulting in a high acid load, results in a hepatic transcriptome signature reflecting increased TG deposition and increased signs of health risk (increased inflammation, alterations in the acid–base equilibrium and oxidative stress). Persistence of this altered metabolic status could have unhealthy consequences.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28454041" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57880" }, "primaryId" : "GEO:GSE57880", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57880" } ] }, "title" : "Resistance to aerobic exercise training causes metabolic dysfunction and reveals novel exercise-regulated signaling networks", "dateAssigned" : "2014-05-21T00:00:00.000-05:00", "summary" : "Low aerobic exercise capacity is a risk factor for diabetes and strong predictor of mortality; yet some individuals are exercise resistant, and unable to improve exercise capacity through exercise training. To test the hypothesis that resistance to aerobic exercise training underlies metabolic disease-risk, we used selective breeding for 15 generation to develop rat models of low- and high-aerobic response to training. Before exercise training, rats selected as low- and high-responders had similar exercise capacities. However, after 8-wks of treadmill training low-responders failed to improve their exercise capacity, while high-responders improved by 54%. Remarkably, low-responders to aerobic training exhibited pronounced metabolic dysfunction characterized by insulin resistance and increased adiposity, demonstrating that the exercise resistant phenotype segregates with disease risk. Low-responders had impaired exercise-induced angiogenes0is in muscle; however, mitochondrial capacity was intact and increased normally with exercise training, demonstrating that mitochondria are not limiting for aerobic adaptation or responsible for metabolic dysfunction in low-responders. Low-responders had increased stress/inflammatory signaling and altered TGFß signaling, characterized by hyperphosphorylation of a novel exercise-regulated phosphorylation site on SMAD2. Using this powerful biological model system we have discovered key pathways for low exercise training response that may represent novel targets for the treatment of metabolic disease.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57924" }, "primaryId" : "GEO:GSE57924", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57924" } ] }, "title" : "Cryptorchidism in the orl rat is associated with muscle patterning defects in the fetal gubernaculum and altered hormonal signaling", "dateAssigned" : "2014-05-23T00:00:00.000-05:00", "summary" : "This study was designed to provide additional insight into testicular hormone production and responsiveness in the orl strain and complement ongoing efforts to characterize the genetic basis of cryptorchidism in this isolated rat colony.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24966393" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57983" }, "primaryId" : "GEO:GSE57983", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE57983" } ] }, "title" : "Short Read Sequencing Data of the Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture or Placebo [tissue 1]", "dateAssigned" : "2014-05-27T00:00:00.000-05:00", "summary" : "We report the application of Illumina HiSeq 2000 sequencing technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis rat model induced by collegen with acupuncture and placebo treatments, at time points before, 1 hour and 34 days after.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28008941" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58009" }, "primaryId" : "GEO:GSE58009", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58009" } ] }, "title" : "Required Enhancer: Matrin-3 Structure Interactions for Homeodomain Transcription Programs", "dateAssigned" : "2014-05-27T00:00:00.000-05:00", "summary" : "Study of the POU-homeodomain transcription factor, has revealed that, binding of Pit1-occupied enhancers to a nuclear matrin-3-rich network/architecture is a key event in effective activation of the Pit1-regulated enhancer / coding gene transcriptional program.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25119036" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58091" }, "primaryId" : "GEO:GSE58091", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58091" } ] }, "title" : "Pesticide Methoxychlor Promotes the Epigenetic Transgenerational Inheritance of Adult-Onset Disease through the Female Germline", "dateAssigned" : "2014-05-29T00:00:00.000-05:00", "summary" : "Environmental compounds including fungicides, plastics, pesticides, dioxin and hydrocarbons can promote the epigenetic transgenerational inheritance of adult-onset disease in future generation progeny following ancestral exposure during the critical period of fetal gonadal sex determination. This study examined the actions of the pesticide methoxychlor to promote the epigenetic transgenerational inheritance of adult-onset disease and associated differential DNA methylation regions (i.e. epimutations) in sperm. Gestating F0 generation female rats were transiently exposed to methoxychlor during fetal gonadal development (gestation days 8 to 14) and then adult-onset disease was evaluated in adult F1 and F3 (great-grand offspring) generation progeny for control (vehicle exposed) and methoxychlor lineage offspring. There were increases in the incidence of kidney disease, ovary disease, and obesity in the methoxychlor lineage animals. In females and males the incidence of disease increased in both the F1 and the F3 generations and the incidence of multiple disease increased in the F3 generation. There was increased disease incidence in F4 generation reverse outcross (female) offspring indicating disease transmission was primarily transmitted through the female germline. Analysis of the F3 generation sperm epigenome of the methoxychlor lineage males identified differentially DNA methylated regions (DMR) termed epimutations in a genome-wide gene promoters analysis. These epimutations were found to be methoxychlor exposure specific in comparison with other exposure specific sperm epimutation signatures. Observations indicate that the pesticide methoxychlor has the potential to promote the epigenetic transgenerational inheritance of disease and the sperm epimutations appear to provide exposure specific epigenetic biomarkers for transgenerational disease and ancestral environmental exposures.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25057798" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58156" }, "primaryId" : "GEO:GSE58156", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58156" } ] }, "title" : "Protective role of Apolipoprotein E in experimental acute renal allogaft rejection", "dateAssigned" : "2014-06-02T00:00:00.000-05:00", "summary" : "Conclusions: ApoE plays a protective role in acute organ rejection. Further studies are needed to understand the exact mechanism how ApoE reverses acute rejection.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58197" }, "primaryId" : "GEO:GSE58197", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58197" } ] }, "title" : "Oxidative Stress and Reduced Responsiveness of Challenged Circulating Leukocytes Following Pulmonary Instillation of Metal-Rich Particulate Matter in Rats", "dateAssigned" : "2014-06-03T00:00:00.000-05:00", "summary" : "Exposure to welding fume consists of a mixed exposure of metal-rich particulate matter with gases (ozone, carbon monoxide) and/or vapors (VOCs). Data suggests that welders are immune compromised. Given the inability of pulmonary leukocytes to properly respond to a secondary infection, the question arose concerning how far upstream the dysfunction persisted. Our aim was to evaluate circulating leukocyte functionality after welding fume exposure. The results showed that welding fume exposure has rapid effects on the circulating leukocyte population as identified by relative mRNA expression changes. Instillation of MMA-SS reduced inflammatory protein production of circulating leukocytes when challenged with the secondary stimulus LPS. The effects were not related to transcription, but were observed in conjunction with oxidative stress.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25123171" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58204" }, "primaryId" : "GEO:GSE58204", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58204" } ] }, "title" : "Rat Life Cycle (RLC) Heart Gene Expression Data", "dateAssigned" : "2014-06-03T00:00:00.000-05:00", "summary" : "Cardiovascular disease (CVD) is the leading cause of mortality, with sex and age being strong risk factors. Mitochondria are vital for normal cardiac function, and regulation of mitochondrial structure and function may impact susceptibility to CVD. We analyzed the basal expression levels of mitochondria-related genes in the hearts of male and female untreated control rats at different ages to identify potential role of mitochondria in differential susceptibility to CVD between the sexes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25615628" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58225" }, "primaryId" : "GEO:GSE58225", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58225" } ] }, "title" : "A rat toxicogenomics study with Calcium Sensitizer EMD 82571 reveals a pleiotropic cause and adverse outcome pathway of teratogenicity", "dateAssigned" : "2014-06-04T00:00:00.000-05:00", "summary" : "The aim of reprotoxicity testing is to reveal adverse effects of chemicals and drugs on reproduction and on pre and postnatal fetal development. There is very limited data available on gene expression profiling for elucidation of the teratogenic effects of nongenotoxic teratogens. Therefore, research was undertaken to obtain knowledge on the molecular effects of MSC1096199 (previously known as EMD 82571), a calcium sensitizer that was abandoned in the preclinical development phase due to its teratogenic effects in some foetuses. Pregnant wistar rats were dose daily with either MSC1096199 (50 or 150 mg/kg) or Retinoic acid (12 mg/kg) on gestational days 6-17. Microarray experiment were performed using four different tissues (maternal liver, embryo liver (GD20), embryo bone (GD20), and whole embryo (GD12)) under four different conditions (vehicle, low dose and high dose of MSC1096199 and Retinoic acid) to determine the drug regulated genes. In the high dose treatment group, approximately 58% of the fetuses showed malformations i.e. exencephaly and agnathia, and toxicogenomics evidenced that the genes critically involved in osteogenesis, odontogenesis and extra cellular matrix components to be significantly regulated by MSC1096199, therefore providing a molecular rational for the observed teratogenic effects.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24977338" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58229" }, "primaryId" : "GEO:GSE58229", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58229" } ] }, "title" : "Mapping genetic modifiers of ARPKD", "dateAssigned" : "2014-06-04T00:00:00.000-05:00", "summary" : "Autosomal recessive polycystic kidney disease (ARPKD) is caused by mutations in the PKHD1 gene in both humans and the orthologous PCK rat model. Although ARPKD results solely from PKHD1 mutations, the disease onset and severity are highly variable, indicating that other unknown genetic risk factor(s) modify ARPKD-associated phenotypes. To identify genetic modifiers of ARPKD severity, we created two genetically distinct Pkhd1 congenic rat strains on the Fawn-Hooded Hypertensive (FHH) and the Dahl S (SS) rat backgrounds (denoted FHH.Pkhd1 and SS.Pkhd1, respectively) that harbor the PCK-derived Pkhd1 allele. The FHH.Pkhd1 and SS.Pkhd1 strains had lower renal cyst formation at 30 days-of-age (5±2% and 8±2% cystic, respectively; P<0.001) compared to the PCK kidneys (26±4% cystic), which coincided with significantly reduced kidney weights in the FHH.Pkhd1 and SS.Pkhd1. Liver cyst formation and liver weight did not differ between PCK, FHH.Pkhd1, and SS.Pkhd1. These data indicated that the PCK genome harbors genetic modifier(s) of ARPKD severity that are not present in the FHH and SS genomes. Using high density SNP array genotyping and microarray expression analysis, we identified 50 potential modifiers of ARPKD severity in the PCK rat. Of these candidates, a damaging nonsynonymous variant in Nphp4 stood out as the most likely candidate based on variant segregation, protein modeling, network analysis, and gene ontology. Nphp4 is widely associated with the autosomal recessive cilliopathy and nephronopthisis, but had not been previously implicated in the molecular or cellular pathophysiology of ARPKD. Collectively, these data provide genetic evidence of disease modifier(s) in the PCK model of ARPKD and prioritized multiple candidates, including NPHP4, for further investigation in ARPKD pathogenesis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58302" }, "primaryId" : "GEO:GSE58302", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58302" } ] }, "title" : "10nM insulin stimulation of Fao Cells", "dateAssigned" : "2014-06-09T00:00:00.000-05:00", "summary" : "To confirm how many and what kind of gene changes within 1 hour treatment of insulin stimulation, we have performed whole genome microarray expression profiling. And we found that 276 genes increased (>2 fold) or decreased (<0.5 fold)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25131207" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58404" }, "primaryId" : "GEO:GSE58404", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58404" } ] }, "title" : "Identification of a Mammalian Silicon Transporter", "dateAssigned" : "2014-06-11T00:00:00.000-05:00", "summary" : "Silicon (Si) has long been known to play a major physiological role in certain organisms, including some sponges and many diatoms and higher plants, leading to the recent identification of multiple proteins responsible for silicon transport in a range of algal and plant species. In mammals, despite several convincing studies suggesting that silicon is an important factor in bone development and connective tissue health, there is a critical lack of understanding in biochemical pathways that enable silicon homeostasis. Here we report the identification of a mammalian efflux silicon transporter, namely Slc34a2 (also known as NaPiIIb), which was upregulated in the kidneys of rats following chronic dietary silicon deprivation. When heterologously expressed in Xenopus laevis oocytes, the protein displayed marked silicon transport activity, specifically efflux, comparable to plant OsLsi2 transfected in the same fashion and independent of sodium and/or phosphate influx. This is the first evidence for a specific active transporter protein for silicon in mammals and suggests an important role for silicon in vertebrates.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28179233" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58438" }, "primaryId" : "GEO:GSE58438", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58438" } ] }, "title" : "Renoprotective Effects of Valproic Acid and Dexamethasone in Acute Kidney Ischemia-Reperfusion Injury", "dateAssigned" : "2014-06-12T00:00:00.000-05:00", "summary" : "Introduction: Renal ischemia-reperfusion (IR) causes acute kidney injury (AKI) with high mortality and morbidity. The objective of this study was to ameliorate kidney IR injury and identify novel biomarkers for kidney injury and repair. Methods: Left renal ischemia was induced in rats by clamping renal artery for 45 minutes, followed by reperfusion and right nephrectomy. Thirty minutes prior to ischemia, rats (n=8/group) received Valproic Acid (150 mg/kg; VPA), Dexamethasone (3 mg/kg; Dex) or Vehicle (Saline) intraperitoneally. Animals were sacrificed at 3h, 24h or 120h post- IR and blood, urine and kidney were collected. Results: Serum creatinine (mg/dL) at 24 h IR in VPA (2.7±1.8) and Dex (2.3±1.2) was reduced (P<0.05) compared to Vehicle (3.8±0.5). At 3h post-IR, urine albumin (mg/ml) was higher in Vehicle (1.47±0.10), VPA (0.84±0.62) and Dex (1.04±0.73) compared to uninjured/untreated control (0.14±0.26) group. At 24h post-IR urine Lipocalin-2 (µg/ml) was significantly higher (P<0.05) in VPA, Dex and Vehicle groups (9.61-11.36) compared to uninjured/untreated control (0.67±o.29); also, Kidney Injury Molecule-1 (KIM-1; ng/ml) was significantly higher in VPA, Dex and Vehicle groups (13.7-18.7) compared uninjured/untreated control (1.7±1.9). KIM-1 levels were significantly (P<0.05) higher in all groups compared to uninjured/untreated control levels. Histopathology at 3h post IR demonstrated (P<0.05) reduction in ischemic injury in the renal cortex in VPA (Grade 1.6± 1.5) compared to Vehicle (Grade 2.9±1.1) group. Inflammatory cytokines IL1ß and IL6 were down-regulated in VPA and Dex groups. BCL2 was higher in VPA group. DNA microarray analysis demonstrated reduced stress response and injury, and improved recovery related gene expression in the kidneys of VPA treated animals. Conclusions: VPA administration reduced kidney IR injury and improved regeneration. KIM-1 and Lipocalin-2 appear to be promising early urine biomarkers of acute ischemic kidney injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25970334" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58456" }, "primaryId" : "GEO:GSE58456", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58456" } ] }, "title" : "Affymetrix Chip Data of the Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture (Affymetrix, mRNA, batch 2)", "dateAssigned" : "2014-06-13T00:00:00.000-05:00", "summary" : "We report the application of Affymetrix technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA), with acupuncture and Methotrexate+acupuncture treatment, as well as epidermal needle manipulation on healthy rat model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28008941" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58458" }, "primaryId" : "GEO:GSE58458", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58458" } ] }, "title" : "Agilent Chip Data of the Post-Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture (Agilent, miRNA, batch 1)", "dateAssigned" : "2014-06-13T00:00:00.000-05:00", "summary" : "We report the application of Agilent technology for high-throughput profiling of the post-transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA), with acupuncture, Methotrexate, Isofluorane anesthetic and placebo treatments, as well as the healthy control.\t\t\t\t\t\t\t\t\t\t", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28008941" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58459" }, "primaryId" : "GEO:GSE58459", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58459" } ] }, "title" : "Short Read Sequencing Data of the Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture (HiSeq 2000, miRNA, batch 1)", "dateAssigned" : "2014-06-13T00:00:00.000-05:00", "summary" : "We report the application of Illumina Hiseq2000 sequencing technology for high-throughput miRNA profiling of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA), with acupuncture and placebo treatments.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28008941" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58537" }, "primaryId" : "GEO:GSE58537", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58537" } ] }, "title" : "Supplemental carnitine affects the microRNA expression profile in skeletal muscle of obese Zucker rats", "dateAssigned" : "2014-06-16T00:00:00.000-05:00", "summary" : "Background In the past, numerous studies revealed that supplementation with carnitine has multiple effects on performance characteristics and gene expression in livestock and model animals. The molecular mechanisms underlying these observations are still largely unknown. Increasing evidence suggests that microRNAs (miRNAs), a class of small non-coding RNA molecules, play an important role in post-transcriptional regulation of gene expression and thereby influencing several physiological and pathological processes. Based on these findings, the aim of the present study was to investigate the influence of carnitine supplementation on the miRNA expression profile in skeletal muscle of obese Zucker rats using miRNA microarray analysis. Results miRNA expression profiling in skeletal muscle revealed a subset of 152 miRNAs out of the total number of miRNAs analysed (259) were identified to be differentially regulated (adjusted P-value ¿ 0.05) by carnitine supplementation. Compared to the obese control group, 111 miRNAs were up-regulated and 41 down-regulated by carnitine supplementation (adjusted P-value ¿ 0.05). 14 of these miRNAs showed a log2 ratio = 0.5 and 7 miRNAs showed a log2 ratio = -0.5 (adjusted P-value ¿ 0.05). Conclusion The present study shows for the first time that supplementation of carnitine affects a large set of miRNAs in skeletal muscle of obese Zucker rats suggesting a novel mechanism through which carnitine exerts its multiple effects on gene expression, which were observed during the past.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24952657" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58548" }, "primaryId" : "GEO:GSE58548", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58548" } ] }, "title" : "Paradoxical neurobehavioral rescue by cues associated with infant trauma: Amygdala 5-HT and CORT", "dateAssigned" : "2014-06-16T00:00:00.000-05:00", "summary" : "We show that infant trauma, as modeled by infant paired odor-shock conditioning, results in later life depressive-like behavior that can be modulated by learned infant cues (i.e., odor previously paired with shock). We have previously shown that this infant attachment odor learning paradigm results in the creation of a new artificial maternal odor that is able to control pup behavior and retain its value throughout development. Here, we assess the mechanism by which this artificial maternal odor is able to rescue depressive-like behavior and show that this anti-depressant like effect results in glucocorticoid and serotonin (5-HT) related changes in amygdala gene expression and is dependent on amygdala 5-HT. Furthermore, increasing amygdala 5-HT and blocking corticosterone (CORT) in the absence of odor mimics the adult rescue effects elicited by the artificial maternal odor, suggesting a mechanism by which odor presentation exerts its repair effects.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25561533" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58575" }, "primaryId" : "GEO:GSE58575", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58575" } ] }, "title" : "Expression data from adipose tissue of WNIN/Ob lean and obese rats", "dateAssigned" : "2014-06-17T00:00:00.000-05:00", "summary" : "We used Microarrays to delinate the alted gene expression in adipose tissue of WNIN/Ob obese rats", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58576" }, "primaryId" : "GEO:GSE58576", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58576" } ] }, "title" : "Expression data from liver of WNIN/Ob lean and obese rats", "dateAssigned" : "2014-06-17T00:00:00.000-05:00", "summary" : "We used Microarrays to delinate the alted gene expression in liver of WNIN/Ob obese rats", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58690" }, "primaryId" : "GEO:GSE58690", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58690" } ] }, "title" : "MiRNA profiling in Rattus norvegicus pancreatic cells: RIN-5F cells during infection with Coxsackie B4 virus", "dateAssigned" : "2014-06-20T00:00:00.000-05:00", "summary" : "This study aims at elucidating how Coxsackie B virus infection perturbs the host's miRNA regulatory pathways that may lead to different pathological events using the miRNA microarray approach.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58691" }, "primaryId" : "GEO:GSE58691", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58691" } ] }, "title" : "MiRNA profiling in Rattus norvegicus pancreatic cells: INS-1E cells during infection with Coxsackie B4 virus", "dateAssigned" : "2014-06-20T00:00:00.000-05:00", "summary" : "This study aims at elucidating how Coxsackie B virus infection perturbs the host's miRNA regulatory pathways that may lead to different pathological events using the miRNA microarray approach.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58693" }, "primaryId" : "GEO:GSE58693", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58693" } ] }, "title" : "MicroRNA (miRNA) expression of IMCD tubule suspension", "dateAssigned" : "2014-06-20T00:00:00.000-05:00", "summary" : "The microarray assay revealed that relative expression of miRNAs in the kidney IMCD cells was changed by desmopressin (dDAVP) stimulation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58701" }, "primaryId" : "GEO:GSE58701", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58701" } ] }, "title" : "Genome-wide identification of rat long non-coding RNAs", "dateAssigned" : "2014-06-20T00:00:00.000-05:00", "summary" : "In the current study, we have focused on a distinct group of non-coding elements, lncRNA, and profiled renal tissues from three different inbred rat strains. We chose the three strains S, SHR and R for the main purpose of cataloging lncRNA annotations from the most widely used rat models of cardiovascular and renal disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25385761" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58710" }, "primaryId" : "GEO:GSE58710", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58710" } ] }, "title" : "Time Course of Gene Expression in the Substantia Nigra in Response to Intrastriatal 6-hydroxydopamine in the rat.", "dateAssigned" : "2014-06-20T00:00:00.000-05:00", "summary" : "Comprehensive gene expression analysis was conducted to detect significant differences in gene expression. Comparisons were conducted within the same treatment groups over time as well as across treatments within the same post-treatment interval. Longitudinal expression patterns were parsed using a k-means clustering algorithm as a method for finding patterns indicative of neuronal loss, upregulation in response to lesion or surgical damage exclusive of lesion.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25992874" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58777" }, "primaryId" : "GEO:GSE58777", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58777" } ] }, "title" : "Effects of two strains of Lactobacillus fermentum on germ free rats", "dateAssigned" : "2014-06-24T00:00:00.000-05:00", "summary" : "Transcription profiling of intestinal tissue from germ free rats mono-colonised with one of two strains of Lactobacillus fermentum; AGR1485 or AGR 1487", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58803" }, "primaryId" : "GEO:GSE58803", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58803" } ] }, "title" : "Transcript Profiling of Periaqueductal Gray in Response to Electroacupuncture on Rats", "dateAssigned" : "2014-06-25T00:00:00.000-05:00", "summary" : "The electroacupuncture-induced analgesic effect has been used widely to alleviate diverse pains. However, significant individual variations in analgesic effect of EA for both experiments and clinics were reported. According to the sensitivity of the analgesic response to EA stimulation, the subjects could be categorized into high responders (HR) and low responders (NR). However, the molecular mechanism of individual variability in the analgesic response to acupuncture stimulation is still uncertain. This study aims to investigate the potential gene expression in spinal dorsal horn induced by 2Hz/100Hz electroacupuncture in HR and NR rats. Rats were given 2Hz or 100Hz electroacupuncture for 30 min and using cDNA microarrays to compare different gene expression in dorsal horn. Transcriptome profiling analysis found that some co-regulated genes related with electroacupuncture or 2Hz or 100Hz fruqencies. These co-regulated genes were plasticity-related by GO analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25346229" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58866" }, "primaryId" : "GEO:GSE58866", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58866" } ] }, "title" : "Expression data of rat insulinoma cells induced with ER stress +/- IRE1 inhibitor treatment", "dateAssigned" : "2014-06-26T00:00:00.000-05:00", "summary" : "We used microarray gene expression arrays to analyze the IRE1-dependent activation of genes in response to misfolded proinsulin expression in an inducible mutant proinsulin (C96Y) insulinoma cell line by inhibiting the IRE1 endoribonucleas activity with a specific inhibitor, 4u8c.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25011481" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58875" }, "primaryId" : "GEO:GSE58875", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58875" } ] }, "title" : "Influence of dietary sucrose and copper content in a rat model of non-alcoholic fatty-liver disease", "dateAssigned" : "2014-06-27T00:00:00.000-05:00", "summary" : "Nutrigenomics analysis was used to investigate the molecular responses to dietary Cu deficiency independently and in combination with 30% (w/w) sucrose in a mature rat model of NAFLD. Low Cu significantly decreased hepatic and serum Cu, and induced NAFLD-like histopathology, mild steatosis, up-regulated transcripts in inflammation and hepatic stellate cell activation, and significantly increased oxidative stress. Rats fed low Cu together with 30% sucrose also developed insulin resistance, increased ATP citrate lyase and FASN expression, and greater oxidative stress. High sucrose with adequate Cu also promoted inflammation and fibrosis, but not steatosis. This study indicates that low dietary Cu and sucrose consumption are singular and synergistic dietary factors in promotion of NAFLD and NASH that act independently of obesity or severe steatosis, likely by promoting oxidative stress and activation of inflammation and fibrosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26033743" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58978" }, "primaryId" : "GEO:GSE58978", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE58978" } ] }, "title" : "Short Read Sequencing Data of the Transcriptome of the Rheumatoid Arthritis and Treated with Acupuncture or not", "dateAssigned" : "2014-07-01T00:00:00.000-05:00", "summary" : "We report the application of Illumina Hiseq2000 sequencing technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA) and treated with acupuncture or not.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28008941" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59039" }, "primaryId" : "GEO:GSE59039", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59039" } ] }, "title" : "Transcriptomics of rat born to dams fed a diet deficient in methyl group donors", "dateAssigned" : "2014-07-02T00:00:00.000-05:00", "summary" : "It is clearly established that the maternal diet during pregnancy can induce physiological and metabolic adaptations in the developing fetus which determine its susceptibility later in life to develop diabetes, obesity... The molecular and genomic mechanisms underlying the programming of the metabolic syndrome remain largely unknown but may involve resetting of epigenetic marks and fetal gene expression. We analyzed the profile of the liver transcriptome in 21-day-old rats born to mothers fed with a standard diet or a diet lacking methyl donor nutrients (Vitamin B12 and folates) during gestation and lactation. From a total of 44,000 probes for 26,456 genes, we found two gene clusters whose expression levels had statistically significant differences between control and deficient rats: 3,269 up-regulated and 2,841 down-regulated genes. Bioinformatics analysis revealed that these genes are mainly involved in glucose and lipid metabolism, nervous system, coagulation, endoplasmic reticulum (ER) stress and mitochondrial function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25380481" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59043" }, "primaryId" : "GEO:GSE59043", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59043" } ] }, "title" : "G9a is essential for epigenetic silencing of K+ channel genes in acute-to-chronic pain transition", "dateAssigned" : "2014-07-02T00:00:00.000-05:00", "summary" : "RESULTS: We were able to map 16876 genes, from which 2035 changed their expression values at least two fold when we compared SNL to Sham operated (p= 0.01). There were 1205 upregulated and 832 down-regulated genes. Next, we focused on genes whose expression was either up or down-regulated 2 fold due to nerve ligation, and the values would be normalized to control level after G9a/GLP inhibito (UNC0638)r treatment. We identified 639 genes in our data set that behave this way", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26551542" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59109" }, "primaryId" : "GEO:GSE59109", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59109" } ] }, "title" : "Environmentally Induced Epigenetic Transgenerational Inheritance of Altered Sertoli Cell Transcriptome and Epigenome: Molecular Etiology of Male Infertility [NimbleGen]", "dateAssigned" : "2014-07-06T00:00:00.000-05:00", "summary" : "Environmental toxicants have been shown to induce the epigenetic transgenerational inheritance of adult onset disease, including testis disease and male infertility. The current study was designed to determine the impact of an altered sperm epigenome on the subsequent development of an adult somatic cell (Sertoli cell) that influences the onset of a specific disease (male infertility). A gestating female rat (F0 generation) was exposed to the agriculture fungicide vinclozolin during gonadal sex determination and then the subsequent F3 generation progeny used for the isolation of Sertoli cells and assessment of testis disease. As previously observed, enhanced spermatogenic cell apoptosis was observed. The Sertoli cells provide the physical and nutritional support for the spermatogenic cells. Over 400 genes were differentially expressed in the F3 generation control versus vinclozolin lineage Sertoli cells. A number of specific cellular pathways were identified to be transgenerationally altered. One of the key metabolic processes affected was pyruvate/lactate production that is directly linked to spermatogenic cell viability. The Sertoli cell epigenome was also altered with over 100 promoter differential DNA methylation regions (DMR) modified. The genomic features and overlap with the sperm DMR were investigated. Observations demonstrate that the transgenerational sperm epigenetic alterations subsequently alters the development of a specific somatic cell (Sertoli cell) epigenome and transcriptome that correlates with adult onset disease (male infertility). The environmentally induced epigenetic transgenerational inheritance of testis disease appears to be a component of the molecular etiology of male infertility.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23555832" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59120" }, "primaryId" : "GEO:GSE59120", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59120" } ] }, "title" : "Cross-species transcriptome profiling identifies new alveolar epithelial type I cell-specific genes", "dateAssigned" : "2014-07-07T00:00:00.000-05:00", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27749084" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59164" }, "primaryId" : "GEO:GSE59164", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59164" } ] }, "title" : "Lipoic acid induced endoplasmic reticulum stress-mediated apoptosis in rat hepatoma cells:identification of new ER stress aggravator (ERSA)", "dateAssigned" : "2014-07-07T00:00:00.000-05:00", "summary" : "Study gene expression during apoptotic process α Lipoic acid-induced.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59165" }, "primaryId" : "GEO:GSE59165", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59165" } ] }, "title" : "Genome-wide identification of rat long non-coding RNAs (microarray)", "dateAssigned" : "2014-07-07T00:00:00.000-05:00", "summary" : "In the current study, we have focused on a distinct group of non-coding elements, lncRNA, and profiled renal tissues from three different inbred rat strains. We chose the three strains S, SHR and R for the main purpose of cataloging lncRNA annotations from the most widely used rat models of cardiovascular and renal disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25385761" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59191" }, "primaryId" : "GEO:GSE59191", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59191" } ] }, "title" : "Epigenomics of rat born to dams fed a diet deficient in methyl group donors (MDD)", "dateAssigned" : "2014-07-08T00:00:00.000-05:00", "summary" : "It is clearly established that the maternal diet during pregnancy can induce physiological and metabolic adaptations in the developing fetus which determine its susceptibility later in life to develop diabetes, obesity... The molecular and genomic mechanisms underlying the programming of the metabolic syndrome remain largely unknown but may involve resetting of epigenetic marks and fetal gene expression. We analyzed the profile of the liver methylome in 21-day-old rats born to mothers fed with a standard diet or a diet lacking methyl donor nutrients (Vitamin B12 and folates) during gestation and lactation. Modifications of DNA methylation were found in the promoter regions of 1,032 genes out of 14,981 genes. Bioinformatics analysis revealed that these genes are mainly involved in glucose and lipid metabolism, nervous system, coagulation, endoplasmic reticulum (ER) stress and mitochondrial function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25380481" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59277" }, "primaryId" : "GEO:GSE59277", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59277" } ] }, "title" : "Environmentally Induced Epigenetic Transgenerational Inheritance of Ovarian Disease [NimbleGen]", "dateAssigned" : "2014-07-10T00:00:00.000-05:00", "summary" : "The actions of environmental toxicants and relevant mixtures in promoting the epigenetic transgenerational inheritance of ovarian disease was investigated with the use of a fungicide, a pesticide mixture, a plastic mixture, dioxin and a hydrocarbon mixture. After transient exposure of an F0 gestating female rat during embryonic gonadal sex determination, the F1 and F3 generation progeny adult onset ovarian disease was assessed. Transgenerational disease phenotypes observed included an increase in cysts resembling human polycystic ovarian disease (PCO) and a decrease in the ovarian primordial follicle pool size resembling primary ovarian insufficiency (POI). The F3 generation granulosa cells were isolated and found to have a transgenerational effect on the transcriptome and epigenome (differential DNA methylation). Epigenetic biomarkers for environmental exposure and associated gene networks were identified. Epigenetic transgenerational inheritance of ovarian disease states was induced by all the different classes of environmental compounds, suggesting a role of environmental epigenetics in ovarian disease etiology.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22570695" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59287" }, "primaryId" : "GEO:GSE59287", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59287" } ] }, "title" : "The Chronic Gavage Toxicity/Carcinogenicity Study of Indole-3-Carbinol (I3C) in Harlan Sprague-Dawley Rats (G823524-B), CAS No 700-06-1", "dateAssigned" : "2014-07-10T00:00:00.000-05:00", "summary" : "Indole-3-carbinol is used as a dietary supplement and has potential use as a therapeutic agent for the prevention of various types of cancer. While substantial evidence exists that indole-3-carbinol can reduce the risk of cancers induced by several known carcinogens when administered to animals, indole-3-carbinol can also function as an initiator and tumor promoter in certain models. The carcinogenic potential of indole-3-carbinol has not been studied in a 2-year bioassay. The objective of the microarray study was to evaluate the transcriptional changes in liver from rats exposed to 0 or 300 mg/kg indole-3-carbinol. At 3 months, livers were analyzed from female Harlan Sprague Dawley rats in the 2-year gavage study of indole-3-carbinol.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59329" }, "primaryId" : "GEO:GSE59329", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59329" } ] }, "title" : "Inhaled Ozone (O3)-Induces Changes in Serum Metabolomic and Liver Transcriptomic Profiles in Rats", "dateAssigned" : "2014-07-11T00:00:00.000-05:00", "summary" : "Long-term exposure to particulate air pollutants has been linked to increased incidence of Type 2 Diabetes (T2DM). Recently, we showed that the gaseous pollutant, O3, induced glucose intolerance, and increased serum leptin and epinephrine in Brown Norway rats. In this study, we hypothesized that O3 exposure will cause broad scale changes in metabolic homeostasis involving liver, muscle and adipose tissues, and that serum metabolomic and liver transcriptomic profiling will provide mechanistic insights into pollutant-induced metabolic alterations. In the first experiment, male Wistar Kyoto (WKY) rats were exposed to filtered air (FA) or O3 at 0.25, 0.50, or 1.00 ppm, 6h/day for two consecutive days to establish concentration-related effects on glucose tolerance and lung injury. In a second experiment, rats were exposed to FA or 1.0 ppm O3, 6h/day for either one day or two consecutive days and systemic metabolic responses were determined immediately after each exposure or after an 18h recovery period. In WKY rats, O3 increased serum fasting glucose and leptin on day 1. Glucose intolerance persisted through two days of exposure but reversed 18h post second exposure. O3 exposure increased circulating metabolites of glycolysis, long-chain free fatty acids, branched chain amino acids (BCAA) and cholesterol while 1,5- anhydroglucitol, bile acids and metabolites of TCA cycle were decreased, indicating impaired glycemic control, muscle proteolysis and adipose lipolysis. Liver gene expression profile after O3 exposure reflected a response to the serum metabolite changes, as evidenced by increased expression of genes for glycolysis, TCA cycle and gluconeogenesis, and decreased expression of genes involved in steroid and fat biosynthesis. In conclusion, short-term O3 exposure induced hormonal changes and global metabolic disorder reflective of changes in peripheral glucose, lipid, and amino acid metabolism, representative of a stress-response. It remains to be examined if these metabolic alterations contribute to insulin resistance upon chronic exposure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59401" }, "primaryId" : "GEO:GSE59401", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59401" } ] }, "title" : "Gene expression profiles of rat enamel organs (secretory--stage and maturation stage)", "dateAssigned" : "2014-07-14T00:00:00.000-05:00", "summary" : "We conducted the genome-wide mRNA expression profiling in parallel with miRNA expression profiling using RNA samples extracted from rat incisor enamel organs, so as to refine the number of predicted gene targets for miRNA regulators.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25406666" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59456" }, "primaryId" : "GEO:GSE59456", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59456" } ] }, "title" : "Gene expression in rat ovaries treated with DHT", "dateAssigned" : "2014-07-16T00:00:00.000-05:00", "summary" : "Polycystic ovarian syndrome (PCOS) is an endocrine disorder of the reproductive and metabolic axis in women during the reproductive age. In this study, we used a rat model exhibiting reproductive and metabolic abnormalities similar to human PCOS to unravel the molecular mechanisms underlining this complex syndrome.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25887459" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59495" }, "primaryId" : "GEO:GSE59495", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59495" } ] }, "title" : "Microarray Analysis of Microcystin-LR", "dateAssigned" : "2014-07-16T00:00:00.000-05:00", "summary" : "Microcystins are produced by the cyanobacteria, most commonly Microcystis aerµginosa. Upon ingestion, toxic microcystins are actively absorbed by fish, birds and mammals where they are primarily liver toxins.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59510" }, "primaryId" : "GEO:GSE59510", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59510" } ] }, "title" : "Environmentally Induced Transgenerational Epigenetic Reprogramming of Primordial Germ Cells and Subsequent Germline [NimbleGen]", "dateAssigned" : "2014-07-17T00:00:00.000-05:00", "summary" : "A number of environmental factors (e.g. toxicants) have been shown to promote the epigenetic transgenerational inheritance of disease and phenotypic variation. Transgenerational inheritance requires the germline transmission of altered epigenetic information between generations in the absence of direct environmental exposures. The primary periods for epigenetic programming of the germ line are those associated with primordial germ cell development and subsequent fetal germline development. The current study examined the actions of an agricultural fungicide vinclozolin on gestating female (F0 generation) progeny in regards to the primordial germ cell (PGC) epigenetic reprogramming of the F3 generation (i.e. great-grandchildren). The F3 generation germline transcriptome and epigenome (DNA methylation) were altered transgenerationally. Interestingly, disruptions in DNA methylation patterns and altered transcriptomes were distinct between germ cells at the onset of gonadal sex determination at embryonic day 13 (E13) and after cord formation in the testis at embryonic day 16 (E16). A larger number of DNA methylation abnormalities (epimutations) and transcriptional alterations were observed in the E13 germ cells than in the E16 germ cells. These observations indicate that altered transgenerational epigenetic reprogramming and function of the male germline is a component of vinclozolin induced epigenetic transgenerational inheritance of disease. Insights into the molecular control of germline transmitted epigenetic inheritance are provided.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23869203" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59552" }, "primaryId" : "GEO:GSE59552", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59552" } ] }, "title" : "Dioxin (TCDD) Induces Epigenetic Transgenerational Inheritance of Adult Onset Disease and Sperm Epimutations", "dateAssigned" : "2014-07-18T00:00:00.000-05:00", "summary" : "Environmental compounds can promote epigenetic transgenerational inheritance of adult-onset disease in subsequent generations following ancestral exposure during fetal gonadal sex determination. The current study examined the ability of dioxin (2,3,7,8-tetrachlorodibenzo[p]dioxin, TCDD) to promote epigenetic transgenerational inheritance of disease and DNA methylation epimutations in sperm. Gestating F0 generation females were exposed to dioxin during fetal day 8 to 14 and adult-onset disease was evaluated in F1 and F3 generation rats. The incidences of total disease and multiple disease increased in F1 and F3 generations. Prostate disease, ovarian primordial follicle loss and polycystic ovary disease were increased in F1 generation dioxin lineage. Kidney disease in males, pubertal abnormalities in females, ovarian primordial follicle loss and polycystic ovary disease were increased in F3 generation dioxin lineage animals. Analysis of the F3 generation sperm epigenome identified 50 differentially DNA methylated regions (DMR) in gene promoters. These DMR provide potential epigenetic biomarkers for transgenerational disease and ancestral environmental exposures. Observations demonstrate dioxin exposure of a gestating female promotes epigenetic transgenerational inheritance of adult onset disease and sperm epimutations.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23049995" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59553" }, "primaryId" : "GEO:GSE59553", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59553" } ] }, "title" : "Hydrocarbons (Jet Fuel JP-8) Induce Epigenetic Transgenerational Inheritance of Obesity, Reproductive Disease and Sperm Epimutations", "dateAssigned" : "2014-07-18T00:00:00.000-05:00", "summary" : "Environmental compounds have been shown to promote epigenetic transgenerational inheritance of disease. The current study was designed to determine if a hydrocarbon mixture involving jet fuel (JP-8) promotes epigenetic transgenerational inheritance of disease. Gestating F0 generation female rats were transiently exposed during the fetal gonadal development period. The direct exposure F1 generation had an increased incidence of kidney abnormalities in both females and males, prostate and pubertal abnormalities in males, and primordial follicle loss and polycystic ovarian disease in females. The first transgenerational generation is the F3 generation, and the jet fuel lineage had an increased incidence of primordial follicle loss and polycystic ovarian disease in females, and obesity in both females and males. Analysis of the jet fuel lineage F3 generation sperm epigenome identified 33 differential DNA methylation regions, termed epimutations. Observations demonstrate hydrocarbons can promote epigenetic transgenerational inheritance of disease and sperm epimutations, potential biomarkers for ancestral exposures.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23453003" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59554" }, "primaryId" : "GEO:GSE59554", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59554" } ] }, "title" : "Pesticide and Insect Repellent Mixture (Permethrin and DEET) Induces Epigenetic Transgenerational Inheritance of Disease and Sperm Epimutations", "dateAssigned" : "2014-07-18T00:00:00.000-05:00", "summary" : "Environmental compounds are known to promote epigenetic transgenerational inheritance of disease. The current study was designed to determine if a “pesticide mixture” (pesticide permethrin and insect repellent N,N-Diethyl-meta-toluamide, DEET) promotes epigenetic transgenerational inheritance of disease and associated DNA methylation epimutations in sperm. Gestating F0 generation female rats were exposed during fetal gonadal sex determination and the incidence of disease evaluated in F1 and F3 generations. There were significant increases in the incidence of total diseases in animals from pesticide lineage F1 and F3 generation animals. Pubertal abnormalities, testis disease, and ovarian disease (primordial follicle loss and polycystic ovarian disease) were increased in F3 generation animals. Analysis of the pesticide lineage F3 generation sperm epigenome identified 363 differential DNA methylation regions (DMR) termed epimutations. Observations demonstrate that a pesticide mixture (permethrin and DEET) can promote epigenetic transgenerational inheritance of adult onset disease and potential sperm epigenetic biomarkers for ancestral environmental exposures.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22975477" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59555" }, "primaryId" : "GEO:GSE59555", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59555" } ] }, "title" : "Plastics Derived Endocrine Disruptors (BPA, DEHP and DBP) Induce Epigenetic Transgenerational Inheritance of Obesity, Reproductive Disease and Sperm Epimutations", "dateAssigned" : "2014-07-18T00:00:00.000-05:00", "summary" : "Environmental compounds are known to promote epigenetic transgenerational inheritance of adult onset disease in subsequent generations (F1–F3) following ancestral exposure during fetal gonadal sex determination. The current study was designed to determine if a mixture of plastic derived endocrine disruptor compounds bisphenol-A (BPA), bis(2-ethylhexyl)phthalate (DEHP) and dibutyl phthalate (DBP) at two different doses promoted epigenetic transgenerational inheritance of adult onset disease and associated DNA methylation epimutations in sperm. Gestating F0 generation females were exposed to either the “plastics” or “lower dose plastics” mixture during embryonic days 8 to 14 of gonadal sex determination and the incidence of adult onset disease was evaluated in F1 and F3 generation rats. There were significant increases in the incidence of total disease/abnormalities in F1 and F3 generation male and female animals from plastics lineages. Pubertal abnormalities, testis disease, obesity, and ovarian disease (primary ovarian insufficiency and polycystic ovaries) were increased in the F3 generation animals. Kidney and prostate disease were only observed in the direct fetally exposed F1 generation plastic lineage animals. Analysis of the plastics lineage F3 generation sperm epigenome previously identified 197 differential DNA methylation regions (DMR) in gene promoters, termed epimutations. A number of these transgenerational DMR form a unique direct connection gene network and have previously been shown to correlate with the pathologies identified. Observations demonstrate that a mixture of plastic derived compounds, BPA and phthalates, can promote epigenetic transgenerational inheritance of adult onset disease. The sperm DMR provide potential epigenetic biomarkers for transgenerational disease and/or ancestral environmental exposures.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23359474" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59593" }, "primaryId" : "GEO:GSE59593", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59593" } ] }, "title" : "Expression data for Male Fischer 344 rat exposed to nickel subsulfide", "dateAssigned" : "2014-07-18T00:00:00.000-05:00", "summary" : "To provide insights into the mode of action for Ni3S2 lung carcinogenicity by examining gene expression changes in target cells after inhalation exposure. Gene expression changes were determined in micro-dissected lung broncho-alveolar cells from Fischer F344 rats following inhalation of Ni3S2 at 0.0, 0.04, 0.08, 0.15, and 0.60 mg/m3 (0.03, 0.06, 0.11, and 0.44 mg Ni/m3) for one and four weeks (6 hours per day, 5 days per week). Results: Broncho-alveolar lavage fluid evaluation and lung histopathology provided evidence of inflammation only at the two highest concentrations, which were similar to those tested in the 2-year bioassay. The number of statistically significant up- and down-regulated genes decreased markedly from one to four weeks of exposure, suggesting adaptation. Cell signal pathway enrichment at both time-points primarily reflected responses to toxicity, including inflammatory and proliferative signaling. While proliferative signaling was up-regulated at both time points, some inflammatory signaling reversed from down-regulation at 1 week to up-regulation at 4 weeks. Conclusions: These results support a mode of action for Ni3S2 carcinogenicity driven by chronic toxicity, inflammation and proliferation, leading to mis-replication, rather than by direct genotoxicity. Benchmark dose (BMD) analysis identified the lowest pathway transcriptional BMD exposure concentration as 0.026 mg Ni/m3, for apoptosis/survival signaling. When conducted on the basis of lung Ni concentration the lowest pathway BMD was 0.64 µg Ni/g lung, for immune/inflammatory signaling. Implications: These highly conservative BMDs could be used to derive a point of departure in a nonlinear risk assessment for Ni3S2 toxicity and carcinogenicity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59633" }, "primaryId" : "GEO:GSE59633", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59633" } ] }, "title" : "Nova1 is a master regulator of alternative splicing in pancreatic beta cells", "dateAssigned" : "2014-07-21T00:00:00.000-05:00", "summary" : "Alternative splicing (AS) is a fundamental mechanism for the regulation of gene expression. It affects more than 90% of human genes but its role in the regulation of pancreatic beta cells, the producers of insulin, remains unknown. Our recently published data indicated that the “neuron specific” Nova1 splicing factor is expressed in pancreatic beta cells. We have presently coupled specific knockdown (KD) of Nova1 with RNA-sequencing to determine all splice variants and downstream pathways regulated by this protein in beta cells. Nova1 KD altered the splicing of nearly 5000 transcripts. Pathway analysis indicated that these genes are involved in exocytosis, apoptosis, insulin receptor signalling, splicing and transcription. In line with these findings, Nova1 silencing inhibited insulin secretion and induced apoptosis basally and after cytokine treatment in rodent and human beta cells. These observations identify a novel layer of regulation of beta cell function, namely AS controlled by key splicing regulators such as Nova1.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25249621" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59641" }, "primaryId" : "GEO:GSE59641", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59641" } ] }, "title" : "miR-222 is necessary for exercise-induced cardiac growth and protects against pathological cardiac remodeling.", "dateAssigned" : "2014-07-22T00:00:00.000-05:00", "summary" : "Isolated primary neonatal rat ventricular cardiomyocytes were plated in 6 cm BD Primaria tissue culture dishes. Transfection of microRNA precursors or scramble control (0.4 µM) was carried out using Lipofectamine RNAiMAX (Invitrogen) as recommended by the manufacturer. Forty-eight hours after transfection, RNAs from cultured cells and tissues were isolated with Tryzol (Invitrogen) following the manufactures’ manuals. Total RNA was harvested and submitted to the Dana-Farber Cancer Institute Molecular Diagnostics Laboratory for assay. These results revealed miR-222 regulated gene expression in primary neonatal rat ventricular cardiomyocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25863248" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59645" }, "primaryId" : "GEO:GSE59645", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59645" } ] }, "title" : "Gene expression of whole hippocampus 24hr post-injury in rat", "dateAssigned" : "2014-07-22T00:00:00.000-05:00", "summary" : "Traumatic brain injury (TBI) alters and dysregulates the expression of thousands of genes in the brain. Since some of the most common problems in TBI patients are learning and memory deficits, we are studying the effects of TBI on the hippocampus, a region of the brain which is essential for learning and memory and which is known to be particularly vulnerable to TBI. We are interested in understanding how potential neuroprotective drugs alter the TBI-induced gene expression profile. The objective of this study is to elucidate and compare the differential gene expression profiles in the hippocampus of naive, sham-control, TBI and TBI plus drug treated rats. JM6, PMI-006 and E33 are three compounds with neuroprotective, anti-inflammatory and anti-oxidative effects. Our goal is to determine if different neuroprotective compounds have similar effects on common gene targets. These genes and the cell signaling pathways linked to them would then be the target of new therapeutic strategies for TBI.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59646" }, "primaryId" : "GEO:GSE59646", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59646" } ] }, "title" : "miRNA expression of whole hippocampus 24hr post-injury in rat", "dateAssigned" : "2014-07-22T00:00:00.000-05:00", "summary" : "Traumatic brain injury dysregulates microRNA expression in the brain. We hypothesized that injury-induced epigenetic changes contribute to neurodegeneration and learning and memory deficits after TBI. These changes may provide a mechanistic explanation for neuropsychiatric comorbidities in TBI patients. Our objective is to compare and contrast the effects of several neuroprotective drugs (JM6, PMI-006 and E33-estrogen) on the TBI-induced changes in microRNA expression in the hippocampus, a region of the brain that is critical for learning and memory. We will also study if different neuroprotective drugs have similar effects on common microRNAs which may cooperatively regulate a common set of gene targets.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59727" }, "primaryId" : "GEO:GSE59727", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59727" } ] }, "title" : "The transcriptome of TRPV1-positive sensory neurons revealed by subgroup-elimination transcriptomics", "dateAssigned" : "2014-07-24T00:00:00.000-05:00", "summary" : "We developed an approach to rapidly eliminate the subgroup of sensory neurons expressing the heat-gated cation channel TRPV1 from dissociated rat sensory ganglia using agonist treatment followed by density centrifugation. To identify transcripts predomintly expressed in TRPV1-positive neurons, we compared the transcriptome of all cells within sensory ganglia versus all cells without TRPV1 expressing neurons using RNA-Seq.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25551770" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59893" }, "primaryId" : "GEO:GSE59893", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59893" } ] }, "title" : "DNA methylation profile for male SD Rats upon fructose treatment by RRBS", "dateAssigned" : "2014-07-29T00:00:00.000-05:00", "summary" : "DNA methylation profile for male SD Rats upon fructose treatment by RRBS", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27322469" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59894" }, "primaryId" : "GEO:GSE59894", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59894" } ] }, "title" : "Exposure of rat to a variety of toxicants, bone marrow assayed by CodeLink microarray", "dateAssigned" : "2014-07-29T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59895" }, "primaryId" : "GEO:GSE59895", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59895" } ] }, "title" : "Exposure of rat to a variety of toxicants, brain assayed by CodeLink microarray", "dateAssigned" : "2014-07-29T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59905" }, "primaryId" : "GEO:GSE59905", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59905" } ] }, "title" : "Exposure of rat to a variety of toxicants, heart assayed by CodeLink microarray", "dateAssigned" : "2014-07-30T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59906" }, "primaryId" : "GEO:GSE59906", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59906" } ] }, "title" : "Exposure of rat hepatocytes to a variety of toxicants, assayed by CodeLink microarray.", "dateAssigned" : "2014-07-30T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59907" }, "primaryId" : "GEO:GSE59907", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59907" } ] }, "title" : "Exposure of rat to a variety of toxicants, intestine assayed by CodeLink microarray", "dateAssigned" : "2014-07-30T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59913" }, "primaryId" : "GEO:GSE59913", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59913" } ] }, "title" : "Exposure of rat to a variety of toxicants, kidney assayed by CodeLink microarray", "dateAssigned" : "2014-07-30T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59918" }, "primaryId" : "GEO:GSE59918", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59918" } ] }, "title" : "Gene expression profile for male SD Rats upon fructose treatment by RNA-Seq", "dateAssigned" : "2014-07-30T00:00:00.000-05:00", "summary" : "Gene expression profile for male SD Rats upon fructose treatment by RNA-Seq", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27322469" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59923" }, "primaryId" : "GEO:GSE59923", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59923" } ] }, "title" : "Exposure of rat to a variety of toxicants, liver assayed by Codelink microarray", "dateAssigned" : "2014-07-30T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59925" }, "primaryId" : "GEO:GSE59925", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59925" } ] }, "title" : "Exposure of rat to a variety of toxicants, spleen assayed by Codelink microarray", "dateAssigned" : "2014-07-30T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59926" }, "primaryId" : "GEO:GSE59926", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59926" } ] }, "title" : "Exposure of rat to a variety of toxicants, thigh muscle assayed by CodeLink microarray", "dateAssigned" : "2014-07-30T00:00:00.000-05:00", "summary" : "DrugMatrix is a comprehensive rat toxicogenomics database and analysis tool developed to facilitate the integration of toxicogenomics into hazard assessment. Using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59946" }, "primaryId" : "GEO:GSE59946", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE59946" } ] }, "title" : "Epigenomics of neural cells: REST-induced down- and up-regulation of gene expression in a two clone PC12 cell model.", "dateAssigned" : "2014-07-30T00:00:00.000-05:00", "summary" : "Cell epigenomics depends on the marks released by transcription factors operating via the assembly of complexes that induce focal changes of DNA and histone structure. Among these factors is REST, a repressor that, via its strong decrease, governs both neuronal and neural cell differentiation and specificity. REST operation on thousands of possible genes can occur directly or via indirect mechanisms including repression of other factors. In previous studies of gene down- and up-regulation, processes had been only partially investigated in neural cells. PC12 are well known neural cells sharing properties with neurons. In the widely used PC12 populations, low-REST cells coexist with few, spontaneous high-REST PC12 cells. High- and low-REST PC12 clones were employed to investigate the role and the mechanisms of the repressor action. Among 15,500 expressed genes we identified 1,770 target and non-target, RESTdependent genes. Functionally, these genes were found to operate in many pathways, from synaptic function to extracellular matrix. Mechanistically, downregulated genes were predominantly repressed directly by REST; up-regulated genes were mostly governed indirectly. Among other factors, Polycomb complexes cooperated with REST for down-regulation, Smad3 and Myod1 participated in up-regulation. In conclusion, we have highlighted that PC12 clones are a useful model to investigate REST, opening opportunities to development of epigenomic investigation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26413508" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60003" }, "primaryId" : "GEO:GSE60003", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60003" } ] }, "title" : "Expression data from Control or ShSuz12 rat Intestinal epithelial cells IEC-6", "dateAssigned" : "2014-08-01T00:00:00.000-05:00", "summary" : "Polycomb-group proteins form multimeric protein complexes involved in transcriptional silencing. The Polycomb Repressive complex 2 (PRC2) contains the Suppressor of Zeste-12 protein (Suz12) and the histone methyltransferase Enhancer of Zeste protein-2 (Ezh2). This complex, catalyzing the di- and tri-methylation of histone H3 lysine 27, is essential for embryonic development and stem cell renewal. However, the role of Polycomb-group protein complexes in the control of the intestinal epithelial cell (IEC) phenotype is not known. We investigated the impact of Suz 12 depletion on gene expression in IEC-6 cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23192652" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60013" }, "primaryId" : "GEO:GSE60013", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60013" } ] }, "title" : "EB-mediated NPY expression and release", "dateAssigned" : "2014-08-01T00:00:00.000-05:00", "summary" : "Neuropeptide Y (NPY) is an endogenous modulator of neuronal activity by regulating GABA and glutamate release. Previously, we found that estradiol modulates NPY expression in the hippocampal dentate gyrus. Here we investigated which estrogen receptor type activation is required for the NPY expression. Further, we determined effects of estrogen receptor activation on NPY release. Finally, we determined the contribution of estrogen-mediated remodeling of the GABAergic and glutamatergic network in relation to changes in coupling with NPY in ovariectomized rats. We found that activation of either estrogen receptor type increases NPY expression as well as NPY release in the dentate gyrus. We also found that compared to OVX rats, estrogen replacement increases the likeness of synergistic/antagonistic coupling between the NPY and GABAergic synapse genes while the glutamatergic synapse genes are less likely coupled with NPY. The data together suggest that estrogen plays a critical role in regulation of activity of the NPY system and its coupling to GABAergic and glutamatergic synapses in female rat dentate gyrus.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26541912" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60033" }, "primaryId" : "GEO:GSE60033", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60033" } ] }, "title" : "microRNAs involved in neuropathic pain following a peripheral nerve injury", "dateAssigned" : "2014-08-01T00:00:00.000-05:00", "summary" : "Peripheral nerve injury alters the expression of hundreds of proteins in dorsal root ganglia (DRG). Targeting some of these proteins has led to successful treatments for acute pain, but not for sustained postoperative neuropathic pain. The latter may require targeting multiple proteins. Since a single microRNA (miR) can affect the expression of multiple proteins, here, we describe an approach to identify chronic neuropathic pain-relevant miRs. We used two variants of the spared nerve injury (SNI): Sural-SNI and Tibial-SNI and found distinct pain phenotypes between the two. Both models induced strong mechanical allodynia, but only Sural-SNI rats maintained strong mechanical and cold allodynia, as previously reported. In contrast, we found that Tibial-SNI rats recovered from mechanical allodynia and never developed cold allodynia. Since both models involve nerve injury, we increased the probability of identifying differentially regulated miRs that correlated with the quality and magnitude of neuropathic pain and decreased the probability of detecting miRs that are solely involved in neuronal regeneration. We found seven such miRs in L3-L5 DRG. The expression of these miRs increased in Tibial-SNI. These miRs displayed a lower level of expression in Sural-SNI, with four having levels lower than those in sham animals. Bioinformatics analysis of how these miRs could affect the expression of some ion channels supports the view that, following a peripheral nerve injury, the increase of the 7 miRs may contribute to the recovery from neuropathic pain while the decrease of four of them may contribute to the development of chronic neuropathic pain. The approach used resulted in the identification of a small number of potentially neuropathic pain relevant miRs. Additional studies are required to investigate whether manipulating the expression of the identified miRs in primary sensory neurons can prevent or ameliorate chronic neuropathic pain following peripheral nerve injuries.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60060" }, "primaryId" : "GEO:GSE60060", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60060" } ] }, "title" : "miRNA expression profiles from neurogenic differentiation of mesenchymal stem cells under conditioned microenvironments", "dateAssigned" : "2014-08-04T00:00:00.000-05:00", "summary" : "Objectives: To evaluate the effects of IGF-1 in trans-lineage differentiation of MSCs, we have induced MSCs into neural lineage in 3 groups; Group A (positive control) - EGF+bFGF, Group B (Treatment) - EGF+bFGF+IGF-1, and Group C (negative control/ untreated). To unravel the role of regulatory miRNAs involved in the early differentiation, we have performed detailed miRNA profiling for MSCs-derived NPCs at three time intervals (day 1, day 3 and day 5). The data has explored crucial miRNAs involved in early differentiation of MSCs into NPCs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25938966" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60069" }, "primaryId" : "GEO:GSE60069", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60069" } ] }, "title" : "Characteristics of Long Non-coding RNAs in the Brown Norway Rat and Alterations in the Dahl Salt-Sensitive Rat", "dateAssigned" : "2014-08-04T00:00:00.000-05:00", "summary" : "Using poly(A)-independent and strand-specific RNA-seq, we identified approximately 1,500 to 1,800 lncRNAs expressed in each of the following tissues of Brown Norway rats: the renal cortex, renal outer medulla, liver, cardiac left ventricle, adrenal gland, and hypothalamus.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60118" }, "primaryId" : "GEO:GSE60118", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60118" } ] }, "title" : "Inhalation exposure of hexanal in rats (mRNA)", "dateAssigned" : "2014-08-05T00:00:00.000-05:00", "summary" : "To further development of insight into the mechanism of toxicity, it is important to employ whole genome microarray expression profiling as a discovery platform to ientify genes with the potential to distinguish hexanal exposure across an exposure range relevant for toxicologic mechanisms. However, few reports have described the effect of hexanal on gene expression profiles using animal model. In this respect, we studied the expression profiles of mRNAs in hexanal-exposed in rats by microarray analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60158" }, "primaryId" : "GEO:GSE60158", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60158" } ] }, "title" : "Feedback Inhibition of CREB Signaling Promotes Beta Cell Dysfunction in Insulin Resistance.", "dateAssigned" : "2014-08-06T00:00:00.000-05:00", "summary" : "Although persistent elevations in circulating glucose concentrations promote compensatory increases in pancreatic islet mass, unremitting insulin resistance causes a deterioration in beta cell function that disrupts glucose balance and signals the progression to diabetes 1. Glucagon like Peptide 1 (GLP1) agonists improve glucose tolerance in insulin resistance, although some individuals are unresponsive to treatment. Here we show that increases in GLP1 during feeding promote beta cell function in part through the PKA-mediated activation of CREB and its coactivator CRTC2 2. Mice with a knockout of CRTC2 in beta cells have impaired oral glucose tolerance due to decreases in circulating insulin concentrations. CRTC2 was found to promote beta cell function in part by stimulating the expression of the transcription factor MafA. Chronic hyperglycemia associated with high fat or high carbohydrate diet feeding disrupted cAMP signaling in pancreatic islets. Indeed, prolonged elevations in circulating glucose concentrations interfered with CREB signaling by activating the mTOR pathway and triggering the hypoxia inducible factor (HIF1)-dependent induction of the Protein Kinase A Inhibitor beta (PKIB), a potent inhibitor of PKA catalytic activity 3. As disruption of the PKIB gene restored glucose tolerance and insulin secretion in obesity, our results demonstrate how cross-talk between nutrient and hormonal pathways contributes to loss of pancreatic islet function in insulin resistance.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25704817" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60203" }, "primaryId" : "GEO:GSE60203", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60203" } ] }, "title" : "Inhalation exposure of hexanal in rats (miRNA)", "dateAssigned" : "2014-08-07T00:00:00.000-05:00", "summary" : "To further development of insight into the mechanism of toxicity, it is important to employ whole genome microarray expression profiling to identify and characterize miRNAs profiles as a discovery platform relevant for toxicologic mechanisms of hexanal. miRNAs have prominent role in cell cycle control, apoptosis, cancer development and proliferation-related processes. However, few reports have described the effect of hexanal on miRNA expression profiles using animal model. In this respect, we studied the expression profiles of miRNAs in hexanal-exposed in rats by miRNA microarray analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60280" }, "primaryId" : "GEO:GSE60280", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60280" } ] }, "title" : "Genome-wide analysis of stress-exposure-associated and exposure-related individual differences associated blood gene expression in males and females.", "dateAssigned" : "2014-08-10T00:00:00.000-05:00", "summary" : "Delineating the molecular basis of individual differences in the stress response is critical to understanding the pathophysiology and treatment of posttraumatic stress disorder (PTSD). In this study, 7 d after predator-scent-stress (PSS) exposure, male and female rats were classified into vulnerable (i.e., “PTSD-like”) and resilient (i.e.,minimally affected) phenotypes on the basis of their performance on a variety of behavioral measures. Genome-wide expression profiling in blood and two limbic brain regions (amygdala and hippocampus), followed by quantitative PCR validation, was performed in these two groups of animals, as well as in an unexposed control group. Differentially expressed genes were identified in blood and brain associated with PSS-exposure and with distinct behavioral profiles postexposure. There was a small but significant between-tissue overlap (4–21%) for the genes associated with exposure-related individual differences, indicating convergent gene expression in both sexes. To uncover convergent signaling pathways across tissue and sex, upstream activated/deactivated transcription factorswere first predicted for each tissue and then the respective pathways were identified. Glucocorticoid receptor (GR) signaling was the only convergent pathway associatedwith individual differences when using the most stringent statistical threshold.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25114262" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60302" }, "primaryId" : "GEO:GSE60302", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60302" } ] }, "title" : "Genome-wide analysis of stress-exposure-associated and exposure-related individual differences associated amygdala gene expression in males and females.", "dateAssigned" : "2014-08-11T00:00:00.000-05:00", "summary" : "Delineating the molecular basis of individual differences in the stress response is critical to understanding the pathophysiology and treatment of posttraumatic stress disorder (PTSD). In this study, 7 d after predator-scent-stress (PSS) exposure, male and female rats were classified into vulnerable (i.e., “PTSD-like”) and resilient (i.e.,minimally affected) phenotypes on the basis of their performance on a variety of behavioral measures. Genome-wide expression profiling in blood and two limbic brain regions (amygdala and hippocampus), followed by quantitative PCR validation, was performed in these two groups of animals, as well as in an unexposed control group. Differentially expressed genes were identified in blood and brain associated with PSS-exposure and with distinct behavioral profiles postexposure. There was a small but significant between-tissue overlap (4–21%) for the genes associated with exposure-related individual differences, indicating convergent gene expression in both sexes. To uncover convergent signaling pathways across tissue and sex, upstream activated/deactivated transcription factorswere first predicted for each tissue and then the respective pathways were identified. Glucocorticoid receptor (GR) signaling was the only convergent pathway associatedwith individual differences when using the most stringent statistical threshold.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25114262" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60303" }, "primaryId" : "GEO:GSE60303", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60303" } ] }, "title" : "Genome-wide analysis of stress-exposure-associated and exposure-related individual differences associated hippocampus gene expression in males and females.", "dateAssigned" : "2014-08-11T00:00:00.000-05:00", "summary" : "Delineating the molecular basis of individual differences in the stress response is critical to understanding the pathophysiology and treatment of posttraumatic stress disorder (PTSD). In this study, 7 d after predator-scent-stress (PSS) exposure, male and female rats were classified into vulnerable (i.e., “PTSD-like”) and resilient (i.e.,minimally affected) phenotypes on the basis of their performance on a variety of behavioral measures. Genome-wide expression profiling in blood and two limbic brain regions (amygdala and hippocampus), followed by quantitative PCR validation, was performed in these two groups of animals, as well as in an unexposed control group. Differentially expressed genes were identified in blood and brain associated with PSS-exposure and with distinct behavioral profiles postexposure. There was a small but significant between-tissue overlap (4–21%) for the genes associated with exposure-related individual differences, indicating convergent gene expression in both sexes. To uncover convergent signaling pathways across tissue and sex, upstream activated/deactivated transcription factorswere first predicted for each tissue and then the respective pathways were identified. Glucocorticoid receptor (GR) signaling was the only convergent pathway associatedwith individual differences when using the most stringent statistical threshold.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25114262" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60439" }, "primaryId" : "GEO:GSE60439", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60439" } ] }, "title" : "Expression data from rats esophagi", "dateAssigned" : "2014-08-15T00:00:00.000-05:00", "summary" : "This microarray study was performed to investigate the molecular events in esophageal SCC carcinogenesis in NMBA induced rat esophageal SCC models.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60539" }, "primaryId" : "GEO:GSE60539", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60539" } ] }, "title" : "Identify and characterize the circular RNAs expressed in lactating rat mammary glands", "dateAssigned" : "2014-08-20T00:00:00.000-05:00", "summary" : "Conclusions:The results provide the basis for comparisons with breast cancer profiles and for selection of representative circRNA candidates for future functional characterization in breast development and breast cancer.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26472973" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60752" }, "primaryId" : "GEO:GSE60752", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60752" } ] }, "title" : "Time resolved ribosome profiling study of oxygen and glucose deprivation of rat pheochromocytoma cells", "dateAssigned" : "2014-08-26T00:00:00.000-05:00", "summary" : "Oxygen and glucose metabolism plays a pivotal role in many (patho)physiological conditions. In particular, oxygen and glucose deprivation (OGD) occurs during ischemia and stroke, resulting in extensive tissue injury and cell death. We applied time-resolved ribosome profiling technique to assess early events at the level of gene expression in rat pheochromocytoma PC12 cells during short-term OGD. Most substantial alterations in transcripts levels and their translation were seen to occur in the first 20 minutes of OGD. The rapid adaptation of translation apparatus to OGD is global and involves altered elongation and initiation rates. We also observed salient and reproducible alterations in ribosome densities of individual mRNAs such as increased translation of particular upstream Open Reading Frames (uORFs); induced site-specific arrests of the ribosomes and synthesis of extended protein isoforms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25943107" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60819" }, "primaryId" : "GEO:GSE60819", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60819" } ] }, "title" : "Effects of acute prenatal exposure to ethanol on microRNA expression are ameliorated by environmental manipulation.", "dateAssigned" : "2014-08-27T00:00:00.000-05:00", "summary" : "In this study, we tested if miRNAs are altered in amygdala and ventral striatum as a consequence of prenatal ethanol exposure and/or social enrichment. miRNA samples from 72 male and female adolescent rats were analyzed by RNA-Seq analysis and Affymetrix miRNA arrays. Several miRNAs showed significant changes due to prenatal ethanol exposure or social enrichment in one or both brain regions. Some of the miRNA changes caused by ethanol were reversed by social enrichment. The top predicted gene targets of these miRNAs were mapped and subjected to pathway enrichment analysis. We also directly examined the evidence for modulation of target mRNAs in whole transcriptome microarray data from the same rats. Among the pathways most strongly affected were p53, CREB, Glutamate and GABA signaling. Together, our data suggest a number of novel epigenetic mechanisms for social enrichment to reverse the effects of ethanol exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25309888" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60864" }, "primaryId" : "GEO:GSE60864", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60864" } ] }, "title" : "Microarray analysis of mouse gene expression in metronomic cyclophosphamide-treated rat glioma 9L xenografts implanted in scid mice", "dateAssigned" : "2014-08-27T00:00:00.000-05:00", "summary" : "Cyclophosphamide (CPA) treatment on a six-day repeating metronomic schedule induces a dramatic, innate immune cell-dependent regression of implanted gliomas. However, little is known about the underlying mechanisms of innate immune cell mobilization and recruitment, or about the role of DNA damage and cell stress response pathways in eliciting the anti-tumor immune responses linked to tumor regression. To address these questions, we compared untreated and 6-day metronomic cyclophosphamide-treated rat 9L gliosarcoma xenografts by mouse microarray analysis to identify responsive mouse (host) cell-specific factors.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25952672" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60881" }, "primaryId" : "GEO:GSE60881", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60881" } ] }, "title" : "Multiple sclerosis patient-derived CSF induces transcriptional changes in proliferating oligodendrocyte progenitors", "dateAssigned" : "2014-08-28T00:00:00.000-05:00", "summary" : "This study provides an overview of the transcriptional signature of oligodendrocyte progenitor cells (OPCs) exposed to the CSF collected from multiple sclerosis patients with either a relapsing remitting disease course (RRMS) or a confirmed primary progressive diagnosis (PPMS). Using an Affymetrix microarray we were able to detect a set of common and unique genes for each treatment group. Gene ontology analysis revealed a common group of genes involved in protein transport, actin dynamics and response to stress and DNA damage, while the RRMS-specific genes were grouped according to protein complex biogenesis, nuclear transport and RNA processing. The transcriptional signature of progenitors exposed to PPMS was characterized by an up-regulation of the pro-differentiation adhesion molecule Lgals3. We confirmed increased protein levels of its gene product,product; galectin-3 in proliferating OPCs incubated with CSF from PPMS patients and also found a four-fold increase in mRNA transcript levels of galectin-3 in human post-mortem normal-appearing white matter samples of primary progressive MS patients when compared to non-neurological controls. This study will help to better understand the common and specific transcriptional changes induced in the different subtypes of MS and therefore find more specific molecular targets for each disease subtype.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25948622" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60900" }, "primaryId" : "GEO:GSE60900", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60900" } ] }, "title" : "Effects of acute prenatal exposure to ethanol on microRNA expression are ameliorated by environmental manipulation", "dateAssigned" : "2014-08-28T00:00:00.000-05:00", "summary" : "In this study, we tested if miRNAs are altered in amygdala and ventral striatum as a consequence of prenatal ethanol exposure and/or social enrichment. miRNA samples from 72 male and female adolescent rats were analyzed by RNA-Seq analysis and Affymetrix miRNA arrays. Several miRNAs showed significant changes due to prenatal ethanol exposure or social enrichment in one or both brain regions. Some of the miRNA changes caused by ethanol were reversed by social enrichment. The top predicted gene targets of these miRNAs were mapped and subjected to pathway enrichment analysis. We also directly examined the evidence for modulation of target mRNAs in whole transcriptome microarray data from the same rats. Among the pathways most strongly affected were p53, CREB, Glutamate and GABA signaling. Together, our data suggest a number of novel epigenetic mechanisms for social enrichment to reverse the effects of ethanol exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25309888" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60961" }, "primaryId" : "GEO:GSE60961", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60961" } ] }, "title" : "Alteration of mRNA and microRNA expression profiles in rat muscular type vasculature in early postnatal development [mRNA]", "dateAssigned" : "2014-09-01T00:00:00.000-05:00", "summary" : "This study tested the hypothesis that mRNA expression profiles change in the muscular type rat saphenous artery during early postnatal development. To explore this, we performed mRNA microarray analysis on muscular type saphenous arteries of young (10-12 days) and adult (2-3 months) rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26073182" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60962" }, "primaryId" : "GEO:GSE60962", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60962" } ] }, "title" : "Alteration of mRNA and microRNA expression profiles in rat muscular type vasculature in early postnatal development [miRNA]", "dateAssigned" : "2014-09-01T00:00:00.000-05:00", "summary" : "This study tested the hypothesis that miRNA expression profiles change in the muscular type rat saphenous artery during early postnatal development. To explore this, we performed miRNA microarray analysis on muscular type saphenous arteries of young (10-12 days) and adult (2-3 months) rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26073182" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60966" }, "primaryId" : "GEO:GSE60966", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE60966" } ] }, "title" : "Expression profiling of brain structures of dependent and non-dependent rats self-administering alcohol and naive controls", "dateAssigned" : "2014-09-02T00:00:00.000-05:00", "summary" : "Rats were trained to orally self-administer alcohol in a concurrent, two-lever, free-choice contingency using a modification of the sweet solution fading procedure (O'Dell et al., 2004; Roberts et al., 2000; Vendruscolo et al., 2012). Following acquisition of self-administration, rats were allowed to self-administer unsweetened alcohol (10%) for 4 weeks and were then assigned to two groups matched by levels of responding: one group (dependent group) was exposed to chronic, intermittent ethanol vapors for 4 weeks to induce dependence; the other group (nondependent group) was not exposed to ethanol vapor. After a month of vapor exposure, rats were again tested during acute withdrawal (6-8 hours after removal from the vapor chambers) until stable levels of alcohol intake were achieved. As expected, alcohol vapor-exposed rats self-administered significantly greater amounts of alcohol than control rats not exposed to alcohol vapor during acute withdrawal. Rats were sacrificed during protracted abstinence (3 weeks after the end of alcohol vapor exposure) along with age-matched alcohol naive rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61039" }, "primaryId" : "GEO:GSE61039", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61039" } ] }, "title" : "Transcriptional Profiling of rat hypothalamic response to TCDD", "dateAssigned" : "2014-09-03T00:00:00.000-05:00", "summary" : "In many mammals, halogenated aromatic hydrocarbon (HAH) exposure causes wasting syndrome, defined as lethal weight loss as a result of severe and persistent hypophagia. The most potent HAH in causing wasting is 2,3,7,8-tetrachlorodibenzo-¿-dioxin (TCDD), which exerts its toxic effects through the aryl hydrocarbon receptor (AHR) – a transcription factor. Because TCDD toxicity is thought to predominantly arise from dysregulation of AHR-transcribed genes, we hypothesized that wasting syndrome is due to TCDD-induced dysregulation of genes involved in regulation of food-intake. We therefore focused on the hypothalamus, as it is the regulatory center of food-intake and energy balance in the central nervous system. We profiled mRNA abundance in hypothalamic tissue from two rat strains with widely differing sensitivities to wasting syndrome: TCDD-sensitive Long-Evans rats and TCDD-resistant Han/Wistar rats, 23 hours after exposure to TCDD (100 µg/kg) or corn oil vehicle. We found that TCDD exposure caused minimal transcriptional dysregulation effects in the hypothalamus, with only 6 genes changed in Long-Evans rats and 15 genes in Han/Wistar rats. Two of the most dysregulated genes were Cyp1a1 and Nqo1, which are induced by TCDD across a wide range of tissues and are considered sensitive markers of TCDD exposure. The minimal response of the hypothalamic transcriptome to a lethal dose of TCDD at an early time-point suggests that the hypothalamus is not the predominant site of initial events leading to hypophagia and associated wasting. TCDD may affect feeding behaviour via events upstream or downstream of the hypothalamus, and further work is required to evaluate this at the level of individual hypothalamic nuclei and subregions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25529477" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61072" }, "primaryId" : "GEO:GSE61072", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61072" } ] }, "title" : "Time-Dependent miRNA Profiling Following Ischemia/Reperfusion Injury in Rat Retina", "dateAssigned" : "2014-09-03T00:00:00.000-05:00", "summary" : "The purpose of the present study was to investigate time-dependent changes in the expression profile of miRNAs, following induction of IR in the rat retina, and to characterize the affected pathways, networks and processes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61083" }, "primaryId" : "GEO:GSE61083", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61083" } ] }, "title" : "Expression data from rat dissected dendrites", "dateAssigned" : "2014-09-03T00:00:00.000-05:00", "summary" : "Using microdissected dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague-Dawley), we investigate via microarrays, subcellular localization of mRNAs in dendrites of neurons to assay the evolutionary differences in subcellular dendritic transcripts localization.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25301173" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61085" }, "primaryId" : "GEO:GSE61085", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61085" } ] }, "title" : "Expression data from Soma dissected from single-cell rat Hippocampal neurons", "dateAssigned" : "2014-09-03T00:00:00.000-05:00", "summary" : "To assess neuronal expression divergence between mice and rats, we used the Affymetrix array platform to assay the transcriptomes of micro-dissected individual soma and pool of dendrites of hippocampal neurons in dispersed primary cell cultures from rat and mouse.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25301173" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61087" }, "primaryId" : "GEO:GSE61087", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61087" } ] }, "title" : "Expression data from rat adult and pups heart and hippocampal tissue.", "dateAssigned" : "2014-09-03T00:00:00.000-05:00", "summary" : "To assess in order to assess potential disparities in gene expression due to developmental differences we performed a comparison between hippocampus and heart tissues from rat and mouse pup (one week old) and adult (10 week old) animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25301173" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61090" }, "primaryId" : "GEO:GSE61090", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61090" } ] }, "title" : "Beta-cell maturation is associated with miRNA expression changes", "dateAssigned" : "2014-09-03T00:00:00.000-05:00", "summary" : "We found that in rodents, postnatal beta-cell maturation is associated with changes in the expression of several islet microRNAs and discovered that these modifications are driven by changes in the nutrient supply. Mimicking the microRNA changes observed during ß-cell maturation in newborn rat islet cells was sufficient to promote glucose-induced insulin release and to achieve a mature ß-cell secretory phenotype. Moreover, the modifications in the level of some of these microRNAs reduced the proliferation of newborn ß-cells, suggesting that they contribute to the limited proliferative capacity of adult ß-cells. These findings demonstrated that miRNAs contribute to postnatal beta-cell maturation and development. Their role is likely to promote beta-cell adaptation to fuel supply and to maintain glucose homeostasis by regulating insulin release and proliferation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61131" }, "primaryId" : "GEO:GSE61131", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61131" } ] }, "title" : "Expression data from primary rat aortic smooth muscle cells", "dateAssigned" : "2014-09-04T00:00:00.000-05:00", "summary" : "We used microarrays for identification and functional characterization of [Na+]i/]K+]i-sensitive transcriptome in RASMC", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25375852" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61179" }, "primaryId" : "GEO:GSE61179", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61179" } ] }, "title" : "Islet-specific microRNA changes driven by nutrient shift trigger postnatal beta-cell maturation - intact islet mRNAs", "dateAssigned" : "2014-09-05T00:00:00.000-05:00", "summary" : "We found that in rodents, postnatal beta-cell maturation is associated with changes in the expression of several islet microRNAs and discovered that these modifications are driven by changes in the nutrient supply. Mimicking the microRNA changes observed during ß-cell maturation in newborn rat islet cells was sufficient to promote glucose-induced insulin release and to achieve a mature ß-cell secretory phenotype. Moreover, the modifications in the level of some of these microRNAs reduced the proliferation of newborn ß-cells, suggesting that they contribute to the limited proliferative capacity of adult ß-cells. These findings demonstrated that miRNAs contribute to postnatal beta-cell maturation and development. Their role is likely to promote beta-cell adaptation to fule supply and to maintain glucose homeostasis by regulating insulin release and proliferation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61180" }, "primaryId" : "GEO:GSE61180", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61180" } ] }, "title" : "Islet-specific microRNA changes driven by nutrient shift trigger postnatal beta-cell maturation - intact islet microRNAs", "dateAssigned" : "2014-09-05T00:00:00.000-05:00", "summary" : "We found that in rodents, postnatal beta-cell maturation is associated with changes in the expression of several islet microRNAs and discovered that these modifications are driven by changes in the nutrient supply. Mimicking the microRNA changes observed during ß-cell maturation in newborn rat islet cells was sufficient to promote glucose-induced insulin release and to achieve a mature ß-cell secretory phenotype. Moreover, the modifications in the level of some of these microRNAs reduced the proliferation of newborn ß-cells, suggesting that they contribute to the limited proliferative capacity of adult ß-cells. These findings demonstrated that miRNAs contribute to postnatal beta-cell maturation and development. Their role is likely to promote beta-cell adaptation to fule supply and to maintain glucose homeostasis by regulating insulin release and proliferation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61181" }, "primaryId" : "GEO:GSE61181", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61181" } ] }, "title" : "Islet-specific microRNA changes driven by nutrient shift trigger postnatal beta-cell maturation - dispersed islet cell mRNAs after miR-17-5p transfection", "dateAssigned" : "2014-09-05T00:00:00.000-05:00", "summary" : "We found that in rodents, postnatal beta-cell maturation is associated with changes in the expression of several islet microRNAs and discovered that these modifications are driven by changes in the nutrient supply. Mimicking the microRNA changes observed during ß-cell maturation in newborn rat islet cells was sufficient to promote glucose-induced insulin release and to achieve a mature ß-cell secretory phenotype. Moreover, the modifications in the level of some of these microRNAs reduced the proliferation of newborn ß-cells, suggesting that they contribute to the limited proliferative capacity of adult ß-cells. These findings demonstrated that miRNAs contribute to postnatal beta-cell maturation and development. Their role is likely to promote beta-cell adaptation to fule supply and to maintain glucose homeostasis by regulating insulin release and proliferation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61204" }, "primaryId" : "GEO:GSE61204", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61204" } ] }, "title" : "Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPKMEF2 signaling [ChIP-seq]", "dateAssigned" : "2014-09-08T00:00:00.000-05:00", "summary" : "Identfification of MEF2A target genes using ChIP-exo in skeletla muscle and primary cardiomyocytes. Identfification of MEF2A target genes using ChIP-exo and RNA-seq in skeletal muscle and primary cardiomyocytes. MEF2 plays a profound role in the regulation of transcription in cardiac and skeletal muscle lineages. To define the overlapping and unique MEF2A genomic targets, we utilized ChIP-exo analysis of cardiomyocytes and skeletal myoblasts. Of the 2783 and 1648 MEF2A binding peaks in skeletal myoblasts and cardiomyocytes, respectively, 294 common binding sites were identified. Genomic targets were compared to differentially expressed genes in RNA-seq analysis of MEF2A depleted myogenic cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25217591" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61301" }, "primaryId" : "GEO:GSE61301", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61301" } ] }, "title" : "Gene expression of 7 day combinatorial yohimbine and imipramine treated rat hippocampi", "dateAssigned" : "2014-09-10T00:00:00.000-05:00", "summary" : "Rats treated on 7 consecutive days with either 2 injections of vehicle (Ctl) (DMSO for yohimbine, saline for imipramine) or Y+I (2mg/kg Yohimbine + 20mg/kg Imipramine) were sacrificed 2 hours post the last injection and their hippocampi used for gene expression analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61319" }, "primaryId" : "GEO:GSE61319", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61319" } ] }, "title" : "Gene expression profiles in rat alveolar macrophages exposure to impurity-free single-wall carbon nanotubes", "dateAssigned" : "2014-09-10T00:00:00.000-05:00", "summary" : "To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the transcriptional level, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish characterization of physicochemical properties of impurity-free single-wall carbon nanotubes (SWCNTs), namely, relatively small bundles and a short linear shape (CNT-1) and large bundles and a long linear shape (CNT-2).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25865113" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61326" }, "primaryId" : "GEO:GSE61326", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61326" } ] }, "title" : "Vitamin D Prevents Cognitive Decline and Enhances Hippocampal Synaptic Function in Aging Rats", "dateAssigned" : "2014-09-11T00:00:00.000-05:00", "summary" : "Vitamin D is an important calcium-regulating hormone with diverse functions in numerous tissues including the brain. Increasing evidence suggests that vitamin D may play a role in maintaining cognitive function and that vitamin D deficiency may accelerate age-related cognitive decline. Using aging rodents, we attempted to model the range of human serum vitamin D levels, from deficient to sufficient, to test whether vitamin D could preserve or improve cognitive function with aging. For 5-6 months, middle-aged F344 rats were fed diets containing low, medium (typical amount) or high vitamin D3 (100, 1000 or 10,000 IU/kg diet, respectively) and then hippocampal-dependent learning and memory were tested in the Morris water maze. Rats on high vitamin D achieved the highest blood levels (in the sufficient range) and significantly outperformed low and medium groups on maze reversal, a particularly challenging task that detects more subtle changes in memory. In addition to calcium-related processes, hippocampal gene expression microarrays identified pathways pertaining to synaptic transmission, cell communication and G-protein function as being up-regulated with high vitamin D. Basal synaptic transmission also was enhanced corroborating observed effects on gene expression and learning and memory. Our studies demonstrate a causal relationship between vitamin D status and cognitive function and suggest that vitamin D-mediated changes in hippocampal gene expression may improve the likelihood of successful brain aging.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25267625" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61480" }, "primaryId" : "GEO:GSE61480", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61480" } ] }, "title" : "Environmentally Induced Epigenetic Transgenerational Inheritance of Sperm Epimutations Promotes Genetic Mutations [CGH]", "dateAssigned" : "2014-09-17T00:00:00.000-05:00", "summary" : "A variety of environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation. This involves the germline transmission of epigenetic information between generations. Exposure specific sperm epimutations have been previously observed. The current study was designed to investigate the potential role genetic mutations have in the process, using copy number variations (CNV). In the first (F1) generation following exposure negligible CNV were identified, but in the transgenerational F3 generation a significant increase in CNV were identified in the sperm. The genome-wide differential DNA methylation regions (epimutations) were correlated with the genome locations of the CNV. Observations indicate the environmental induction of the epigenetic transgenerational inheritance of sperm epimutations promotes genome instability such that genetic CNV mutations are acquired in later generations. A combination of epigenetics and genetics is suggested to be involved in the transgenerational phenotypes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61483" }, "primaryId" : "GEO:GSE61483", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61483" } ] }, "title" : "Gene expression profiles in rat lung following intratracheal instillation with impurity-free single-wall carbon nanotubes", "dateAssigned" : "2014-09-17T00:00:00.000-05:00", "summary" : "To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the transcriptional level, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish characterization of physicochemical properties of impurity-free single-wall carbon nanotubes (SWCNTs). We have prepared two types of dispersed the SWCNTs, namely relatively small bundles and a short linear shape (CNT-1) and large bundles and a long linear shape (CNT-2), and attempted to characterize time-dependent changes in the gene expression of lung tissues until 90 days after intratracheal instillation with SWCNTs suspensions at 0.4 mg injected dose per rat.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25865113" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61498" }, "primaryId" : "GEO:GSE61498", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61498" } ] }, "title" : "Development of gene expression for stress in heat- and shake-induced injury in the rat jejunum", "dateAssigned" : "2014-09-17T00:00:00.000-05:00", "summary" : "To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish radiation dose across an exposure range relevant for medical decision-making in a radiological emergency. Human peripheral blood from healthy donors was irradiated ex vivo, and a 74-gene consensus signature was identified that distinguished between four radiation doses (0.5, 2, 5 and 8 Gy) and control samples. The same set of genes separated samples by exposure level at both six and 24 hours after treatment, with overlap evident only at the highest two doses (5 and 8 Gy). Expression of five genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61543" }, "primaryId" : "GEO:GSE61543", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61543" } ] }, "title" : "Analysis of the placental tissue transcriptome from normal and testosterone treated rat pregnancy", "dateAssigned" : "2014-09-18T00:00:00.000-05:00", "summary" : "Elevated testosterone levels increase maternal blood pressure and decrease uterine blood flow in pregnancy, resulting in abnormal perinatal outcomes. The placenta is the key in understanding the pathophysiological processes associated with pregnancy. The current study is designed to characterize the genes essential for placental function to understand the mechanisms underlying normal and pathological gestation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61616" }, "primaryId" : "GEO:GSE61616", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61616" } ] }, "title" : "The effect of XUESAITONG on gene expression profile after focal cerebral ischemia in rats", "dateAssigned" : "2014-09-22T00:00:00.000-05:00", "summary" : "Male Sprague Dawley rat model of MCAO and reperfusion were administered XST for 7 days while the control group was not treated.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61617" }, "primaryId" : "GEO:GSE61617", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61617" } ] }, "title" : "Human transcripts up-regulated in the human mesenchymal stem cells migrated within the rat synovium; rat transcripts up-regulated in the rat synovium after human mesenchymal stem cells injection", "dateAssigned" : "2014-09-22T00:00:00.000-05:00", "summary" : "After the injection of human synovial mesenchymal stem cells into the rat (Lewis strain) knee joint, synovium was investigated using species specific microarray analyses of human and rat transcripts to investigate the gene expression change after injection.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61731" }, "primaryId" : "GEO:GSE61731", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61731" } ] }, "title" : "Real-time quantitative PCR analysis of undifferentiated rat embryonic stem cells and induced pluripotent stem cells", "dateAssigned" : "2014-09-24T00:00:00.000-05:00", "summary" : "Validation study of a focused microarray for evaluation of undifferentiated rat ESCs.Using a focused microarray, undifferentiated embryonic stem cells (ESCs) can be distinguished from differentiated ESCs and other cells derived from the early embryo since they have a unique gene expression pattern associated with pluripotency and lack of markers of differentiation. To date, however, such an array has not been developed for the rat species and differences in genomes of rat and human or rat and mouse preclude the use of ESC focused human or mouse microarrays for the rat. Here, we developed a focused microarray for screening rat ESCs and provide validation data that this array can distinguish undifferentiated rat ESCs from rat trophoblast stem cells (TS), rat extraembryonic endoderm cells (XEN), mouse embryonic fibroblast feeder cells (MEFs) and rat ESCs that have been differentiated in vitro. We used this tool to compare rat ESCs which have been expanded in a conventional rat ESC medium containing two inhibitors, e.g., GSK3 and MEK inhibitors, and leukemia inhibitory factor (LIF), and found expression of Cdx2, a gene associated with trophoblast determination. The rat ESC focused microarray described in this report has utility for rapid screening rat ESCs. This will enable optimization of culture conditions in the future.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61770" }, "primaryId" : "GEO:GSE61770", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61770" } ] }, "title" : "microRNA sequencing of HEK293 and H9c2 cells", "dateAssigned" : "2014-09-25T00:00:00.000-05:00", "summary" : "The human HEK293 / 293T and rat cardiomyoblast H9c2 cell lines are commonly employed for microRNA-mRNA interaction studies. Here, I provide microRNA sequencing data obtained from each of these lines to better document which microRNAs are endogenously expressed at high or low levels.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61784" }, "primaryId" : "GEO:GSE61784", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61784" } ] }, "title" : "Gene expression profile in DRG neurons over-expressing NRG1 type III intracellular domain", "dateAssigned" : "2014-09-25T00:00:00.000-05:00", "summary" : "In DRG neurons NRG1 type III intacellular domain (ICD) moves to the nucleus upon contact with Schwann cells. We aimed to investigate genes up/down regulated by ICD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25362470" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61840" }, "primaryId" : "GEO:GSE61840", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61840" } ] }, "title" : "Genome-wide profiling of gene expression under electro-acupuncture pretreatment on myocardial I/R injury in rats", "dateAssigned" : "2014-09-29T00:00:00.000-05:00", "summary" : "Conclusions: Our results for the first time generated genome-wide gene expression profiles both in the rat I/R model and in acupuncture treatment by high throughput sequencing. The optimized data analysis workflows reported here should provide a framework for acupuncture investigations of expression profiles.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25302705" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61991" }, "primaryId" : "GEO:GSE61991", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE61991" } ] }, "title" : "Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity", "dateAssigned" : "2014-10-02T00:00:00.000-05:00", "summary" : "In addition, following a homeostatic downscaling of neuronal activity many circRNAs exhibit significant up or down-regulation. These data indicate that brain circRNAs are positioned to respond to and regulate synaptic function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25714049" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62026" }, "primaryId" : "GEO:GSE62026", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62026" } ] }, "title" : "Transcriptomics Analysis and Hormonal Changes of Male and Female Rats Treated Chronically with a Low Dose of Acrylamide in their Drinking Water", "dateAssigned" : "2014-10-03T00:00:00.000-05:00", "summary" : "Acrylamide is known to produce follicular cell tumors of the thyroid in rats. RccHan Wistar rats were exposed in utero to a carcinogenic dose of acrylamide (3 mg/Kg bw/day) from gestation day 6 to delivery and then through their drinking water to postnatal day 35. In order to identify potential mechanisms of carcinogenesis in the thyroid glands, we used a transcriptomics approach. Thyroid glands were collected from male pups at 10 PM and female pups at 10 AM or 10 PM in order to establish whether active exposure to acrylamide influenced gene expression patterns or pathways that could be related to carcinogenesis. While all animals exposed to acrylamide showed changes in expected target pathways related to carcinogenesis, such as DNA repair, DNA replication, chromosome segregation, among others, animals that were sacrificed while actively drinking acrylamide-laced water during their active period at night showed increased changes in pathways related to oxidative stress, detoxification pathways, metabolism, and activation of checkpoint pathways, among others. In addition, thyroid hormones, T3 and T4, were increased in acrylamide-treated rats sampled at night, but not in quiescent animals, compared to controls. The data clearly indicate that time of day for sample collection is critical to identifying molecular pathways that are altered by the exposures. These results suggest that carcinogenesis in the thyroids of acrylamide treated rats may ensue from several different mechanisms such as hormonal changes and oxidative stress and not only from direct genotoxicity, as has been assumed to date.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62028" }, "primaryId" : "GEO:GSE62028", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62028" } ] }, "title" : "Differences in gene expression between fast and slow muscle or between normal and denervated slow muscles", "dateAssigned" : "2014-10-03T00:00:00.000-05:00", "summary" : "Characters of slow muscle are strongly dependent on the level of muscular activity. Denervation silences the muscular activity. Therefore, we determined the effects of denervation on gene expression in slow soleus muscle of adult rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26404615" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62041" }, "primaryId" : "GEO:GSE62041", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62041" } ] }, "title" : "Characterization of changes in global genes expression in the distal colon of loperamide-induced constipation SD rats in response to the laxative effects of Liriope platyphylla", "dateAssigned" : "2014-10-03T00:00:00.000-05:00", "summary" : "In order to characterize the changes in global gene expression in the distal colon of constipated SD rats in response to the laxative effects induced by aqueous extract of Liriope platyphylla (AEtLP) including isoflavone, saponin, oligosaccharide, succinic acid and hydroxyproline, total RNA extracted from the distal colon of AEtLP-treated constipation rats was hybridized to oligonucleotide microarrays.Overall, 581 genes were up-regulated and 216 genes were down-regulated by constipation induced by loperamide, while 67 genes were up-regulated and 421 genes were down-regulated by AEtLP treatment in constipated rats compared to controls. Among the transcripts up-regulated by constipation, 89 were significantly down-regulated and 20 were recovered to normal levels by AEtLP treatment. The major genes in the down-regulated categories included Slc9a5, klk10, Fgf15 and Alpi, while the major genes in the recovered categories were Cyp2b2, Ace, G6pc and Setbp1. However, nine of these genes that were down-regulated by constipation were significantly up-regulated and four were recovered to normal levels by AEtLP treatment. The major genes in the up-regulated categories included Serpina3n, Lcn2 and Slc5a81, while the major genes in the recovered categories were Tmem45a, Rerg and Rgc32.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62092" }, "primaryId" : "GEO:GSE62092", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62092" } ] }, "title" : "Gene Expression of Kidney from HSRA-S (congenital solitary kidney) and HSRA-C (two-kidney) using Rat Gene 1.1 ST Array [RaGene-1_1-st]", "dateAssigned" : "2014-10-06T00:00:00.000-05:00", "summary" : "Whole transcriptome analysis was evaluated at month 1 to identify early changes in genes/networks that may be involved in increased susceptibility of HSRA-S to develop kidney injury in the long-term.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25349207" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62204" }, "primaryId" : "GEO:GSE62204", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62204" } ] }, "title" : "Transcription in wounded rat vocal folds and vocal fold fibroblasts", "dateAssigned" : "2014-10-09T00:00:00.000-05:00", "summary" : "We used microarrays to characterize transcriptome profiles of rat vocal fold tissue following surgical injury (vs. naive tissue); rat vocal fold fibroblasts harvested from scar tissue at the 60 d time point (vs. naive fibroblasts); rat vocal fold scar fibroblasts treated with siRNA against the collagen chaperone protein rat gp46 (vs. scramble siRNA).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25592437" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62282" }, "primaryId" : "GEO:GSE62282", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62282" } ] }, "title" : "S100 calcium-binding proteins A8/A9 initiate the early inflammatory program in injured peripheral nerve", "dateAssigned" : "2014-10-11T00:00:00.000-05:00", "summary" : "To shed light on the early processes of immune response to peripheral nerve injury, we first used genome-wide transcriptional profiling and bioinformatics (Ingenuity, NextBio) pathway analyses of the proximal (P; regenerating) and distal (D; degenerating) nerve stumps at day 1 in the sciatic nerve axotomy model in rats. We identified a number of specific immunomodulatory genes and pathways that were regulated shortly post-injury in both the P and D segments, including all members of the interleukin (IL), chemokine, tumor necrosis factor (TNF), matrix metalloproteinase (MMP), toll-like receptor (TLR), tissue inhibitor of metalloproteinase (TIMP), ion channel and myosin families. Immunomodulatory calcium-binding S100A8 and S100A9 were the top up-regulated genes in both the D and P segments. In cultured Schwann cells stimulated with the purified S100A8/A9 heterodimer we recorded a high level of similarity of the activated genes and pathways with that of the injured nerve, especially in the activation of the chemokine and cytokine gene networks that support agranulocyte and granulocyte chemotaxis, adhesion, transmigration and rolling signaling pathways. We also confirmed activation of multiple cell death related gene networks supporting TNFR1, natural killer cell receptor and death receptor apoptosis signaling in the D stump, and the gluconeogenesis/glycolysis and cytoskeletal motility signaling in the P stump, corroborated by activation of ERK, PI3K and JNK kinase pathways. As compared to the D segment, multiple additional pathways were more efficiently upregulated in the P stump, including the IL-6 and -17, MMP-9, calcium, activated agranulocyte, leukocyte rolling and glutathione-mediated detoxification signaling pathways. These data suggest that shortly after nerve injury, upregulation of S100A8/A9 is responsible for the expression and release of chemokines and cytokines by Schwann cells, necessary to generate the initial chemotactic gradient and guide the hematogenous immune cells into the injury site.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25792748" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62368" }, "primaryId" : "GEO:GSE62368", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62368" } ] }, "title" : "Transcript expression in circulating whole blood after saline injections", "dateAssigned" : "2014-10-15T00:00:00.000-05:00", "summary" : "These experiments were designed to produce the appropriate controls so that their cohort's transcript (mRNA) changes in whole circulating blood could be determined. The cohorts were exposed to D-amphetamine under a neurotoxic and non-neurotoxic condition or subjected to elevated environmental temperatures that produced a hyperthermia very similar to heat stroke. The cohort data is in a separate, but linked, GEO file.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26177368" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62383" }, "primaryId" : "GEO:GSE62383", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62383" } ] }, "title" : "DNA Methylation Patterns in Rat Mammary Carcinomas Induced by Pre- and Post-Pubertal Irradiation", "dateAssigned" : "2014-10-15T00:00:00.000-05:00", "summary" : "Several lines of evidence indicate one's age at exposure to radiation strongly modifies the risk of radiation-induced breast cancer. We previously reported that rat mammary carcinomas induced by pre- and post-pubertal irradiation have distinct gene expression patterns, but the changes underlying these differences have not yet been characterized. The aim of this investigation was to see if differences in CpG DNA methylation were responsible for the differences in gene expression between age at exposure groups observed in our previous study.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27711132" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62387" }, "primaryId" : "GEO:GSE62387", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62387" } ] }, "title" : "In vivo activation of a conserved microRNA program induces robust mammalian heart regeneration (RNA-Seq)", "dateAssigned" : "2014-10-15T00:00:00.000-05:00", "summary" : "Heart failure is a leading cause of mortality and morbidity in the developed world, partly because mammals lack the ability to regenerate heart tissue. Whether this is due to evolutionary loss of regenerative mechanisms present in other organisms or to an inability to activate such mechanisms is currently unclear. Here, we decipher mechanisms underlying heart regeneration in adult zebrafish and show that the molecular regulators of this response are conserved in mammals. We identified miR-99/100 and Let-7a/c, and their protein targets smarca5 and fntb, as critical regulators of cardiomyocyte dedifferentiation and heart regeneration in zebrafish. Although human and murine adult cardiomyocytes fail to elicit an endogenous regenerative response following myocardial infarction, we show that in vivo manipulation of this molecular machinery in mice results in cardiomyocyte dedifferentiation and improved heart functionality after injury. These data provide a proof-of-concept for identifying and activating conserved molecular programs to regenerate the damaged heart.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25517466" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62388" }, "primaryId" : "GEO:GSE62388", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62388" } ] }, "title" : "Expression data from muscle samples following synergist ablation", "dateAssigned" : "2014-10-15T00:00:00.000-05:00", "summary" : "We used microarrays to detail the program of gene expression underlying the growth of the plantaris muscle following synergist ablation-induced supraphysiological overload", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27979985" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62426" }, "primaryId" : "GEO:GSE62426", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62426" } ] }, "title" : "Environmentally Induced Epigenetic Transgenerational Inheritance of Sperm Epimutations Promotes Genetic Mutations [MeDIP-Chip]", "dateAssigned" : "2014-10-16T00:00:00.000-05:00", "summary" : "A variety of environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation. This involves the germline transmission of epigenetic information between generations. Exposure specific sperm epimutations have been previously observed. The current study was designed to investigate the potential role genetic mutations have in the process, using copy number variations (CNV). In the first (F1) generation following exposure negligible CNV were identified, but in the transgenerational F3 generation a significant increase in CNV were identified in the sperm. The genome-wide differential DNA methylation regions (epimutations) were correlated with the genome locations of the CNV. Observations indicate the environmental induction of the epigenetic transgenerational inheritance of sperm epimutations promotes genome instability such that genetic CNV mutations are acquired in later generations. A combination of epigenetics and genetics is suggested to be involved in the transgenerational phenotypes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62556" }, "primaryId" : "GEO:GSE62556", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62556" } ] }, "title" : "The evolution of genic piRNA cluster loci expression patterns", "dateAssigned" : "2014-10-21T00:00:00.000-05:00", "summary" : "This study examines the conservation of Piwi-interacting RNA (piRNA) clusters that come from protein coding gene transcripts. By sequencing small RNA libraries from gonad tissues of Drosophilids and Glires we discover a diverse set of genic piRNA clusters conserved across animals. This dataset reveals new expression patterns for genic piRNA clusters and examines whether changing piRNA expression patterns correlates with sequence changes in piRNA cluster genomic sequence across a variety of animal species.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26588211" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62686" }, "primaryId" : "GEO:GSE62686", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62686" } ] }, "title" : "PRR7 is a novel NMDA-dependent inhibitor of c-Jun ubiquitination in neurons", "dateAssigned" : "2014-10-24T00:00:00.000-05:00", "summary" : "Elevated c-Jun levels result in apoptosis and are evident in neurodegenerative disorders such as Alzheimer's disease and dementia and after global cerebral insults such as stroke and epilepsy. NMDA receptor (NMDAR) antagonists block c-Jun upregulation and prevent neuronal cell death following excitotoxic insults. However, little is known about the molecular mechanisms that regulate c-Jun abundance in neurons. Here we show that PRR7, a component of synaptic junctions, can upregulate c-Jun levels by inhibiting its ubiquitination in neurons. PRR7 interacts with the GLUN1 subunit of NMDARs and is upregulated in the nucleus following NMDAR activation. We show that PRR7 interacts with the E3 ligase SCFFBW7 (FBW7) and blocks the FBW7-mediated ubiquitination of c-Jun. PRR7 overexpression increases c-Jun-dependent transcriptional activity and promotes neuronal death. Microarray assays indicate that both Prr7 knockdown or overexpression alter the abundance of c-Jun-regulated transcripts associated with cellular viability as well as synaptic function. Moreover, Prr7 knockdown attenuates NMDA-mediated excitotoxicity in primary neuronal cultures. Our results show that PRR7 links NMDAR activity to c-Jun function and provide insight into the processes that underlie NMDA-dependent excitotoxicity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27458189" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62688" }, "primaryId" : "GEO:GSE62688", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62688" } ] }, "title" : "Transcriptome profiling based study of early gene responses in susceptible and tolerant rat lung tissues during acute hypobaric hypoxia", "dateAssigned" : "2014-10-24T00:00:00.000-05:00", "summary" : "Conclusion: The differential gene expression patterns in different experimental sets elucidated the physiological mechanisms associated with progressive damage in the lung tissues of susceptible and normal (moderate) rats, and tissue protective measures in tolerant rats during acute hypobaric hypoxia.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62760" }, "primaryId" : "GEO:GSE62760", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62760" } ] }, "title" : "T Cell Deficiency in Spinal Cord Injury: Altered Locomotor Recovery and Whole-Genome Transcriptional Analysis", "dateAssigned" : "2014-10-28T00:00:00.000-05:00", "summary" : "T cells undergo autoimmunization following spinal cord injury (SCI) and play both protective and destructive roles during the recovery process. T-cell deficient athymic nude (AN) rats recover better than immunocompetent Sprague-Dawley (SD) rats following spinal cord transection. In the present study, we evaluated locomotor recovery in SD and AN rats following moderate spinal cord contusion. To explain variable locomotor outcome, we assessed whole-genome expression using RNA sequencing, in the acute (1 week post-injury) and chronic (8 weeks post-injury) phases of recovery. AN rats demonstrated greater locomotor function than SD rats only at 1 week post-injury, coinciding with peak T cell infiltration in immunocompetent rats. Genetic markers for T cells and helper T cells were acutely enriched in SD rats, while AN rats expressed genes for Th2 cells, cytotoxic T cells, NK cells, mast cells, IL-1a, and IL-6 at higher levels. Acute enrichment of cell death-related genes suggested that SD rats undergo secondary tissue damage from T cells. Additionally, SD rats exhibited increased acute expression of voltage-gated potassium (Kv) channel-related genes. However, AN rats demonstrated greater chronic expression of cell death-associated genes and less expression of axon-related genes. We put forth a model in which T cells facilitate early tissue damage, demyelination, and Kv channel dysregulation in SD rats following contusion SCI. However, compensatory features of the immune response in AN rats cause delayed tissue death and limit long-term recovery. T cell inhibition combined with other neuroprotective treatment may thus be a promising therapeutic avenue.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26546062" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62770" }, "primaryId" : "GEO:GSE62770", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62770" } ] }, "title" : "Epigenetic regulation of Atrophin1 by lysine-specific demethylase 1 is required for cortical progenitor maintenance", "dateAssigned" : "2014-10-28T00:00:00.000-05:00", "summary" : "Lysine-specific demethylase 1 (LSD1) is involved in gene regulation and development; however, its precise function, molecular targets and underlying mechanisms during development are poorly understood. Here, we show that LSD1 is required for neuronal progenitor cell (NPC) maintenance during cortical development. A ChIP-seq analysis identified a LSD1 binding site (LBAL) downstream of Atrophin1 (ATN1). Surprisingly, tranylcypromine (LSD1 inhibitor) treatment increased H3K4 methylation at LBAL, leading to ATN1 repression and NPC differentiation. Knockdown of LSD1 and ATN1 phenocopied each other in inducing NPC premature differentiation and depletion which could be rescued by ATN1 overexpression, suggesting that LSD1 controls NPC differentiation via regulation of ATN1 methylation status and expression. The involvement of LSD1 in ATN1 expression and NPC maintenance were confirmed in knockout mice. These findings hint at the potential application for the clinical drug, tranylcypromine, in the prevention and/or treatment of ATN1-associated degenerative disease, dentatorubral-pallidoluysian atrophy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25519973" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62806" }, "primaryId" : "GEO:GSE62806", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62806" } ] }, "title" : "Toxicogenomic Assessment of Liver Responses following subchronic exposure to furan in Fischer F344 rats [cRNA]", "dateAssigned" : "2014-10-29T00:00:00.000-05:00", "summary" : "Furan is a widely used industrial chemical and a common contaminant in heated foods. Chronic furan exposure has been shown to cause cholangiocarcinoma and hepatocellular tumors at doses of 2 mg/kg bw/day with gender differences in frequency and severity. The hepatic transcriptional alterations induced by low doses of furan (doses below those inducing liver tumors) and the potential mechanisms underlying gender differences are largely unexplored. We used DNA microarrays to examine the global hepatic mRNA and microRNA transcriptional profiles of male and female rats exposed to 0, 0.03, 0.12, 0.5 or 2 mg/kg bw/day furan over 90 days. Marked gender differences in gene expression responses to furan were observed, with many more altered genes in exposed males than females, confirming the increased sensitivity of males even at the low doses. Pathway analysis supported that key events in furan-induced hepatotoxicity in males included gene expression changes related to oxidative stress, apoptosis and inflammatory response, while pathway changes in females were consistent with primarily adaptive responses (regeneration). Pathway benchmark doses (BMDs) were estimated and compared to relevant apical endpoints. Transcriptional BMDs could be examined in males, they ranged from 0.08 – 1.43 mg/kg bw/day and approximated those derived from traditional histopathology. MiR-34a (a target of P53 signalling) was the only microRNA significantly increased at the 2 mg/kg bw/day, providing evidence in support of the importance of apoptosis and cell proliferation in furan hepatotoxicity. Overall, this study demonstrates the use of transcriptional profiling to discern mode of action and mechanisms involved in gender differences.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62807" }, "primaryId" : "GEO:GSE62807", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62807" } ] }, "title" : "Toxicogenomic Assessment of Liver Responses following subchronic exposure to furan in Fischer F344 rats [miRNA]", "dateAssigned" : "2014-10-29T00:00:00.000-05:00", "summary" : "Furan is a widely used industrial chemical and a common contaminant in heated foods. Chronic furan exposure has been shown to cause cholangiocarcinoma and hepatocellular tumors at doses of 2 mg/kg bw/day with gender differences in frequency and severity. The hepatic transcriptional alterations induced by low doses of furan (doses below those inducing liver tumors) and the potential mechanisms underlying gender differences are largely unexplored. We used DNA microarrays to examine the global hepatic mRNA and microRNA transcriptional profiles of male and female rats exposed to 0, 0.03, 0.12, 0.5 or 2 mg/kg bw/day furan over 90 days. Marked gender differences in gene expression responses to furan were observed, with many more altered genes in exposed males than females, confirming the increased sensitivity of males even at the low doses. Pathway analysis supported that key events in furan-induced hepatotoxicity in males included gene expression changes related to oxidative stress, apoptosis and inflammatory response, while pathway changes in females were consistent with primarily adaptive responses (regeneration). Pathway benchmark doses (BMDs) were estimated and compared to relevant apical endpoints. Transcriptional BMDs could be examined in males, they ranged from 0.08 – 1.43 mg/kg bw/day and approximated those derived from traditional histopathology. MiR-34a (a target of P53 signalling) was the only microRNA significantly increased at the 2 mg/kg bw/day, providing evidence in support of the importance of apoptosis and cell proliferation in furan hepatotoxicity. Overall, this study demonstrates the use of transcriptional profiling to discern mode of action and mechanisms involved in gender differences.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62883" }, "primaryId" : "GEO:GSE62883", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62883" } ] }, "title" : "Expression profiling of small, noncoding RNAs in physiologically hypertrophied rat hearts", "dateAssigned" : "2014-10-31T00:00:00.000-05:00", "summary" : "Conclusions: This is the first report to reveal the involvement of a large number of apoptotic miRNAs during physiological cardiac hypertrophy including the previously unknown cardiac players like miR-99, miR-100, miR-191, miR-181 and miR-19. Our data indicates that regulation of these apoptotic miRNAs can be one of the major key factor in determining pathological or physiological hypertrophy by controlling apoptosis, fibrosis and cell death mechanisms.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62994" }, "primaryId" : "GEO:GSE62994", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE62994" } ] }, "title" : "Microarray analysis of the therapeutic effects of the mixture of salvianolic acids from Salvia miltiorrhiza and total flavonoids from Anemarrhena asphodeloides on sulfur mustard-induced damages", "dateAssigned" : "2014-11-05T00:00:00.000-06:00", "summary" : "To further investigate the potential molecular basis of the therapeutic effects of the mixture of salvianolic acids from Salvia miltiorrhiza and total flavonoids from Anemarrhena asphodeloides (MSTF) on sulfur mustard (SM) damage, gene expression analysis was conducted on rats liver tissues using microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63004" }, "primaryId" : "GEO:GSE63004", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63004" } ] }, "title" : "The effects of UVB and the organic osmolyte betaine on rat epidermal keratinocytes in an organotypic culture system", "dateAssigned" : "2014-11-05T00:00:00.000-06:00", "summary" : "The expression of several genes relevant to epidermal biology, proliferation/differentiation or malignancy as well as solute transport were verified by independent methods (qRT-PCR, western blotting). The data concerning changes in calcium metabolism after UVB exposure has been published separately (Bart et al., Br. J. Dermatol. 171:376-387, 2014).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26391144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63096" }, "primaryId" : "GEO:GSE63096", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63096" } ] }, "title" : "Malnutrition-associated hepatic steatosis and ATP depletion is caused by peroxisomal and mitochondrial dysfunction and rescued by fenofibrate", "dateAssigned" : "2014-11-07T00:00:00.000-06:00", "summary" : "disturbances associated with malnutrition and have potentially profound clinical consequences with respect to the management of malnourished children worldwide.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27312946" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63103" }, "primaryId" : "GEO:GSE63103", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63103" } ] }, "title" : "Enhancer Analysis in Peripheral Nerve Injury", "dateAssigned" : "2014-11-07T00:00:00.000-06:00", "summary" : "ChIP-seq of H3K27acetylation in sham and injured nerve. Schwann cells play an important role in the response of peripheral nerve to injury. This study was designed to identify enhancers that are altered in sciatic nerve at 3 days post-injury to help identify pathways that mediate the gene expression reprogramming that occurs in Schwann cells after nerve injury. We employed ChIP-seq analysis of H3K27 acetylation as a mark of actively engaged enhancers, and compared enhancers in the distal stump of transected sciatic nerve compared to contralateral (sham) condition. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25614629" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63200" }, "primaryId" : "GEO:GSE63200", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63200" } ] }, "title" : "3 Week IV Study of RGMC Ab in Female Sprague Dawley Rats", "dateAssigned" : "2014-11-12T00:00:00.000-06:00", "summary" : "High levels of hepcidin, the main regulator of systemic iron metabolism leads to various diseases. Targeting hepcidin and lowering its concentration is a possible form of intervention in order to treat these diseases. High turnover rate of hepcidin is a major drawback of therapies directly targeting this peptide. We developed two monoclonal antibodies (mAbs) ABT-207 and h5F9-AM8 which inhibit hemojuvelin also known as repulsive guidance molecule c (RGMc) and downregulate hepcidin. After a single application of these antibodies hepcidin expression in liver and its concentration in serum were reduced. Serum iron increased for several weeks. The RGMc antibodies show a pronounced dose response relationship in rats with h5F9-AM8 having an IC50 (UIBC) of ~80 fold higher than ABT-207. When hepcidin levels were downregulated iron deposition in the liver was visible histologically one week post application. The anitbody-mediated iron deposition was not associated with any toxicologically relevant effect at the doses and timepoints evaluate. Iron depositions seen after 14 weekly treatments with ABT-207 were partially reversible in rats and in cynomolgus monkeys. Due to their long-lasting effects and excellent safety profile, both RGMc-blocking antibodies ABT-207 and h5F9-AM8 are favorable clinical candidates for diseases characterized by high serum hepcidin levels like anemia of chronic disease.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63295" }, "primaryId" : "GEO:GSE63295", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63295" } ] }, "title" : "Gene expression comparision in the developing striatum between transgenic rats expressing full-length human mutant huntingtin and time-matching controls", "dateAssigned" : "2014-11-14T00:00:00.000-06:00", "summary" : "The mechanisms involved in the pathogenesis of HD that result in late, and fatal, neurodegeneration are still not fully understood. The monogenic nature of HD is in contradiction with the complexity of the cellular alterations found in patients with HD. Huntingtin interacts with a broad range of proteins within the cell, and it is altered by the expanded polyglutamine tract. Transcriptional dysregulation is a common finding in genetic models and in human HD patients, and it is thought to play an important role in the disease. Although the onset of the disease is late in life, growing lines of evidence suggest that mHtt causes alterations in development. In this microarray study, the effects of mHtt on the transcriptome were investigated with a full-length human huntingtin (96 CAG repeats) expressing transgenic rat model of HD at an early stage of development (E14).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63305" }, "primaryId" : "GEO:GSE63305", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63305" } ] }, "title" : "Gene expression profiling of basal cells in rat epididymis", "dateAssigned" : "2014-11-14T00:00:00.000-06:00", "summary" : "Basal cells represent a specific cell type in the epididymis, with specific functions. We performed gene expression analysis to detect differentially regulated genes in basal cells versus other, non-basal, cells in rat epididymis, in order to understand basal cell functions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26400399" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63309" }, "primaryId" : "GEO:GSE63309", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63309" } ] }, "title" : "RNA-Seq of the rat pineal transcriptome, with in-vivo and in-vitro samples, under various treatment and surgical conditions", "dateAssigned" : "2014-11-14T00:00:00.000-06:00", "summary" : "Pineal function follows a 24-hour schedule, dedicated to the conversion of night and day into a hormonal signal, melatonin. In mammals, 24-hour changes in pineal activity are controlled by a neural pathway that includes the central circadian oscillator in the suprachiasmatic nucleus and the superior cervical ganglia (SCG), which innervate the pineal gland. In this study, we have generated the first next-generation RNA sequencing evidence of neural control of the daily changes in the pineal transcriptome. We found over 3000 pineal transcripts that are differentially expressed (p <0.001) on a night/day basis (70% of these genes increase at night, 376 with fold change >4 or <1/4), the majority of which had not been previously identified as such. Nearly all night/day differences were eliminated by neonatal removal or decentralization of the SCG, confirming the importance of neural input for differential night/day changes in transcript abundance. In contrast, very few non-rhythmic genes showed evidence of changes in expression due to the surgical procedure itself, which is consistent with the hypothesis that post neonatal neural stimulation is not required for cell fate determination and maintenance of phenotype. Many of the transcripts that exhibit marked differential night/day expression exhibited similar changes in response to in vitro treatment with norepinephrine, the SCG neurotransmitter which mediates pineal regulation. Similar changes were also seen following treatment with an analog of the norepinephrine second messenger, cyclic AMP.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26367423" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63362" }, "primaryId" : "GEO:GSE63362", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63362" } ] }, "title" : "Identification of sexually dimorphically expressed genes in rat tissues", "dateAssigned" : "2014-11-17T00:00:00.000-06:00", "summary" : "The sexually dimorphic expression of genes across 26 somatic rat tissues was using Affymetrix RAE-230 genechips. We considered probesets to be sexually dimorphically expressed (SDE) if they were measurably expressed above background in at least one sex, there was at least a two-fold difference in expression (dimorphism) between the sexes, and the differences were statistically significant after correcting for false discovery. 14.5% of expressed probesets were SDE in at least one tissue, with higher expression nearly twice as prevalent in males compared to females. Most were SDE in a single tissue. Surprisingly, nearly half of the probesets that were (SDE) in multiple tissues were oppositely sex biased in different tissues, and most SDE probesets were also expressed without sex bias in other tissues. Two genes were widely SDE: Xist (female-only) and Eif2s3y (male-only). The frequency of SDE probesets varied widely between tissues, and was highest in the duodenum (6.2%), whilst less than 0.05% in over half of the surveyed tissues. The occurrence of SDE probesets was not strongly correlated between tissues. Within individual tissues, however, relational networks of SDE genes were identified. In the liver, networks relating to differential metabolism between the sexes were seen. The estrogen receptor was implicated in differential gene expression in the duodenum. To conclude, sexually dimorphic gene expression is common, but highly tissue-dependent. Sexually dimorphic gene expression may provide insights into mechanisms underlying phenotypic sex differences.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25548914" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63377" }, "primaryId" : "GEO:GSE63377", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63377" } ] }, "title" : "Gene expression change in the cerebellum and prefrontal cortex of depression rats", "dateAssigned" : "2014-11-17T00:00:00.000-06:00", "summary" : "The depressive-like behavior in animals is usually assessed by standardized behavioral tests such as the forced swimming test. However, the findings of these tests may be affected by individual variability among animals, which may hinder the discovery of genes responsible for depression. Few reports have showed the influence of individual variability in identifying the genes associated with depressive-like behavior. In this study, we measured the immobility ratio (% immobility in 5 min) in the forced swimming test in 106 male Wistar rats. According to the distribution of individual immobility ratio, the rats were divided into three groups: the control group with immobility ratio -1 to +1 standard deviation (SD) from the mean, the depressive group with immobility ratio +1 to +2 SD above the mean, and the anti-depressive group with immobility ratio -1 to -2 SD below the mean. Microarray analysis was used to identify the genes differentially expressed by depressive group rats in the prefrontal cortex and cerebellum. The differentially expressed genes in both brain regions of the depressive group were Alas2, Gh1, Hba-a2, Hbb, Hbb-b1, Hbe2, LOC689064, Mrps10, Mybpc, Olf6415, and Pfkb1. Ingenuity pathway analysis identified Gh1 as a hub gene in the networks of the differentially expressed genes in both brain regions. This study indicates that inherent differences in depressive-like behavior may be related to the Gh1 expression in the cerebellum and prefrontal cortex.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26484268" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63401" }, "primaryId" : "GEO:GSE63401", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63401" } ] }, "title" : "Beyond acid suppression: Novel therapeutic targets for gastro-esophageal reflux disease based on a murine model (esophageal tissue)", "dateAssigned" : "2014-11-18T00:00:00.000-06:00", "summary" : "Background & Aims: Because the pathophysiology of GERD is not fully understood, presently used drug target only one or more of the known underlying mechanisms but are not fully effective in all patients. 1Identifying novel central targets may pave the way to develop more effective agents. Methods: A surgical model of sub-chronic reflux esophagitis was developed. Wistar rats were pretreated for 7days with omeprazole (standard proton pump inhibitor) or STW5 (herbal preparation of established efficacy in gastro-intestinal disorders). Treatment was continued for 10days after surgery, rats were sacrificed and esophagi excised. Histological, proteomic and transcriptomic methods were applied to identify reflux induced changes and treatment responses. Results: Protection against reflux induced inflammation was achieved by both test drugs. Both reduced macroscopic and microscopic lesions of the esophagi as well as most measured pro-inflammatory cytokines without significantly affecting NF-kB activity. Proteomic and transcriptomic analysis identified CINC1-3, MIP-1/3a, MIG, RANTES and IL-1ß as highly relevant mediators in GERD. Other highly regulated genes were those of IL-6, CCL3, CCL7 and LOX-1. Many affected cyto-/chemokines were involved in the TREM-1 signaling pathway. The fatty acid receptor GPR84 was highly up-regulated in esophagitis but down-regulated by both drugs. This was confirmed by Western blot and immune-histochemical staining, showing for the first time expression of this receptor in esophageal tissue and its possible involvement in GERD. Conclusion: STW5 and omeprazole target a broad spectrum of molecules involved in immunological and inflammatory processes, of which IL-8 (CINC1-3), TREM-1 pathway and GPR84 are proposed to be most promising novel targets for the treatment of GERD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26650186" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63402" }, "primaryId" : "GEO:GSE63402", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63402" } ] }, "title" : "Beyond acid suppression: Novel therapeutic targets for gastro-esophageal reflux disease based on a murine model (whole blood)", "dateAssigned" : "2014-11-18T00:00:00.000-06:00", "summary" : "Background & Aims: Because the pathophysiology of GERD is not fully understood, presently used drug target only one or more of the known underlying mechanisms but are not fully effective in all patients. 1Identifying novel central targets may pave the way to develop more effective agents. Methods: A surgical model of sub-chronic reflux esophagitis was developed. Wistar rats were pretreated for 7days with omeprazole (standard proton pump inhibitor) or STW5 (herbal preparation of established efficacy in gastro-intestinal disorders). Treatment was continued for 10days after surgery, rats were sacrificed and esophagi excised. Histological, proteomic and transcriptomic methods were applied to identify reflux induced changes and treatment responses. Results: Protection against reflux induced inflammation was achieved by both test drugs. Both reduced macroscopic and microscopic lesions of the esophagi as well as most measured pro-inflammatory cytokines without significantly affecting NF-kB activity. Proteomic and transcriptomic analysis identified CINC1-3, MIP-1/3a, MIG, RANTES and IL-1ß as highly relevant mediators in GERD. Other highly regulated genes were those of IL-6, CCL3, CCL7 and LOX-1. Many affected cyto-/chemokines were involved in the TREM-1 signaling pathway. The fatty acid receptor GPR84 was highly up-regulated in esophagitis but down-regulated by both drugs. This was confirmed by Western blot and immune-histochemical staining, showing for the first time expression of this receptor in esophageal tissue and its possible involvement in GERD. Conclusion: STW5 and omeprazole target a broad spectrum of molecules involved in immunological and inflammatory processes, of which IL-8 (CINC1-3), TREM-1 pathway and GPR84 are proposed to be most promising novel targets for the treatment of GERD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26650186" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63442" }, "primaryId" : "GEO:GSE63442", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63442" } ] }, "title" : "A novel functional role for the serine protease inhibitor SerpinA3N and its substrate leukocyte elastase in neuropathic pain", "dateAssigned" : "2014-11-19T00:00:00.000-06:00", "summary" : "Two out-bred rat selection lines were separated to produce different hypersensitivity phenotypes following nerve injury. These lines were termed High Pain and Low Pain (HP or LP). Each sub-strain was either subject to a Sham surgery or a Spinal Nerve Ligation (SNL) surgery to the L4 and L5 spinal nerves. Three days following surgery L4/L5 Dorsal Root Ganglia (DRG) were dissected from these animals. For the rat line separation protocol see: Devor M, Raber P (1990) Heritability of symptoms in an experimental model of neuropathic pain. Pain 42:51-67.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63489" }, "primaryId" : "GEO:GSE63489", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63489" } ] }, "title" : "Levator Ani Satellite Cells (LASCs) treated with Nonsteroidal Androgen Receptor Agonist (NARA)", "dateAssigned" : "2014-11-19T00:00:00.000-06:00", "summary" : "Primary objectives: 1) Identify biomarkers of satellite cell growth and differentiation, 2) Characterize a novel muscle satellite cell line, 3) Understand the effects of androgen (NARA) on rat satellite cell activation and recruitment.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63504" }, "primaryId" : "GEO:GSE63504", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63504" } ] }, "title" : "miRNA profile of microglial cells under oxygen-glucose deprivation", "dateAssigned" : "2014-11-20T00:00:00.000-06:00", "summary" : "Migroglia cells were exposed to oxygen-glucose deprivation (OGD) for 3 h. The miRNA was isolated and the expression profiles of OGD-activated cells were compared with the profiles of resting cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25545945" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63505" }, "primaryId" : "GEO:GSE63505", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63505" } ] }, "title" : "Gene expression profile of microglial cells under oxygen-glucose deprivation", "dateAssigned" : "2014-11-20T00:00:00.000-06:00", "summary" : "Migroglia cells were exposed to oxygen-glucose deprivation (OGD) for 3 h. The mRNA was isolated and the expression profiles of OGD-activated cells were compared with the profiles of resting cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25545945" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63527" }, "primaryId" : "GEO:GSE63527", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63527" } ] }, "title" : "Tissue-specific DNA methylation is conserved across species and driven by primary sequence conservation", "dateAssigned" : "2014-11-21T00:00:00.000-06:00", "summary" : "Tissue specific differentially methylated regions (DMRs) have been shown to play important roles in tissue specification, but little is known about the conservation pattern of genome-wide DNA methylation distribution that encodes tissue specifity. Using a comparative approach, we identified and compared the tissue-specific DNA methylation patterns of the rat against that of mouse and human across three common tissue types. We found that 10%-40% of this tissue-specific DNA methylation pattern is conserved, and this epigenetic onservation is associated with the conservation of tissue specific TFBS.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28899353" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63561" }, "primaryId" : "GEO:GSE63561", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63561" } ] }, "title" : "Prenatal alcohol exposure alters steady-state and activated gene expression in the adult rat brain", "dateAssigned" : "2014-11-21T00:00:00.000-06:00", "summary" : "Background: Prenatal alcohol exposure (PAE) is associated with alterations in numerous physiological systems, including the stress and immune systems. We have previously shown that PAE increases the course and severity of arthritis in an adjuvant-induced arthritis (AA) model. While the molecular mechanisms underlying these effects are not fully known, changes in neural gene expression are emerging as important factors in the etiology of PAE effects. As the prefrontal cortex (PFC) and hippocampus (HPC) play key roles in neuroimmune function, PAE-induced alterations to their transcriptome may underlie abnormal steady-state functions and responses to immune challenge. The current study examined brains from adult PAE and control females from our recent AA study to determine whether PAE causes long-term alterations in gene expression and whether these mediate the altered severity and course of arthritis in PAE females Methods: Adult females from PAE, pair-fed [PF], and ad libitum-fed control [C]) groups were injected with either saline or complete Freund’s adjuvant. Animals were terminated at the peak of inflammation or during resolution (days 16 and 39 post-injection, respectively); cohorts of saline-injected PAE, PF and C females were terminated in parallel. Gene expression was analyzed in the PFC and HPC using whole genome mRNA expression microarrays. Results: Significant changes in gene expression in both the PFC and HPC were found in PAE compared to controls in response to ethanol exposure alone (saline-injected females), including genes involved in neurodevelopment, apoptosis, and energy metabolism. Moreover, in response to inflammation (adjuvant-injected females), PAE animals showed unique expression patterns, while failing to exhibit the activation of genes and regulators involved in the immune response observed in control and pair-fed animals. Conclusions: These results support the hypothesis that PAE affects neuroimmune function at the level of gene expression, demonstrating long-term effects of PAE on the CNS response under steady-state conditions and following an inflammatory insult. Key words: prenatal alcohol exposure (PAE), ethanol, inflammation, arthritis, gene expression, rat.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25684047" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63639" }, "primaryId" : "GEO:GSE63639", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63639" } ] }, "title" : "Genome-wide DNA Microarray Analysis Unravels Rapid Changes in the Transcriptome of MK-801 treated Rat Brain", "dateAssigned" : "2014-11-25T00:00:00.000-06:00", "summary" : "N-Methyl-D-aspartate receptors (NMDAr), widely located around the central nervous system, are known to be involved in behavioral disorders. Dizocilpine (commonly referred to as MK-801) is a well known non-competitive NMDAr antagonist. We treated rats with intraperitoneal injection [0.08 (low-dose) and 0.16 (high-dose) mg/kg] of MK-801. In one experiment, 40 min after NaCl (vehicle control) and MK-801 (0.08 mg/kg) injection, electrocorticogram (ECoG) signals were analyzed. In the second experiment, 40 min post-injection, the whole brain of each animal was rapidly removed and separated into amyglada, cerebral cortex, hippocampus, hypothalamus, midbrain and ventral striatum) on ice, followed by analysis using a 4x44K DNA microarray chip. Spectral analysis revealed that a single systemic injection of MK-801 significantly and selectively augmented the power of baseline (30-80 Hz) frequency oscillations. DNA microarray analysis showed the largest number (up- and down- regulations) of gene expressions in the cerebral cortex (378), midbrain (376), hippocampus (375), ventral striatum (353), amygdala (301), and hypothalamus (201) under low-dose of MK-801. Under high-dose, ventral striatum (811) showed the largest number of gene expression changes. Gene expression changes were functionally categorized to reveal expression of genes and function varies with each brain region. MK-801 increases the synchrony of baseline oscillations, causing very early changes in gene expressions in rat brain after acute MK-801 treatment, a first report.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63640" }, "primaryId" : "GEO:GSE63640", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63640" } ] }, "title" : "A DNA Microarray Analysis of Rat Intestine, Spleen and Liver Transcriptome after Oral Administration of Lavender Oil", "dateAssigned" : "2014-11-25T00:00:00.000-06:00", "summary" : "Lavender oil (LO) – a commonly used oil in aromatherapy with well defined volatile components linalool and linalyl acetate – use in non-traditional medicine is increasing globally. To understand and provide evidence for the potential positive effects of LO on the body, we have established an animal model for investigating in this current study, orally administered LO effects genome-wide in rat intestine, spleen and liver. The rats were administrated LO at 5 mg/kg (usual threaupeutic dose in humans) followed by screeing of differentially expressed genes in the tissues utlilizing a 4x44K whole genome rat chip (Agilent microarray platform) in conjunction with a dye-swap approach, one of the novelties of this study. Fourteen days after treatment (LO) and in comparison with a control group (sham), a total of 156 and 154 up (>1.5 fold)- and down (<0.75 fold)-regulated genes, 174 and 66 up- (>1.5 fold)- and down (<0.75 fold)-regulated genes, and 222 and 322 up- (>1.5 fold)- and down (<0.75 fold)-regulated genes showed differential expression at the mRNA level, in the intestine, spleen and liver, respectively. Reverse transcription-polymerase chain reaction (RT-PCR) validation of highly up- and down-expressed genes revealed the regulation of Papd4, Lrp1b, Alb, Cyr61, Cyp2c, and Cxcl1 genes, by LO, as examples in these tissues. Using bioinformatics functionally categorization of differentially expressed genes was done by their Gene Ontology (GO) revealing their diverse functions and potential roles in LO-mediated effects in rat. Present results are a first such inventory of genes affected by the essential oil of Lavender (LO) in an animal model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26161641" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63650" }, "primaryId" : "GEO:GSE63650", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63650" } ] }, "title" : "Aging-associated inflammatory and oxidative changes in the rat urinary bladder and dorsal root ganglia - preventive effect of caloric restriction [bladder]", "dateAssigned" : "2014-11-26T00:00:00.000-06:00", "summary" : "Purpose: To disclose the molecular mechanisms of aging-related functional impairments of the rat bladder, and to determine whether long-term caloric restriction (CR) may have preventive effects on these mechanisms. Materials and Methods: Male Fischer 344 rats were divided into three groups: young (6 months-old) fed ad libitum (Y, N = 16), old (25-28 months-old) fed ad libitum (O+AL, N = 15), and old (25-28 months-old) fed restrictedly three days a week since 6 weeks-old (O+CR, N = 16). cDNA microarray analysis and real-time polymerase chain reaction (RT-PCR) of the bladder and L6 dorsal root ganglia (L6DRG) were performed. The bladder was subjected to oxidative stress measurement and immunohistochemistry. Results: In the O+AL group, 83 genes in the bladder and 48 genes in the L6DRG were up-regulated than compared with those of the Y and O+CR groups (fold change > 2). These genes were mostly related to immune- and inflammatory-responses. Immunohistochemistry showed that Granzyme B, a cytotoxic T-lymphocyte-associated serine protease, and matrix metalloproteinase 13 (Mmp13), an interstitial collagenase, were more strongly expressed in the bladder of the O+AL than the Y and O+CR groups. The level of Malondialdehyde (MDA), an oxidative stress marker, was higher in the O+AL than the Y group, whereas there were no significant differences between the O+CR and Y groups. Conclusions: In the rat, aging is associated with up-regulation of immune and inflammatory genes in the bladder and DRG as well as with oxidative and fibrotic changes of the bladder. Long-time CR reduced these aging-related changes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63651" }, "primaryId" : "GEO:GSE63651", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63651" } ] }, "title" : "Aging-associated inflammatory and oxidative changes in the rat urinary bladder and dorsal root ganglia - preventive effect of caloric restriction [L6 dorsal root ganglia]", "dateAssigned" : "2014-11-26T00:00:00.000-06:00", "summary" : "Purpose: To disclose the molecular mechanisms of aging-related functional impairments of the rat bladder, and to determine whether long-term caloric restriction (CR) may have preventive effects on these mechanisms. Materials and Methods: Male Fischer 344 rats were divided into three groups: young (6 months-old) fed ad libitum (Y, N = 16), old (25-28 months-old) fed ad libitum (O+AL, N = 15), and old (25-28 months-old) fed restrictedly three days a week since 6 weeks-old (O+CR, N = 16). cDNA microarray analysis and real-time polymerase chain reaction (RT-PCR) of the bladder and L6 dorsal root ganglia (L6DRG) were performed. The bladder was subjected to oxidative stress measurement and immunohistochemistry. Results: In the O+AL group, 83 genes in the bladder and 48 genes in the L6DRG were up-regulated than compared with those of the Y and O+CR groups (fold change > 2). These genes were mostly related to immune- and inflammatory-responses. Immunohistochemistry showed that Granzyme B, a cytotoxic T-lymphocyte-associated serine protease, and matrix metalloproteinase 13 (Mmp13), an interstitial collagenase, were more strongly expressed in the bladder of the O+AL than the Y and O+CR groups. The level of Malondialdehyde (MDA), an oxidative stress marker, was higher in the O+AL than the Y group, whereas there were no significant differences between the O+CR and Y groups. Conclusions: In the rat, aging is associated with up-regulation of immune and inflammatory genes in the bladder and DRG as well as with oxidative and fibrotic changes of the bladder. Long-time CR reduced these aging-related changes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63726" }, "primaryId" : "GEO:GSE63726", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63726" } ] }, "title" : "Gene expression profiles of fractionated cells from cirrhotic rat livers", "dateAssigned" : "2014-12-01T00:00:00.000-06:00", "summary" : "Gene expression profiling was performed in each of hepatocyte fraction and non-parenchymal cell fraction enriched with activated hepatic stellate cells/myofibroblasts from cirrhotic rat livers induced by repeated, low-dose diethylnitrosamine (DEN) treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27960085" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63740" }, "primaryId" : "GEO:GSE63740", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63740" } ] }, "title" : "Persistence of furan-induced epigenetic aberrations in the livers of Fisher 344 rats", "dateAssigned" : "2014-12-01T00:00:00.000-06:00", "summary" : "Furan is a heterocyclic organic compound produced in the chemical manufacturing industry and also found in a broad range of food products, including infant formulas and baby foods. Previous reports have indicated that the adverse biological effects of furan, including its liver tumorigenicity, may be associated with epigenetic abnormalities. In the present study we investigated the persistence of epigenetic alterations in rat liver. Male Fisher 344 (F344) rats were treated by gavage 5 days per week with 8 mg furan/kg body weight (bw)/day for 90 days. After the last treatment, rats were divided randomly into four groups; one group of rats was sacrificed 24 hours after the last treatment, while other groups were maintained without further furan treatment for an additional 90, 180, or 360 days. Treatment with furan for 90 days resulted in alterations in histone lysine methylation and acetylation, oxidative damage to DNA, and changes in the gene expression in the livers. A majority of these furan-induced molecular changes was transient and disappeared after the cessation of furan treatment. In contrast, histone H3 lysine 9, H3 lysine 27, and H3 lysine 56 showed a sustained and time-depended decrease in acetylation, which was associated with formation of heterochromatin and altered gene expression. These results indicate that furan-induced adverse effects may be mechanistically related to sustained changes in histone lysine acetylation that compromise the ability of cells to maintain and control properly the expression of genetic information.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25539665" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63742" }, "primaryId" : "GEO:GSE63742", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63742" } ] }, "title" : "Expression data from rat liver tissue during liver regeneration after partial hepatectomy.", "dateAssigned" : "2014-12-01T00:00:00.000-06:00", "summary" : "We used microarrays to further highlight the regulatory role of rat liver tissue in liver regeneration at gene transcription level.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63783" }, "primaryId" : "GEO:GSE63783", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63783" } ] }, "title" : "Next Generation Sequencing Facilitates Quantitative Analysis of Pressure Type and control Transcriptomes", "dateAssigned" : "2014-12-02T00:00:00.000-06:00", "summary" : "With the aim to reveal the function of microRNAs in Hepatic stellate cells (HSCs) in response to portal hypertension, primary rat HSCs were exposed to pressure (10mmHg, 1 h) by using a pressure induced apparatus. Appling next-generation sequencing screened the pressurization induced miRNAs expression profile in HSCs. Among them miR-9a-5p was confirmed to be significantly increased after loading pressure in HSC by RT-PCR. It was found that inhibition of miR-9a-5p could significantly restrain HSCs proliferation and activation under pressure overload. Moreover, the results showed that the induction of miR-9a-5p upon pressure load might by increasing the phosphorylation of Akt but not FAK and Erk1/2. Luciferase reporter assay and western blot suggested that Sirt1 was a potential target gene of miR-9a-5p. Finally, we revealed that miR-9a-5p level was apparently higher in rat liver fibrotic model than in the normal control while Sirt1 level was decreased in fibrotic liver tissue. In conclusion, our results suggest that miR-9a-5p regulate HSCs proliferation through negative regulation of Sirt1 and suggest a potential biomarker for portal hypertension.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26379395" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63854" }, "primaryId" : "GEO:GSE63854", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63854" } ] }, "title" : "Global Genome Analysis of the Downstream Binding Targets of Testis Determining Factor SRY and SOX9 [SRY ChIP]", "dateAssigned" : "2014-12-04T00:00:00.000-06:00", "summary" : "A major event in mammalian male sex determination is the induction of the testis determining factor Sry and its downstream gene Sox9. The current study provides one of the first genome wide analyses of the downstream gene binding targets for SRY and SOX9 to help elucidate the molecular control of Sertoli cell differentiation and testis development. A modified ChIP-Chip analysis using a comparative hybridization was used to identify 71 direct downstream binding targets for SRY and 109 binding targets for SOX9. Interestingly, only 5 gene targets overlapped between SRY and SOX9. In addition to the direct response element binding gene targets, a large number of atypical binding gene targets were identified for both SRY and SOX9. Bioinformatic analysis of the downstream binding targets identified gene networks and cellular pathways potentially involved in the induction of Sertoli cell differentiation and testis development. The specific DNA sequence binding site motifs for both SRY and SOX9 were identified. Observations provide insights into the molecular control of male gonadal sex determination.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63855" }, "primaryId" : "GEO:GSE63855", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63855" } ] }, "title" : "Global Genome Analysis of the Downstream Binding Targets of Testis Determining Factor SRY and SOX9 [SOX9 ChIP]", "dateAssigned" : "2014-12-04T00:00:00.000-06:00", "summary" : "A major event in mammalian male sex determination is the induction of the testis determining factor Sry and its downstream gene Sox9. The current study provides one of the first genome wide analyses of the downstream gene binding targets for SRY and SOX9 to help elucidate the molecular control of Sertoli cell differentiation and testis development. A modified ChIP-Chip analysis using a comparative hybridization was used to identify 71 direct downstream binding targets for SRY and 109 binding targets for SOX9. Interestingly, only 5 gene targets overlapped between SRY and SOX9. In addition to the direct response element binding gene targets, a large number of atypical binding gene targets were identified for both SRY and SOX9. Bioinformatic analysis of the downstream binding targets identified gene networks and cellular pathways potentially involved in the induction of Sertoli cell differentiation and testis development. The specific DNA sequence binding site motifs for both SRY and SOX9 were identified. Observations provide insights into the molecular control of male gonadal sex determination.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63902" }, "primaryId" : "GEO:GSE63902", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63902" } ] }, "title" : "Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity.", "dateAssigned" : "2014-12-05T00:00:00.000-06:00", "summary" : "Combinations of anticancer agents may have synergistic anti-tumor effects, but enhanced hematological toxicity often limit their clinical use. We examined whether “microarray profiles” could be used to compare early molecular responses following a single dose of agents administered individually with that of the agents administered in a combination. Six patterns of co-expressed genes were detected at the 1-hour time point which indicate regulatory expression of genes dependent on the order of the administration. When topotecan is given first, several signal transduction transcription factors associated with cancer or inactivation of a tumor suppressor were co-regulating gene expression. These results suggest alterations in histone biology, chromatin remodeling, DNA repair, bone regeneration, and respiratory and oxidative phosphorylation are among the prominent pathways modulated in bone marrow from animals treated with an oxaliplatin/topotecan combination.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25729387" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63930" }, "primaryId" : "GEO:GSE63930", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63930" } ] }, "title" : "Transcriptomic Responses to Prion Disease in Rats", "dateAssigned" : "2014-12-05T00:00:00.000-06:00", "summary" : "While prion infections have been extensively characterized in the laboratory mouse, little is known regarding the molecular responses to prions in other rodents. To explore these responses and make comparisons, we generated a prion disease in the laboratory rat by successive passage of mouse RML prions. Here we describe the accumulation of prions and associated pathology in the rat and describe the transcriptional impact throughout prion disease. Comparative transcriptional profiling between laboratory mice and rats suggests that similar molecular processes are unfolding in response to prion infection. At the level of individual transcripts, however, variability exists between mice and rats and many genes deregulated in mouse scrapie are not affected in rats. Notwithstanding these differences, many transcriptome responses are conserved between mice and rats infected with scrapie. Our findings highlight the usefulness of comparative approaches to understanding neurodegeneration and prion diseases in particular.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26341492" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63959" }, "primaryId" : "GEO:GSE63959", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE63959" } ] }, "title" : "A modular analysis reveals that kinase-associated gene groups are involved in taurolithocholic acid 3-sulfate (TLC-S)-induced biological processes of AR42J cells", "dateAssigned" : "2014-12-08T00:00:00.000-06:00", "summary" : "Background: Bile acids can act on pancreatic acinar cells and induce intracellular trypsinogen activation, but the underlying molecular mechanism remains unknown.The present study aimed to investigate taurolithocholic acid 3-sulfate (TLC-S)-induced alterations of gene groups in AR42J cells using a modular analysis.Methods: After the pancreatic acinar AR42J cells were stimulated by TLC-S for 20 min, gene chip technology was applied to identify genes that were differentially expressed. Subsequently, the regulatory sub-networks of genetic interactions among the differentially expressed genes were constructed using the protein–protein interaction (PPI) network. Finally, the CFinder software was utilized to generate genetic modules, which were then subjected to a functional enrichment analysis.Results: The gene chip assay demonstrated that the expression levels of 1124 genes were upregulated and that those of 498 genes were downregulated in the TLC-S", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64126" }, "primaryId" : "GEO:GSE64126", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64126" } ] }, "title" : "Identification of the gene(s) responsible for ocular abnormalities of Hirosaki Small Eye Rat (HiSER)", "dateAssigned" : "2014-12-12T00:00:00.000-06:00", "summary" : "HiSER, established in our laboratory, exhibits ocular abnormalities including opacity, lens involution, and retinal detachment. To identify a causative gene(s) of the HiSER phenotype, microarray analysis was performed between HiSER and normal (SDR) eyes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26303524" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64239" }, "primaryId" : "GEO:GSE64239", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64239" } ] }, "title" : "Long non-coding RNA expression profile in the kidney of male low birth weight rats exposed to maternal protein restriction at postnatal day 10", "dateAssigned" : "2014-12-16T00:00:00.000-06:00", "summary" : "To investigate the lncRNA profiles in low birth weight rats with reduced nephron endowment induced by restriction of maternal protein intake. Low birth weight by reduced nephron endowment is a risk factor for hypertension and end-stage renal disease in adulthood.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25826617" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64265" }, "primaryId" : "GEO:GSE64265", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64265" } ] }, "title" : "Expression data from kidneys of rats with and without glomerulonephritis", "dateAssigned" : "2014-12-17T00:00:00.000-06:00", "summary" : "To obtain insight into molecular processes during GN pathogenesis, mRNA expression was investigated in WKY and SD kidneys. The immunopathological processes during GN are still not fully understood and likely involve both innate and adaptive immunity. In the present study, several hundred mRNAs were found deregulated, which functionally were mostly associated with inflammation and regeneration. The ß-chain of the major histocompatibility complex class II RT1.B (Rt1-Bb) and complement component 6 (C6) were identified as two mRNAs differentially expressed between WKY and SD rat strains which could be related to known different susceptibilities to NTS of different rat strains; both were increased in WKY and decreased in SD rats. Increased Rt1-Bb expression in WKY rats could indicate a stronger and more persistent cellular reaction of the adaptive immune system in this strain, in line with findings indicating adaptive immune reactions during GN. The complement cascade is also known to be essential for GN development, especially terminal cascade products like C6.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25758243" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64345" }, "primaryId" : "GEO:GSE64345", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64345" } ] }, "title" : "Neuronal changes induced by Varicella Zoster Virus in a rat model of Post Herpetic Neuralgia", "dateAssigned" : "2014-12-18T00:00:00.000-06:00", "summary" : "Animals which had developed VZV-dependent nocifensive behaviours at 10 days were euthanized, and dorsal root ganglia (L4,5) ipsilateral to inoculation were taken for microarray analysis. Dorsal root ganglia from matching control animals were also analyzed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25880108" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64362" }, "primaryId" : "GEO:GSE64362", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64362" } ] }, "title" : "Translational characterization of hepatic miR-301a as a biomarker for acute rejection in experimental and clinical liver transplantation", "dateAssigned" : "2014-12-19T00:00:00.000-06:00", "summary" : "Using a rat orthotopic liver transplantation (OLT) model and microarray, we compared the expression profiles of microRNAs in naïve and AR livers at day 7 after OLT obtained from the rats with short-term (<14 days, DA-LEW) or long-term (>60 days, DA-PVG) survival fate. AR-related microRNAs and pro-inflammatory cytokines were validated by using a quantitative real-time PCR. AR-related microRNA-mediated inflammatory responses were evaluated by overexpression of a target microRNA in rat primary hepatocytes. Human liver biopsies from recipients with AR or abnormal liver function were used for clinical verification. The microarray revealed that miR-301a was significantly upregulated in lethal AR livers of DA-LEW, while it was comparable to the naïve livers in DA-PVG, which spontaneously overcomes AR.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64450" }, "primaryId" : "GEO:GSE64450", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64450" } ] }, "title" : "Unique gene program of rat mesenteric arteries as revealed by Deep RNA Sequencing", "dateAssigned" : "2014-12-22T00:00:00.000-06:00", "summary" : "Results: ~900 genes were identified that were expressed at least 2-fold difference between meseteric artery and aorta", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26156969" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64561" }, "primaryId" : "GEO:GSE64561", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64561" } ] }, "title" : "Small RNA expression in wild-type sciatic nerves during myelination", "dateAssigned" : "2014-12-29T00:00:00.000-06:00", "summary" : "miRNAs are critical for myelination in the peripheral nervous system. We report the differential expression of miRNAs during myelination in sciatic nerves of wild-type mice. This data serves as a starting point to identify physiologically relevant regulatory miRNAs in the peripheral nervous system.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26466203" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64617" }, "primaryId" : "GEO:GSE64617", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64617" } ] }, "title" : "Gene expression and complex network analyis of effects of anaethesia", "dateAssigned" : "2014-12-31T00:00:00.000-06:00", "summary" : "We used complex systems analyis of gene expression data to study brain gene expression in rats following a brief period of anaesthesia using isoflurane", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64636" }, "primaryId" : "GEO:GSE64636", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64636" } ] }, "title" : "Expression data from the mammary gland of ovariectomized (ovx) rats treated for three days with E2, 3-MC, E2+3-MC", "dateAssigned" : "2015-01-02T00:00:00.000-06:00", "summary" : "The study was designed to see the overall gene-expression change in the mammary gland induced by AHR ligand 3-MC alone and in combination with E2.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26372666" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64692" }, "primaryId" : "GEO:GSE64692", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64692" } ] }, "title" : "Gene expression profiles of hexadecyl-4-124I-iodobenzoate(124I-HIB)-labeled adipose-derived stem cells (ADSCs) in vitro and in vivo", "dateAssigned" : "2015-01-06T00:00:00.000-06:00", "summary" : "[2] Microarray analysis in the rat adipose derived stem cells: 124I-HIB-labeled ADSCs Vs. Unlabeled ADSCs", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64703" }, "primaryId" : "GEO:GSE64703", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64703" } ] }, "title" : "Sox10 Binding Analysis in the Central and Peripheral Nervous System", "dateAssigned" : "2015-01-06T00:00:00.000-06:00", "summary" : "ChIP-seq of Sox10 in spinal cord and sciatic nerve was performed to determine shared and unique binding sites for Sox10 in oligodendrocytes and Schwann cells, respectively. Sox10 is required for both Schwann cell and oligodendrocyte development. In addition, differentiation of myelinating glia is dependent upon axonal signaling, so these studies were performed in vivo. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23966833" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64733" }, "primaryId" : "GEO:GSE64733", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64733" } ] }, "title" : "Identification of molecules from dying cells that act as signals to promote proliferation of surrounding cells", "dateAssigned" : "2015-01-07T00:00:00.000-06:00", "summary" : "To elucidate the mechanisms underlying epithelial homeostasis, we explored molecules that might serve as “danger” signals in mediating epithelial regeneration with microarray. We hypothesize that soluble factors may have been released from damaged cells to stimulate the proliferation of surviving epithelial cells. In elucidating the mechanism of dying cell-to-surviving cell communication using normal rat kidney NRK-52E epithelial cells, we observed gene expression profiles in these cells after the induction of cell death using hydrogen peroxide. The results demonstrated up-regulation of Interleukin-6, Heme oxygenase-1 and Hypoxia inducible factor-1 alpha in dying cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64778" }, "primaryId" : "GEO:GSE64778", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64778" } ] }, "title" : "Changes in transcript expression in circulating whole blood resulting from exposure to neurotoxic doses of D-amphetamine or Heat Stroke/Hyperthermia", "dateAssigned" : "2015-01-08T00:00:00.000-06:00", "summary" : "Amphetamine effects on gene expression are dependent on body temperature and indicate that many significant changes in genes related to the immune system occur, some likely in response to damage, even when animals remain normothermic during amphetamine exposure. Also, hyperthermia alone produces many changes in immune related genes in blood", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26177368" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64815" }, "primaryId" : "GEO:GSE64815", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64815" } ] }, "title" : "Gene expression profile for male SD Rats upon fructose and DHA treatment by RNA-Seq", "dateAssigned" : "2015-01-09T00:00:00.000-06:00", "summary" : "To investigate the beneficial effects of DHA (omega-3) on affecting fructose induced brain dysfunction and metabolic disorders by sequencing the transcripome (RNA-Seq) in the hypothalamus and hippocampus of male SD rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27322469" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64816" }, "primaryId" : "GEO:GSE64816", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64816" } ] }, "title" : "DNA methylation profile for male SD Rats upon fructose and DHA treatment by RRBS", "dateAssigned" : "2015-01-09T00:00:00.000-06:00", "summary" : "To investigate the beneficial effects of DHA (omega-3) on affecting fructose induced brain dysfunction and metabolic disorders by sequencing the methylome (RRBS) in the hypothalamus and hippocampus of male SD rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27322469" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64818" }, "primaryId" : "GEO:GSE64818", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64818" } ] }, "title" : "Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs", "dateAssigned" : "2015-01-09T00:00:00.000-06:00", "summary" : "Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: identifying truly non-coding genes from de novo reconstructed transcriptomes, and prioritizing the hundreds of resulting putative lncRNAs for downstream experimental interrogation. We present slncky, a computational lncRNA discovery tool that produces a high-quality set of lncRNAs from RNA-sequencing data and further uses evolutionary constraint to prioritize lncRNAs that are likely to be functionally important. Our automated filtering pipeline is comparable to manual curation efforts and more sensitive than previously published computational approaches. Furthermore, we develop a sensitive alignment pipeline for aligning lncRNA loci and propose new evolutionary metrics relevant for analyzing sequence and transcript evolution. Our analysis reveals that evolutionary selection acts in several distinct patterns, and uncovers two notable classes of intergenic lncRNAs: one showing strong purifying selection on RNA sequence and another where constraint is restricted to the regulation but not the sequence of the transcript.\t\t\t\t\t\t", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26838501" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64838" }, "primaryId" : "GEO:GSE64838", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64838" } ] }, "title" : "Human umbilical cord matrix mesenchymal stem cells suppress the growth of breast cancer by expression of tumor suppressor genes [rat]", "dateAssigned" : "2015-01-09T00:00:00.000-06:00", "summary" : "Human and rat umbilical cord matrix mesenchymal stem cells (UCMSC) possess the ability to control the growth of breast carcinoma cells. Comparative analyses of two types of UCMSC suggest that rat UCMSC-dependent growth regulation is significantly stronger than that of human UCMSC. Their different tumoricidal abilities were clarified by analyzing gene expression profiles in the two types of UCMSC. Microarray analysis revealed differential gene expression between untreated naïve UCMSC and those co-cultured with species-matched breast carcinoma cells. The analyses screened 17 differentially expressed genes that are commonly detected in both human and rat UCMSC. The comparison between the two sets of gene expression profiles identified two tumor suppressor genes, adipose-differentiation related protein (ADRP) and follistatin (FST), that were specifically up-regulated in rat UCMSC, but down-regulated in human UCMSC when they were co-cultured with the corresponding species' breast carcinoma cells. Over-expression of FST, but not ADRP, in human UCMSC enhanced their ability to suppress the growth of MDA-231 cells. The growth of MDA-231 cells was also significantly lower when they were cultured in medium conditioned with FST, but not ADRP over-expressing human UCMSC. In the breast carcinoma lung metastasis model generated with MDA-231 cells, systemic treatment with FST-overexpressing human UCMSC significantly attenuated the tumor burden. These results suggest that FST may play an important role in exhibiting stronger tumoricidal ability in rat UCMSC than human UCMSC and also implies that human UCMSC can be transformed into stronger tumoricidal cells by enhancing tumor suppressor gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25942583" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64842" }, "primaryId" : "GEO:GSE64842", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64842" } ] }, "title" : "Rat Life Cycle Kidney miRNA Expression Data", "dateAssigned" : "2015-01-09T00:00:00.000-06:00", "summary" : "Kidney miRNA expression was examined in F344 rats at 2, 5, 6, 8, 15, 21, 78, and 104 weeks of age in both sexes using Agilent miRNA microarrays. 311 miRNAs were found to be expressed in at least one age and sex. Filtering criteria of =1.5 fold change and ANOVA (FDR <5%) revealed 174 differentially expressed miRNAs in the kidney; 173 and 34 miRNAs exhibiting age and sex effects, respectively. Principal component analysis revealed age effects predominated over sex effects, with 2 week miRNA expression being much different from other ages. No significant sexually dimorphic miRNA expression was observed from 5 to 8 weeks, while the most differential expression (13 miRNAs) was observed at 21 weeks. Potential target genes of these differentially expressed miRNAs were identified. Pathway analysis was used to investigate the possible roles of these target genes in age- and sex-specific differences.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25653823" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64886" }, "primaryId" : "GEO:GSE64886", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64886" } ] }, "title" : "Effect of Traumatic Brain Injury, Erythropoietin and Anakinra on Hepatic Metabolizing Enzymes and Transporters in an Experimental Rodent Model", "dateAssigned" : "2015-01-12T00:00:00.000-06:00", "summary" : "In contrast to the considerable in vitro and in vivo data demonstrating a decrease in cytochrome P450 (CYP) activity in inflammation and infection, clinically, traumatic brain injury (TBI) results in an increase in CYP and UDP glucuronosyltransferases (UGT) activity. The objective of this study was to determine the effects of TBI alone and along with treatment with either erythropoietin (EPO) or anakinra on gene expression of hepatic inflammatory proteins and drug metabolizing enzymes and transporters in a cortical contusion impact (CCI) injury animal model. Microarray-based transcriptional profiling was used to determine the effect on gene expression at 24 h, 72 h and 7 days post-CCI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26068867" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64902" }, "primaryId" : "GEO:GSE64902", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64902" } ] }, "title" : "Extra-coding RNAs regulate neuronal DNA methylation and long-term memory formation [RNA-seq]", "dateAssigned" : "2015-01-12T00:00:00.000-06:00", "summary" : "This dataset contains whole-genome RNA sequencing results from cortical neuronal cultures and serves as the basis for characterization of extra-coding RNA species from neuronal systems.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27384705" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64947" }, "primaryId" : "GEO:GSE64947", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64947" } ] }, "title" : "Gene expression profile for male SD rats treated with high fat diet (HFD) and DNA methyltransferase (DNMT) inhibitor 5-aza-2′-deoxycytidine (5-AzaD) by RNA-Seq", "dateAssigned" : "2015-01-13T00:00:00.000-06:00", "summary" : "To investigate the effects of HFD on affecting the gene expressions, as well as the methylation inhibitor 5-AzaD reversing such effects in the frontal cortex of male SD rats by RNA-Seq.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64948" }, "primaryId" : "GEO:GSE64948", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64948" } ] }, "title" : "DNA methylation profile for male SD rats treated with high fat diet (HFD) and DNA methyltransferase (DNMT) inhibitor 5-aza-2′-deoxycytidine (5-AzaD) by RRBS", "dateAssigned" : "2015-01-13T00:00:00.000-06:00", "summary" : "To investigate the effects of HFD on affecting the DNA methylation, as well as the methylation inhibitor 5-AzaD reversing such effects in the frontal cortex of male SD rats by sequencing the methylome (RRBS).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64970" }, "primaryId" : "GEO:GSE64970", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64970" } ] }, "title" : "Rapid increase of fibroblast growth factor 21 under protein malnutrition and its impact on growth and lipid metabolism", "dateAssigned" : "2015-01-14T00:00:00.000-06:00", "summary" : "FGF21 is a polypeptide hormone that regulates glucose and lipid metabolism. Using transgenic mice, FGF21 has also been shown to promote a growth hormone-resistant state and suppress IGF-I. Therefore, to further determine whether the up-regulation of Fgf21 under protein malnutrition causes hepatic steatosis and growth retardation following decrease in IGF-I, we fed isoenergetic low protein diet to Fgf21-knockout (KO) mice. Fgf21-KO did not rescue growth retardation and reduced plasma IGF-I concentration of mice fed the low-protein diet. Meanwhile, Fgf21-KO mice showed greater epididymal white adipose tissue weight as well as hepatic triglyceride and cholesterol levels under protein malnutrition (P<0.05). Taken together, we showed that protein deprivation directly increases Fgf21 expression. However, growth retardation and decreased IGF-I were not mediated by increased FGF21 expression under protein malnutrition. Furthermore, up-regulated FGF21 rather appears to have a protective effect against obesity and hepatic steatosis in protein malnourished animals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64971" }, "primaryId" : "GEO:GSE64971", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64971" } ] }, "title" : "Enhancer Analysis in Peripheral Nerve: ChIP-seq of H3K27ac in P15 sciatic nerve", "dateAssigned" : "2015-01-14T00:00:00.000-06:00", "summary" : "ChIP-seq of H3K27ac in P15 sciatic nerve was used to identify actively engaged enhancers in Schwann cells, which constitute the majority of nuclei in peripheral nerve. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25974668" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64978" }, "primaryId" : "GEO:GSE64978", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64978" } ] }, "title" : "Gene expression profile for male SD Rats with and without traumatic brain injury (TBI) by RNA-Seq", "dateAssigned" : "2015-01-14T00:00:00.000-06:00", "summary" : "To investigate the effects of TBI on affecting the gene expressions in the hippocampus of male SD rats by RNA-Seq..", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28174132" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64984" }, "primaryId" : "GEO:GSE64984", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64984" } ] }, "title" : "DNA methylation profile for male SD rats with and without traumatic brain injury (TBI) by RRBS", "dateAssigned" : "2015-01-14T00:00:00.000-06:00", "summary" : "To investigate the effects of TBI on affecting the DNA methylation in the hippocampus of male SD rats by sequencing the methylome (RRBS).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28174132" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64987" }, "primaryId" : "GEO:GSE64987", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE64987" } ] }, "title" : "Extra-coding RNAs regulate neuronal DNA methylation and long-term memory formation [MBD-seq]", "dateAssigned" : "2015-01-14T00:00:00.000-06:00", "summary" : "This dataset contains whole-genome MBD (methylbinding domain) sequencing results from cortical neuronal cultures and serves as the basis for characterization of DNA methylation profiles from neuronal systems.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27384705" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65017" }, "primaryId" : "GEO:GSE65017", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65017" } ] }, "title" : "Effect of Egg Protein Ovotransferrin-derived Peptide, IRW on Gene Expression of Vascular Tissues in Spontaneously Hypertensive Rats", "dateAssigned" : "2015-01-15T00:00:00.000-06:00", "summary" : "In this study we tested the effect of orraly administered egg white ovotransferrin derived pepide, IRW on gene expression in spontaneously hypertensive rats. IRW is previously identified with antihypertensive effect and in this study we evaluated how IRW treatment can modulate various gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26016560" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65051" }, "primaryId" : "GEO:GSE65051", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65051" } ] }, "title" : "Transcriptomic analysis of colonic epithelial cells in adult rats born with intra-uterine growth retardation.", "dateAssigned" : "2015-01-16T00:00:00.000-06:00", "summary" : "The hypothesis tested in this study was that IUGR induces sustainable effects on colonocyte transcriptome that may alter further nutritional adaptations at adulthood, especially to high-fat diet.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65053" }, "primaryId" : "GEO:GSE65053", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65053" } ] }, "title" : "Gene expression signatures following nerve injury in a rat model (0.5h-9h)", "dateAssigned" : "2015-01-16T00:00:00.000-06:00", "summary" : "We used microarrays to distinguish the gene expression differences among different time points after injury", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65064" }, "primaryId" : "GEO:GSE65064", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65064" } ] }, "title" : "Transcriptomic analysis of prefrontal medial cortex, hippocampus and nucleus accumbens of alcohol-preferring and nonpreferring rats", "dateAssigned" : "2015-01-16T00:00:00.000-06:00", "summary" : "This study was supported through funding from the following grants: Polish Scientific Committee Grant 2011/03/N/NZ29/05222, Polish Ministry of Science and Higher Education Grants “Iuventus Plus” (IP2011 030371) and N N519 657940.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65119" }, "primaryId" : "GEO:GSE65119", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65119" } ] }, "title" : "Genome-wide maps of Wnt effector Tcf7l2/Tcf4 occupancy in oligodendrocyte during CNS myelination", "dateAssigned" : "2015-01-20T00:00:00.000-06:00", "summary" : "We performed genome-wide profiling of Tcf7l2 occupancy during oligodendrocyte differentiation and identified the key enzymes involved in cholesterol metabolism and essential for CNS myelination.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26955760" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65169" }, "primaryId" : "GEO:GSE65169", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65169" } ] }, "title" : "Liver miRNA Expression during the Rat Life Span in both Sexes", "dateAssigned" : "2015-01-21T00:00:00.000-06:00", "summary" : "Global miRNA expression was examined in liver tissues from male and female F344 rats over the life span for the purpose of evaluating their possible roles in susceptibility to liver toxicity and disease. Hepatic miRNA expression was characterized at 2, 5, 6, 8, 15, 21, 52, 78, and 104 weeks of age in both sexes using Agilent 8x15k rat miRNA microarrays containing multiple probes for 677 unique miRNAs. Data processing, 75% normalization, and statistical analysis of microarray data were performed in SAS. Functional analysis (Ingenuity) was performed on select miRNAs exhibiting prominent age and sex expression differences. +", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28174625" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65182" }, "primaryId" : "GEO:GSE65182", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65182" } ] }, "title" : "mRNA expression in white adipose tissue of adult F2 female offspring from F0-fathers fed a chow or high-fat diet", "dateAssigned" : "2015-01-22T00:00:00.000-06:00", "summary" : "White adipose tissue mRNA expression profiling of F2-female offspring from F0-founders fed either a chow or a chronic HFD challenged. Adult females were challenged or not a high-fat diet for 12 weeks. White adipose tissue was dissected at an endpoint experiment. Rats were subjected to 4 hours fasting prior to anesthesia with pentobarbital and tissue collection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26977389" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65198" }, "primaryId" : "GEO:GSE65198", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65198" } ] }, "title" : "Temporal Changes in Rat Liver Gene Expression after Acute Cadmium and Chromium Exposure", "dateAssigned" : "2015-01-22T00:00:00.000-06:00", "summary" : "U.S. Service Members and civilians are at risk of exposure to a variety of environmental health hazards throughout their normal duty activities and in industrial occupations. Metals are widely used in large quantities in a number of industrial processes and are a common environmental toxicant, which increases the possibility of being exposed at toxic levels. While metal toxicity has been widely studied, the exact mechanisms of toxicity remain unclear. In order to further elucidate these mechanisms and identify candidate biomarkers, rats were exposed via a single intraperitoneal injection to three concentrations of CdCl2 and Na2Cr2O7, with livers harvested at 1, 3, or 7 days after exposure. Cd and Cr accumulated in the liver at 1 day post exposure. Cd levels remained elevated over the length of the experiment, while Cr levels declined. Metal exposures induced ROS, including hydroxyl radical (•OH), resulting in DNA strand breaks and lipid peroxidation. Interestingly, ROS and cellular damage appeared to increase with time post-exposure in both metals, despite declines in Cr levels. Differentially expressed genes were identified via microarray analysis. Both metals perturbed gene expression in pathways related to oxidative stress, metabolism, DNA damage, cell cycle, and inflammatory response. This work provides insight into the temporal effects and mechanistic pathways involved in acute metal intoxication, leading to the identification of candidate biomarkers.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25993096" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65220" }, "primaryId" : "GEO:GSE65220", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65220" } ] }, "title" : "Microarray analysis among non-alcoholic fatty liver, non-alcoholic steatohepatitis, and type 2 diabetes mellitus rats", "dateAssigned" : "2015-01-22T00:00:00.000-06:00", "summary" : "Non-alcoholic fatty liver disease (NAFLD) is recognized as a low-grade systemic inflammatory state with both hepatic and extra-hepatic manifestations. We aimed to identify common key regulators and adaptive pathways in different NAFLD phenotypes. NAFL, NASH and NAFL+T2DM rat models were used to represent simple fatty liver, fatty liver with severe hepatic manifestations, and fatty liver with severe metabolic manifestations, respectively. We applied microarray analysis to characterize the key regulators and adaptive pathways in different NAFLD phenotypes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65265" }, "primaryId" : "GEO:GSE65265", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65265" } ] }, "title" : "Macrophage gene expression associated with remodeling of the prepartum rat cervix: Microarray and pathway analyses", "dateAssigned" : "2015-01-24T00:00:00.000-06:00", "summary" : "Perfused cervix from prepartum day 21 postbreeding (D21) or nonpregnant (NP) rats, with or without Mfs, had RNA extracted and whole genome microarray analysis performed. By subtractive analyses, expression of 194 and 120 genes related to Mfs in the cervix from D21 rats were increased and decreased, respectively. In both D21 and NP groups, 158 and 57 Mf genes were also more or less up- or down-regulated, respectively.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65300" }, "primaryId" : "GEO:GSE65300", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65300" } ] }, "title" : "Expression data from retinoic acid injections into the third ventricle of F344 rats compared to vehicle injected rats", "dateAssigned" : "2015-01-26T00:00:00.000-06:00", "summary" : "4 rats per group were used giving 8 rats in total.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27225311" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65324" }, "primaryId" : "GEO:GSE65324", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65324" } ] }, "title" : "microRNA expression in parotid acinar cells during terminal differentiation", "dateAssigned" : "2015-01-26T00:00:00.000-06:00", "summary" : "We used both microRNA and mRNA expression measurements along with knowledgebased network analysis was used to develop a prospective gene regulatory network that drives differentiation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26484231" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65374" }, "primaryId" : "GEO:GSE65374", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65374" } ] }, "title" : "Analysis of gene expression profiles from the liver of rats treated with the mitochondrial electron transport chain complex III inhibitor GSK932121A (50mg/kg) or vehicle control", "dateAssigned" : "2015-01-28T00:00:00.000-06:00", "summary" : "BACKGROUND: Correlating in vitro mitochondrial data to outcomes in vivo remains a challenge and improving methods to assess mitochondrial function in vivo would both guide safer candidate selection and support the growing number of discovery programmes targeting mitochondria for pharmacological intervention. OBJECTIVES: The aim was to assess the toxicity profile of a compound with complex III electron transport chain inhibitory activity (GSK932121A) in order to identify markers and mechanisms of mitochondrial perturbation in vivo. METHODS:Crl:CD(SD) rats were dosed IP with GSK932121A for up to 5 hours depending upon the severity of observed clinical signs. Respirometry, microscopy, lactate/pyruvate and transcriptomics profiling were used to aid identification of a mode of action and this data was compared with functional data in isolated mitochondria. RESULTS AND DISCUSSION: GSK932121A administered in vivo caused hypothermia and a metabolic shift in energy production provoking an increased lactate/pyruvate ratio, microvesicular steatosis and glycogen depletion; alongside gene expression changes indicative of a fasted state. Our data improves current understanding of the toxicological consequences of drug induced respiratory chain inhibition and guides endpoint selection for future investigative safety studies with mitochondrially active molecules.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65466" }, "primaryId" : "GEO:GSE65466", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65466" } ] }, "title" : "Effects of N-terminal truncated version of FGF2 on dissociated myelinating cultures", "dateAssigned" : "2015-01-30T00:00:00.000-06:00", "summary" : "Analysis of the effects of different FGF2 variants (human FGFs-hFGF2, wild-type protein and N-terminal truncated FGF2-F2V2) on myelinating cultures generated from dissociated embryonic spinal cord after 24 hours treatment to give insights into the effects of the N-terminal region of FGF2 on FGF signalling and its implications in demyelinating diseases.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65490" }, "primaryId" : "GEO:GSE65490", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65490" } ] }, "title" : "The effects of herb-partitioned moxibustion on miRNA expression profiling in the colons of CD rats", "dateAssigned" : "2015-01-30T00:00:00.000-06:00", "summary" : "Using the highly sensitive miRNA microarray, we screened differentially-expressed miRNAs in colons of normal control (NC) rats, model control (MC) rats and herb-partitioned moxibustion (HPM) rats. We found 40 miRNAs differentially expressed in CD rats’ colons compared with the NC rats, and HPM significantly regulated 26 miRNAs in colon tissues compared with the MC group. Furthermore, the quantitative real-time polymerase chain reaction results showed that down-regulated miR-147 and miR-205 in CD rats’ colons were both significantly up-regulated by HPM, with 2.64- and 3.72-folds increased respectively, indicating that miR-147 and miR-205 are the target genes of HPM in treating CD rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25810742" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65586" }, "primaryId" : "GEO:GSE65586", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65586" } ] }, "title" : "mRNA expression in parotid acinar cells during terminal differentiation", "dateAssigned" : "2015-02-03T00:00:00.000-06:00", "summary" : "We used expression measurements along with knowledgebased network analysis was used to develop a prospective gene regulatory network that drives differentiation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26484231" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65663" }, "primaryId" : "GEO:GSE65663", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65663" } ] }, "title" : "A comparison of physiological and transcriptome responses to water deprivation and salt loading in the rat supraoptic nucleus", "dateAssigned" : "2015-02-05T00:00:00.000-06:00", "summary" : "Salt loading (SL) and water deprivation (WD) are experimental challenges that are often used to study the osmotic circuitry of the brain. Central to this circuit is the supraoptic nucleus (SON) of the hypothalamus, which is responsible for the biosynthesis of the hormones, vasopressin (AVP) and oxytocin (OXT), and their transport to terminals that reside in the posterior lobe of the pituitary. Upon osmotic challenge evoked by a change in blood volume or osmolality, the SON undergoes a function related plasticity that creates an environment that allows for an appropriate hormone response. Here, we have described the impact of SL and WD compared to euhydrated (EU) controls in terms of drinking and eating behaviour, body weight and recorded physiological data including circulating hormone data and plasma and urine osmolality. We have also used microarrays to profile the transcriptome of the SON following SL", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25632023" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65715" }, "primaryId" : "GEO:GSE65715", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65715" } ] }, "title" : "Macrophage epoxygenase determines a pro-fibrotic transcriptomesignature", "dateAssigned" : "2015-02-06T00:00:00.000-06:00", "summary" : "Epoxygenases belong to the cytochrome P450 family and they generate epoxyeicosatrienoic acids (EETs) known to have anti-inflammatory effects but little is known about their role in macrophage function. By high-throughput sequencing of RNA (RNA-seq) in primary macrophages derived fromrodents and humans, we establish the relative expression of epoxygenases in these cells. Zinc-finger nuclease-mediated targeted gene deletion of the major ratmacrophage epoxygenaseCyp2j4 (orthologue of human CYP2J2),resulted inreduced EET synthesis. Cyp2j4-/-macrophages have relatively increased PPAR¿ levels and show a pro-fibrotic transcriptome,displayingover-expression of a specific subset of genes (260 transcripts) primarily involved in extracellular matrix, with fibronectin being the most abundantly expressed transcript.Fibronectin expression is under the control of epoxygenase activity in human and rat primary macrophages. In keeping with the invitro findings, Cyp2j4-/- rats show up-regulation of type I collagen following unilateral ureter obstruction (UUO) of the kidney and quantitative proteomics analysis (LC-MS/MS) showed increased renal type I collagen and fibronectin protein abundance resulting from experimentally induced crescentic glomerulonephritis in these rats. Taken together, these results identify the rat epoxygenase Cyp2j4 as a determinant of a pro-fibrotic macrophage transcriptome that could have implications in various inflammatory conditions depending on macrophage function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25840911" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65779" }, "primaryId" : "GEO:GSE65779", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65779" } ] }, "title" : "Effects of GDM involves alterations in gene specific DNA methylation", "dateAssigned" : "2015-02-09T00:00:00.000-06:00", "summary" : "Gestational diabetes mellitus(GDM) will bring health issues for offspring. The offspring of diabetic mothers often reveal high birth weight and are prone to have obesity, hypertension and dyslipidemia. It was implied that the phenotype of offspring might be influenced by intrauterine environment and planned in utero already in addition to the genetic influences.‘Programming’ refers to the process whereby a stimulus at a critical window of development has long-term effects. A large body of studies investigated the adverse intrauterine environment was correlated with poor fetal growth and increased risk of Type 2 diabetes in the adulthood. Epigenetic mechanism has been proposed to involve in the link between environmental and nutritional factors and gene expression regulation. DNA methylation is one of the major epigenetic modifications. We hypothesized that DNA methylation changes could participate in the gene expression related to glucose intolerance in the offspring. Furthermore, DNA methylation might also determine the transgenerational disease transmission.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65787" }, "primaryId" : "GEO:GSE65787", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65787" } ] }, "title" : "Evidence from mRNA-Sequencing that Acute Olanzapine Infusion is Initiating a Skeletal Muscle Fiber Type Transition In Rat Gastrocnemius", "dateAssigned" : "2015-02-09T00:00:00.000-06:00", "summary" : "The purpose of this study was to examined the acute actions of the second generation antipsychotic (SGA), olanzapine, on skeletal muscle (gastrocnemius) of Sprague Dawley Rats. SGAs cause metabolic side effects including leading to metabolic inflexibility, hyperglycemia, adiposity and diabetes. These effects are preceded by glucose intolerance and increased FFA flux and metabolism in peripheral tissues. Skeletal muscle is a likely target of glucose intolerance, therefore understanding how olanzapine affects the skeletal muscle transcriptome could elucidate approaches for mitigating these side effects. Male Sprague-Dawley rats freely fed on normal chow with comparable body weights (vehicle: 373±9g, olanzapine: 388±11g, p=0.34) were infused with vehicle or olanzapine for 24h using a dosing regimen leading to mild hyperglycemia (vehicle, 98±2mg/dl; olanzapine 127±4mg/dl, p=0.0023). For the olanzapine group, the venous catheter was attached to a syringe pump (Model NE-300) filled with olanzapine (Dr. Reddy’s Laboratories Ltd, Hyderabad, India) in sterile saline (infusion: 1mg/100g BW loading dose for 0.5h and then 0.04mg/100g/h continuously for 23.5h). Gastrocnemius was then surgically removed under isoflurane anesthesia (carried with 100% O2), and frozen between two aluminum blocks cooled to the temperature of liquid nitrogen and then stored at -80oC until RNA was isolated. With anesthesia gas flow continuing, the animals were euthanized by cutting the diaphram and removing the heart. The mRNA was isolated from from these muscles and used for RNA-Seq followed by alignment of the data with the rat genome assembly 5.0. To determine significant differences in FPKM values between control and olanzapine groups, the DEGexp function of the DEGseq 1.18.0 R package was used with the Likelihood Ratio Test (LRT) and default parameters. In the uploaded excel file, P values with p<0.05 and p<0.001 are shown for each row in different columns indicated by the number 1. The value 0 indicates the row is not significantly different.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25893406" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65862" }, "primaryId" : "GEO:GSE65862", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE65862" } ] }, "title" : "Transcriptomic response in colon of rat with increased dietary protein content", "dateAssigned" : "2015-02-11T00:00:00.000-06:00", "summary" : "Increase of fecal hazardous compounds and decrease of butyrate-producing bacteria has been implicated to be detrimental to colonic health during weight loss by high-protein diet in human. The question remains that whether the change of luminal microenvironment were paralleled with the alteration of colonic function in vivo.To reveal the change of gene expression involved in metabolic or immmunological process, we have employed the whole genome microarray profiling to identify differentially expressed genes in rat dietary normal protein (20% protein) or high protein (45% protein) diet. Colonic epithelium were sampled in adult male wistar rats (weighing 180-200g) fed each diet for six weeks.Each group contained six replicates.A total of 181 transcripts were significantly changed: 88 genes were up-regulated and 93 genes were down-regulated in high protein compared with normal protein rats. Transcriptome analysis identified the upregulation of chemotaxis, TNF-a signal process, antigen presentation, apoptosis, glutathione S-transferase activity and downregulation of innate immune, O-linked glycosylation of mucin, oxidative phosphorylation.Expression of ten genes, including calmodulin1,acetyl-CoA acyltransferase 2,isovaleryl-CoA dehydrogenase and occludin, were quantified in the same RNA samples by real-time PCR, validating the microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26843585" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66058" }, "primaryId" : "GEO:GSE66058", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66058" } ] }, "title" : "Wide-scale transcriptome disturbance underlies liver and kidney pathology from chronic ultra low dose Roundup exposure [liver]", "dateAssigned" : "2015-02-18T00:00:00.000-06:00", "summary" : "Glyphosate-based herbicides (GBH) are the major pesticides used worldwide. Converging evidence suggests that GBH residues pose a particular risk to the kidneys and liver. However, the existence of biological effects with negative health implications at low environmentally relevant doses remains unresolved. A previous investigation addressed this issue, by conducting a 2-year feeding study, which included 10 female Sprague Dawley rats administered via drinking water with 0.1 ppb of a major Roundup formulation (50 ng/L glyphosate equivalent dilution). Hepatorenal toxicities, as well as urine and blood biochemistry disturbances at the 15th month of age were observed. In an effort to obtain molecular mechanistic insight into the underlying causes of these pathologies, we have carried out a transcriptome microarray analysis of the liver and kidneys from these same animals. The expression of 4224 and 4447 genes were found to be disturbed respectively in liver and kidney (p<0.01, q<0.08, fold change >1.1). Among the 1319 genes whose expression was altered in both tissues, 3 functional categories were over-represented. First, genes involved in mRNA splicing and small nucleolar RNA were mostly upregulated, suggesting disruption of normal spliceosome activity. Electron microscopic analysis of hepatocytes confirmed nucleolar structural disruption. Second, genes controlling chromatin structure (especially histone-lysine N-methyltransferases) were mostly upregulated. Third, genes related to respiratory chain complex I and the tricarboxylic acid cycle were mostly downregulated. The transcription factor networks that can account for these disruptions were centered on CREB1, ESR1, YY1, c-Myc and Oct3/4 activity, which are known to closely cooperate in the regulation of gene expression after hormonal stimulation. The analysis of pathways and toxicity processes showed that these disturbances in gene expression were representative of fibrosis, necrosis, phospholipidosis, mitochondrial membrane dysfunction and ischemia, which correlate with the pathologies observed at an anatomical and histological level. Our results suggest that new studies incorporating testing principles from endocrinology and developmental epigenetics need to be performed to investigate potential consequences of exposure to low dose, environmental levels of GBH and glyphosate.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26302742" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66059" }, "primaryId" : "GEO:GSE66059", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66059" } ] }, "title" : "Wide-scale transcriptome disturbance underlies liver and kidney pathology from chronic ultra low dose Roundup exposure [kidney]", "dateAssigned" : "2015-02-18T00:00:00.000-06:00", "summary" : "Glyphosate-based herbicides (GBH) are the major pesticides used worldwide. Converging evidence suggests that GBH residues pose a particular risk to the kidneys and liver. However, the existence of biological effects with negative health implications at low environmentally relevant doses remains unresolved. A previous investigation addressed this issue, by conducting a 2-year feeding study, which included 10 female Sprague Dawley rats administered via drinking water with 0.1 ppb of a major Roundup formulation (50 ng/L glyphosate equivalent dilution). Hepatorenal toxicities, as well as urine and blood biochemistry disturbances at the 15th month of age were observed. In an effort to obtain molecular mechanistic insight into the underlying causes of these pathologies, we have carried out a transcriptome microarray analysis of the liver and kidneys from these same animals. The expression of 4224 and 4447 genes were found to be disturbed respectively in liver and kidney (p<0.01, q<0.08, fold change >1.1). Among the 1319 genes whose expression was altered in both tissues, 3 functional categories were over-represented. First, genes involved in mRNA splicing and small nucleolar RNA were mostly upregulated, suggesting disruption of normal spliceosome activity. Electron microscopic analysis of hepatocytes confirmed nucleolar structural disruption. Second, genes controlling chromatin structure (especially histone-lysine N-methyltransferases) were mostly upregulated. Third, genes related to respiratory chain complex I and the tricarboxylic acid cycle were mostly downregulated. The transcription factor networks that can account for these disruptions were centered on CREB1, ESR1, YY1, c-Myc and Oct3/4 activity, which are known to closely cooperate in the regulation of gene expression after hormonal stimulation. The analysis of pathways and toxicity processes showed that these disturbances in gene expression were representative of fibrosis, necrosis, phospholipidosis, mitochondrial membrane dysfunction and ischemia, which correlate with the pathologies observed at an anatomical and histological level. Our results suggest that new studies incorporating testing principles from endocrinology and developmental epigenetics need to be performed to investigate potential consequences of exposure to low dose, environmental levels of GBH and glyphosate.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26302742" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66079" }, "primaryId" : "GEO:GSE66079", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66079" } ] }, "title" : "Expression data of embryonic kidney from MWF E15.5 and SHR 16.0 rats", "dateAssigned" : "2015-02-19T00:00:00.000-06:00", "summary" : "Microarray analysis revealed 311 transcripts representing 253 known genes with differential expression between MWF and SHR (FC >+1.5 or <-1.5, FDR<0.05).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66150" }, "primaryId" : "GEO:GSE66150", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66150" } ] }, "title" : "Gene expression in rat hippocampal CA1 during the consolidation of contextual fear memory", "dateAssigned" : "2015-02-20T00:00:00.000-06:00", "summary" : "Adult rats (male Lister hooded) received a single unsignaled scrambled footshock (0.5 mA for 2 s) 2 min into a 3min exposure to a novel context. One half rats received bilateral microinfusions (1 microlitre/hemisphere) of 2 nmol/microlitre BDNF antisense ODN (BDNFASO, 5’-TCTTCCCCTTTTAATGGT-3’ in PBS, pH 7.4) or BDNF missense ODN (BDNFMSO, 5’ -ATACTTTCTGTTCTTGCC-3’ in PBS, pH 7.4) into the dorsal hippocampus (AP -3.50, relative to bregma), 90 min before contextual fear conditioning (CFC). Infusions were made in awake rats via previously surgically implanted indwelling stainless steel cannula. Rats were housed in the home cages at all times outside the conditioning procedure. Rats were killed by CO2 inhalation 2 hours after CFC. CA1 enriched dorsal hippocampus was immediately dissected on ice before rapid freezing and storage at -80oC. The BDNFASO-infused group represent consolidation-impaired rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66151" }, "primaryId" : "GEO:GSE66151", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66151" } ] }, "title" : "Gene expression in rat hippocampal CA1 during the extinction of contextual fear memory", "dateAssigned" : "2015-02-20T00:00:00.000-06:00", "summary" : "Adult rats (male Lister hooded) were pre-exposed for 3 d for 10 min /d (24 hr interval) to two different novel contexts. On day 4 rats received a single unsignaled scrambled footshock (0.5 mA for 2 s) 2 min into a 3min exposure to one of the two contexts. Rats were either returned to the CS conditioned context (CS+, EXT group) or to the other (CS-, NOR group) context for 10 min, 48h after contextual fear conditioning. Rats were housed in the home cages at all times outside the conditioning and re-exposure components. The novel context chosen to be the conditioned context was counterbalanced across the experimental groups. Rats were killed by CO2 inhalation 2 hours after CS- or CS+ exposure. CA1-enriched dorsal hippocampus was immediately dissected on ice before rapid freezing and storage at -80oC. The CS+ group represents rats that underwent extinction of contextual fear memory.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66152" }, "primaryId" : "GEO:GSE66152", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66152" } ] }, "title" : "Gene expression in rat hippocampal CA1 after the retrieval of contextual fear memory in the absence of extinction.", "dateAssigned" : "2015-02-20T00:00:00.000-06:00", "summary" : "Adult rats (male Lister hooded) received a single unsignaled scrambled footshock (0.5 mA for 2 s) 2 min into a 3min exposure to a novel context. 48 hours later, rats were reexopsed to the condition context for 2 min (TEST). One half rats received bilateral microinfusions (1 microlitre/hemisphere) of 2 nmol/microlitre Zif268 antisense ODN (ZIFASO, 5’- GGTAGTTGTCCATGGTGG-3’in PBS, pH 7.4) or Zif268 missense ODN (ZIFMSO, 5’ -GTGTTCGGTAGGGTGTCA-3’in PBS, pH 7.4) into the dorsal hippocampus (AP -3.50, relative to bregma), 90 min before TEST. Infusions were made in awake rats via previously surgically implanted indwelling stainless steel cannula. Rats were housed in the home cages at all times outside the conditioning and TEST procedures. Rats were killed by CO2 inhalation 2 hours after TEST. CA1-enriched dorsal hippocampus was immediately dissected on ice before rapid freezing and storage at -80oC. The ZIFSO-infused group potentially represents reconsolidation-impaired rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66195" }, "primaryId" : "GEO:GSE66195", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66195" } ] }, "title" : "miRNA profiles of tubular cells (Rodent A and Rodent B)", "dateAssigned" : "2015-02-23T00:00:00.000-06:00", "summary" : "MicroRNAs (miRNAs) are endogenous small RNAs of 18–23 nucleotides that regulate gene expression. Recently, plasma miRNAs have been investigated as biomarkers for various diseases. In the present study, we assessed whether the miRNA expression profiles of tubular tissues could discriminate proximal tubule injury and diagnose acute kidney injury (AKI) and the renal tubular dysfunction without morphological changes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66203" }, "primaryId" : "GEO:GSE66203", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66203" } ] }, "title" : "DNMT inhibition in the Neonatal Preoptic Area", "dateAssigned" : "2015-02-23T00:00:00.000-06:00", "summary" : "PN2 male and female rat pups were treated with vehicle or zebularine. POA RNA was extracted and sequenced to deterime the effects of DNMT inhibition in POA gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25821913" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66275" }, "primaryId" : "GEO:GSE66275", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66275" } ] }, "title" : "Microarray profiling of rats treated for 21 days with haloperidol (0.25 mg/kg/d), risperidone (5 mg/kg/d) or vehicle", "dateAssigned" : "2015-02-24T00:00:00.000-06:00", "summary" : "SD rats were dosed with gold standard antipsychotic therapies, haloperidol or risperidone, at doses aimed at achieving therapeutically relevant drug exposures. Tissues were collected after 21 days of delivery to examine the impact of this treatment on gene expression in frontal cortex, hippocampus and striatum.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66276" }, "primaryId" : "GEO:GSE66276", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66276" } ] }, "title" : "Microarray profiling of rats treated for 21 days with Lithium chloride (0.2% in chow), Lamotrigine (30 mg/kg), or appropriately matched vehicles", "dateAssigned" : "2015-02-24T00:00:00.000-06:00", "summary" : "SD rats were dosed with gold mood stabilizer therapies, lithium or lamotrigine, at doses aimed at achieving therapeutically relevant drug exposures. Tissues were collected after 21 days of delivery to examine the impact of this treatment on gene expression in frontal cortex, hippocampus and striatum.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66287" }, "primaryId" : "GEO:GSE66287", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66287" } ] }, "title" : "Hippocampal response to Hypobaric Hypoxia", "dateAssigned" : "2015-02-25T00:00:00.000-06:00", "summary" : "Sprague Dawley rats were exposed to Hypobaric Hypoxia for 1, 3 and 7 days followed isolation of Hippocampus. Microarray was performed utilizing RNA isolated from these samples. Each group included 5 animals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66316" }, "primaryId" : "GEO:GSE66316", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66316" } ] }, "title" : "Expression data from adult male Sprague Dawley rat liver, investigating how pomegranate skin extract prevents non alcoholic fatty liver diseases", "dateAssigned" : "2015-02-26T00:00:00.000-06:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying the fatty liver development and preventive effect of pomegranate skin extract on fatty liver.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66347" }, "primaryId" : "GEO:GSE66347", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66347" } ] }, "title" : "Rat DNA methylation in the Nucleus Accumbens in Incubation of Cocaine Craving and treatments with DNA methylation modifying drugs", "dateAssigned" : "2015-02-26T00:00:00.000-06:00", "summary" : "DNA methylation profiling of nucleus Accumbens of rats that self administered cocaine, were subjected to 30 withdrawal days, were treated with aCSF, RG108 or SAM and were subjected to extinction tests.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26019323" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66348" }, "primaryId" : "GEO:GSE66348", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66348" } ] }, "title" : "Rat DNA methylation in the Nucleus Accumbens in Incubation of Cocaine Craving", "dateAssigned" : "2015-02-26T00:00:00.000-06:00", "summary" : "DNA methylation profiling of nucleus Accumbens of rats that self administered cocaine and were subjected to 1 or 30 withdrawal days with or without extinction tests.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26019323" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66349" }, "primaryId" : "GEO:GSE66349", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66349" } ] }, "title" : "Rat gene expression in the Nucleus Accumbens in Incubation of Cocaine Craving", "dateAssigned" : "2015-02-26T00:00:00.000-06:00", "summary" : "Gene expression profiling of nucleus Accumbens of rats that self administered cocaine and were subjected to 1 or 30 withdrawal days with or without extinction tests.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26019323" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66371" }, "primaryId" : "GEO:GSE66371", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66371" } ] }, "title" : "Different Effects of Tofu (Soybean Curd) and Fish Oil in Serum Lipoproteins and Hepatic Gene Expressions of Rats", "dateAssigned" : "2015-02-27T00:00:00.000-06:00", "summary" : "Soybean and fish contains various active components that were reported to prevent cardiovasucular diseases. Epidemiological studies indicated that Asian eating patterns, consisting of daily seafood and/or soy consumption, confer protection against cardiovascular diseases. In this context, we expected that simultaneous intake of soybean and fish may be greatly beneficial in a manner different from the ingestion of the individual food. To understand the detailed mechanism for modulating the lipid metabolism by co-ingestion of a soy food (tofu) and fish oil, we investigated the global changes in hepatic mRNA expression in rats by using a microarray analysis. Generally, ingestion of tofu contributed to prevent the mRNA expressions involved in hepatic lipogenesis, whereas fish oil facilitated the mRNA expressions related to the degradation of hepatic fatty acids. In terms of mRNA expression, the interaction of two dietary factors was limited. The expression data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66554" }, "primaryId" : "GEO:GSE66554", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66554" } ] }, "title" : "Expression data of LncRNA from the rat (Sprague-Dawley) knee articular cartilage at different developmental stages", "dateAssigned" : "2015-03-05T00:00:00.000-06:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying the rat knee cartilage and identified distinct classes of age-related lncRNA during this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66566" }, "primaryId" : "GEO:GSE66566", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66566" } ] }, "title" : "Hepatitis B virus-mediated alterations to the primary hepatocyte transcriptome [24 and 48 h]", "dateAssigned" : "2015-03-05T00:00:00.000-06:00", "summary" : "Results: Following this pipeline, we were able to identify a number of HBV-mediated differentially expressed transcripts at 24h and 48h post-infection. Further pathway analysis of these differentially expressed transcripts identified many important cellular pathways, including those involved with cell cycle regulation and metabolism, as being differentially regulated by HBV in primary hepatocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26891448" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66617" }, "primaryId" : "GEO:GSE66617", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66617" } ] }, "title" : "Chaetocin efficacy on Dahl rat", "dateAssigned" : "2015-03-06T00:00:00.000-06:00", "summary" : "Transcriptional profiling of left ventricular tissues of Dahl rat with or without treatment of chaetocin", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28051130" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66623" }, "primaryId" : "GEO:GSE66623", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66623" } ] }, "title" : "Iodine-131 Biomarker Identification in the Rat Thyroid Gland", "dateAssigned" : "2015-03-06T00:00:00.000-06:00", "summary" : "Introduction Iodine-131 (131I) is frequently used in nuclear medicine. Unbound or released 131I accumulate in the thyroid gland and may be detrimental to normal thyroid function. The aim of the present study was to identify biomarkers for 131I exposure in rat thyroid tissue and to assess the effect on thyroid function. Methods Thirty six male Sprague Dawley rats were i.v. injected with 150 µl saline solution containing 9.0, 88, 170, 260, 340, 760, 1300, or 4700 kBq (group A-H) 131I, or mock-treated with 150 µl saline solution only, and killed at 24 h after injection. Total RNA was extracted from individual thyroid tissue samples thyroids and mRNA levels were determined with the Agilent microarray platform. Results Estimated absorbed doses in treatment groups A-H was 0.0058, 0.057, 0.11, 0.17, 0.22, 0.5 Gy, 0.8 Gy, and 3 Gy. Totally, 429 transcripts were identified with a fold change fold change = 1.5 and adjusted p-value = 0.01. A trend with downregulation of thyroid hormone biosynthesis associated genes (e.g. thyroglobulin, thyroid peroxidase, the sodium-iodine symporter) was identified, but only statistically significant after 0.0058 and 0.22 Gy. Three transcripts coding for isoform 1 of the DBP protein showed a pattern with monotonous decrease in downregulation with absorbed dose between 0.0058-0.22 Gy. Changes in Dbp expression were not statistically significant between 0.5-3 Gy. However, a trend with downregulation at 0.5 and 0.8 Gy and upregulation and 3 Gy was identified. Previously, 131I (0.85-17 Gy) and 211At (0.023-32 Gy) exposure resulted in upregulation of Dbp in mice thyroid tissue 24 h after administrations. Additionally, a monotonous decrease in Dbp downregulation has been identified of in mouse kidney tissue at 8 and 12 months after 177Lu-octreotate administrations. Conclusion Conclusively, the Dbp gene is a promising candidate biomarker gene for exposure to 131I and possibly other internal radiation emitters. Further studies should be performed to establish how Dbp expression vary with dose-rate, absorbed dose, time after administration, different radiation qualities, and the function of Dbp.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66624" }, "primaryId" : "GEO:GSE66624", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66624" } ] }, "title" : "Expression of V3 Versican by Arterial Smooth Muscle Cells Promotes Differentiated and Anti-inflammatory Phenotypes", "dateAssigned" : "2015-03-06T00:00:00.000-06:00", "summary" : "Arterial smooth muscle cells (ASMCs) undergo phenotypic changes during development and pathological processes in vivo and during cell culture in vitro. Our previous studies demonstrated that retrovirally-mediated expression of the versican V3 splice variant (V3) that lacks glycosaminoglycan chains by ASMCs retards cell proliferation and migration in vitro and reduces neointimal thickening, macrophage and lipid accumulation in animal models of vascular injury and atherosclerosis. However, the molecular pathways induced by V3 expression that are responsible for these changes are not yet clear. In the present study, we employed a microarray approach to examine how expression of V3 induced changes in gene expression and the molecular pathways in ASMCs. We found that forced expression of V3 by ASMCs affected expression of 521 genes by more than 1.5 fold. Gene ontology (GO) analysis shows that components of extracellular matrix were the most significantly affected by V3 expression, indicating that V3 expression elicits profound remodeling of extracellular matrix. In addition, genes regulating the formation of the cytoskeleton which also serve as markers of contractile smooth muscle cells were significantly upregulated. On the other hand, components of the complement system, chemokines, chemokine receptors, and transcription factors crucial for regulating inflammatory processes were among the genes most downregulated. Consistently, we found that the level of myocardin, a key transcription factor promoting contractile ASMC phenotype, was greatly increased while proinflammatory transcription factors NFkappaB1 and C/EBPß were significantly attenuated in V3-expressing SMCs. Such results indicate that V3 expression reprograms ASMC into differentiated and anti-inflammatory phenotypes. Overall, these findings demonstrate that expression of V3 reprograms ASMCs promoting anti-inflammatory and differentiated smooth muscle cell phenotypes potentially by altering cell-ECM interaction and focal adhesion signaling pathways.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26152723" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66633" }, "primaryId" : "GEO:GSE66633", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66633" } ] }, "title" : "Bisphenol A disrupts HNF4a-regulated gene networks linking to prostate preneoplasia in Noble rats ", "dateAssigned" : "2015-03-06T00:00:00.000-06:00", "summary" : "Exposure of humans to bisphenol A (BPA) is widespread and continuous. We previously showed that perinatal exposure to BPA increased prostate cancer risk in adult rats. Yet the effects of protracted, exposure to BPA during adulthood have not been studied. In this study, we subjected Noble rats to 32 weeks of co-treatment with testosterone (T) and BPA (low- or high-dose) or T and 17ß-estradiol (E2) via Silastic capsule implants. Circulating T levels were comparable in all treatment groups, whereas the levels of free BPA were elevated in the groups that received T+low BPA (1.06 ± 0.05 ng/ml, P<0.05) and T+high BPA (10.37 ± 0.43 ng/ml, P<0.01) when compared with those in controls (0.1 ± 0.05 ng/ml). T+low/high BPA induced prostatic hyperplasia, low-grade prostatic intraepithelial neoplasia (PIN), and intraepithelial infiltration of T-lymphocytes only in the lateral prostates (LPs), whereas T+E2 induced high-grade PIN in this prostatic lobe. Genome-wide transcriptome analysis identified differential changes in the LPs of T+BPA and T+E2 treatments, with aberrant expression of multiple genes in the regulatory network controlled by the transcription factor hepatic nuclear factor 4a (HNF4a) specifically in BPA- but not E2-treated LPs. These findings suggest that the adult rat prostate is susceptible to transcriptomic reprogramming by BPA associated with the development of prostate pathology in a manner distinct from that of E2. The relevance of these data to the previous report demonstrating an association between high urinary levels of BPA and prostate cancer needs to be studied further.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66653" }, "primaryId" : "GEO:GSE66653", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66653" } ] }, "title" : "Methylation of H3K9 by G9a/GLP protects against pathological cardiac hypertrophy", "dateAssigned" : "2015-03-09T00:00:00.000-05:00", "summary" : "The heart adapts to increased workload through hypertrophic growth of cardiomyocytes. Although beneficial when induced physiologically by exercise, pathological cues including hypertension cause reexpression of fetal genes and dysfunctional hypertrophy, with lasting consequences for cardiac health. We hypothesised that these differences are driven by changes in chromatin-encoded cellular memory. We generated genome-wide maps of transcription and of two stable epigenetic marks, H3K9me2 and H3K27me3, specifically in hypertrophied cardiomyocytes, by selectively flow-sorting their nuclei. This demonstrated a pervasive loss of euchromatic H3K9me2 specifically upon pathological but not physiological hypertrophy, derepressing genes associated with pathological hypertrophy. Levels of the H3K9 methyltransferases, G9a and GLP, were correspondingly reduced. Importantly, pharmacological or genetic inactivation of these enzymes was sufficient to induce pathological hypertrophy and the dedifferentiation associated with it. These findings suggest novel therapeutic opportunities by defining an epigenetic state of cardiomyocytes, acquired during maturation, which is required for maintaining cardiac health.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27893464" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66715" }, "primaryId" : "GEO:GSE66715", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66715" } ] }, "title" : "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats", "dateAssigned" : "2015-03-09T00:00:00.000-05:00", "summary" : "Aging is associated with the decline of protein, cell, and organ function. Here, we use an integrated approach to characterize gene expression, bulk translation, and cell biology in the brains and livers of young and old rats. We identify 468 differences in protein abundance between young and old animals. The majority are a consequence of altered translation output, that is, the combined effect of changes in transcript abundance and translation efficiency. In addition, we identify 130 proteins whose overall abundance remains unchanged but whose sub-cellular localization, phosphorylation state, or splice-form varies. While some protein-level differences appear to be a generic property of the rats’ chronological age, the majority are specific to one organ. These may be a consequence of the organ’s physiology or the chronological age of the cells within the tissue. Taken together, our study provides an initial view of the proteome at the molecular, sub-cellular, and organ level in young and old rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66761" }, "primaryId" : "GEO:GSE66761", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66761" } ] }, "title" : "microRNAs expression in kidneys from normal, cisplatin induced AKI rats and those with the restoration of MSCs", "dateAssigned" : "2015-03-10T00:00:00.000-05:00", "summary" : "The availability of mesenchymal stem cells in kidney injury repair has been demonstrated. However, the underlying molecular mechanism remains not well understood. Herein, we profiled the altered microRNAs in renal tissiues from cisplatin-induced acute kidney injury (AKI) rats administrated with or without rat bone marrow mesenchymal stem cells, normal kidneys as control. Sprague Dawley rats were administrated with PBS by caudal vein after 24h peritoneal injection of 6mg/mg cisplatin, short for g2. 1×106 MSCs were injected to rats after 24h peritoneal injection of cisplatin, short for g3. Kidneys from healthey rats were used as control, short for g1. Renal tissues were collected at day 5 after treatment. There were 44 micorRNAs changed with significance between g2 and g3, among which 36 microRNAs upregulated and 8 microRNAs downregulated.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27400799" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66976" }, "primaryId" : "GEO:GSE66976", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE66976" } ] }, "title" : "Age-dependent Response of Isolated Male Germ Cells to Oxidative Stress", "dateAssigned" : "2015-03-17T00:00:00.000-05:00", "summary" : "Study of the response of isolated male germ cells from young and aged Brown Norway Rats to oxidative stress.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26224006" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67022" }, "primaryId" : "GEO:GSE67022", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67022" } ] }, "title" : "Regulation of Rat Hepatic Translation by mTOR", "dateAssigned" : "2015-03-18T00:00:00.000-05:00", "summary" : "Our strategy was to manipulate mTOR signaling in vivo, then characterize the transcriptome and translating mRNA in liver tissue. In adult rats, we used the non-proliferative growth model of refeeding after a period of fasting, and the proliferative model of liver regeneration following partial hepatectomy. We also studied livers from pre-term fetal rats (embryonic day 19-20) in which fetal hepatocytes are asynchronously proliferating. All three models employed rapamycin to inhibit mTOR signaling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25924882" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67036" }, "primaryId" : "GEO:GSE67036", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67036" } ] }, "title" : "Candesartan neuroprotection on Rat Primary cerebellar granule cells (CGCs)", "dateAssigned" : "2015-03-18T00:00:00.000-05:00", "summary" : "Neuronal cultures were treated with candesartan at neuroprotective concentrations followed by excitotoxic glutamate amounts. Candesartan significantly reduced glutamate-induced inflammation. To provide mechanistic insight into the potential targets and pathways that may underlie these benefits, we performed genome wide expression profile analysis and evaluated the data by Ingenuity Pathway Analysis (IPA) and Gene Set Enrichment Analysis (GSEA). We found that the inflammation signal transduction pathways were major components of the neuronal response to glutamate excitotoxicity, and that candesartan significantly ameliorated glutamate-induced alterations in gene expression. Further analysis showed significant associations of these genes with two independent published networks identified by microarray analysis of hippocampal samples obtained post-mortem from brains of patients diagnosed with AD .", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26822027" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67050" }, "primaryId" : "GEO:GSE67050", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67050" } ] }, "title" : "Cytosolic Accumulation of Small Nucleolar RNAs (snoRNAs) is Dynamically Regulated by NADPH Oxidase", "dateAssigned" : "2015-03-19T00:00:00.000-05:00", "summary" : "Small nucleolar RNAs (snoRNAs) guide nucleotide modifications of cellular RNAs in the nucleus. We have previously shown that box C/D snoRNAs from the Rpl13a locus are unexpected mediators of physiologic oxidative stress, independent of their predicted ribosomal RNA modifications. Here, we demonstrate that oxidative stress induced by doxorubicin causes rapid cytoplasmic accumulation of the Rpl13a snoRNAs through a mechanism that requires superoxide and a nuclear splice variant of NADPH oxidase. RNA-sequencing analysis reveals that box C/D snoRNAs as a class are present in the cytoplasm, where their levels are dynamically regulated by NADPH oxidase. These findings suggest that snoRNAs may orchestrate the response to environmental stress through molecular interactions outside of the nucleus.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25792744" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67069" }, "primaryId" : "GEO:GSE67069", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67069" } ] }, "title" : "MRF4 negatively regulates adult skeletal muscle growth by repressing MEF2 activity", "dateAssigned" : "2015-03-19T00:00:00.000-05:00", "summary" : "The myogenic regulatory factor MRF4 is expressed at high levels in myofibers of adult skeletal muscle, but its function is unknown. Here we show that knockdown of MRF4 in adult muscle causes hypertrophy and prevents denervation-induced atrophy. This effect is accompanied by increased protein synthesis and the widespread activation of genes involved in muscle contraction, excitation-contraction coupling and energy metabolism, many of which are known targets of MEF2 transcription factors. Genes regulated by MEF2 represent the top-ranking gene set enriched after Mrf4 RNAi, and a MEF2 reporter is inhibited by co-transfected MRF4 and activated by Mrf4 RNAi. The role of MEF2 in mediating the effect of MRF4 knockdown is supported by the finding that Mrf4 RNAi-dependent increase in fiber size is prevented by dominant negative MEF2, while constitutively active MEF2 is able to induce myofiber hypertrophy. The nuclear localization of the MEF2 co-repressor HDAC4 is impaired by Mrf4 knockdown, suggesting that MRF4 acts by stabilizing a repressor complex that controls MEF2 activity. The demonstration that fiber size in adult skeletal muscle is controlled by the MRF4-MEF2 axis opens new perspectives in the search for therapeutic targets to prevent muscle wasting, in particular sarcopenia and cachexia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27484840" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67146" }, "primaryId" : "GEO:GSE67146", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67146" } ] }, "title" : "Expression data from camptothecin-treated rat primary motor neurons", "dateAssigned" : "2015-03-22T00:00:00.000-05:00", "summary" : "Topoisomerase 1 (TOP1) poisons like camptothecin (CPT), which are used as chemotherapeutic agents in cancer, elicit DNA damage in quiescient neurons. In this study, we examined the effects of CPT and actinomycin D (ActD) on neuronal cells. Motor (MNs) and cortical (CNs) neurons were more susceptible to the toxic effects of CPT and ActD than fibroblasts. MNs and CNs exhibited a delayed DNA damage response—increase in nuclear ¿-H2AX foci—relative to fibroblasts. Neuronal cells expressed higher levels of Top1 mRNA than fibroblasts which could explain their enhanced vulnerability to CPT and ActD toxicity. Microarray analysis was performed to identify differentially regulated transcripts in MNs treated with CPT for 2 hours. Many immediate-early genes including Fos and Egr-1 were upregulated in CPT-treated MNs. Fos mRNA levels were elevated in all cells types treated with CPT; Egr-1 transcript levels, however, were reduced in CPT-treated fibroblasts even though they were elevated in treated MNs and CNs. Pathway and network analysis of the differentially expressed transcripts revealed activation of ERK and JNK signaling cascades in CPT-treated MNs. In conclusion, MNs were more vulnerable than fibroblasts to the damaging effects of TOP1 poisons and they elicit a unique intracellular response to CPT treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27641670" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67175" }, "primaryId" : "GEO:GSE67175", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67175" } ] }, "title" : "SAHA Rat Dental Pulp", "dateAssigned" : "2015-03-23T00:00:00.000-05:00", "summary" : "Transcript profiling of DPC identified several novel genes expression induced and supressed by HDACi at 24 hrs and 14 days under mineralising conditions. SAHA induces several members of the MMP family of endopepsidases (TIMP-1, MMP-9, MMP-13) and other members of the endochondral ossification pathway at 24 h.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26484294" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67203" }, "primaryId" : "GEO:GSE67203", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67203" } ] }, "title" : "Long-term consequences of chronic fluoxetine exposure on the expression of myelination-related genes in the rat hippocampus", "dateAssigned" : "2015-03-24T00:00:00.000-05:00", "summary" : "To more concretely elucidate the long-term effects of chronic SSRI exposure during adulthood, the long-term consequences of chronic fluoxetine (12 mg/kg) versus vehicle treatment during adulthood (postnatal day (PND) 67-88) on gene expression in the hippocampus were investigated. The study showed that adult chronic fluoxetine exposure causes on the long-term changes in the expression of genes related to, amongst others, myelination", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26393488" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67213" }, "primaryId" : "GEO:GSE67213", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67213" } ] }, "title" : "Identification of differential expressed genes among P-RPC, rESC-RPC1 and rESC-RPC2 through genome-wide transcript profiling", "dateAssigned" : "2015-03-24T00:00:00.000-05:00", "summary" : "Degenerative retinal diseases like age-related macular degeneration (AMD) are the leading cause of blindness. Cell transplantation showed promising therapeutic effect for such diseases, and retinal progenitor cell (RPC) derived from embryonic stem cell (ESC) is one of the sources of such donor cells. Here, we established two protocols through which two types of rat ESC-derived RPCs (rESC-RPCs) were obtained and both contained some NPCs and committed retina lineage cells. As P-RPCs have been reported to successfully integrate into host eyes, we sough to identify differentially expressed genes among P-RPCs, rESC-RPC1s and rESC-RPC2s through genome-wide transcript profiling. rESC-RPC2 can integrate into the host retina, form synaptic connections and restore visual function after transplanted into the degenerative retinal disease model RCS rat.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26553210" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67242" }, "primaryId" : "GEO:GSE67242", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67242" } ] }, "title" : "Analysis of the role of miR-21 in liver regeneration after partial hepatectomy (PHx) in chronic ethanol-treated rats through in vivo inhibition using LNAs", "dateAssigned" : "2015-03-24T00:00:00.000-05:00", "summary" : "In this study, we analyzed the role of miR-21 in liver regeneration after partial hepatectomy (PHx) in chronic ethanol-treated rats. Male Sprague-Dawley rats were fed a liquid diet containing 36% of total calories derived from ethanol for 5 weeks; corresponding pair-fed calorie-matched controls were fed diets in which ethanol calories were replaced by carbohydrate. After 5 weeks, locked nucleic acid (LNA)-modified oligo antisense to miR-21 (AM21, Exiqon, Vedbaek, Denmark) was used to inhibit miRNA in vivo, and rats were subjected to 70% PHx. Liver samples were collected at 24h after the surgery. The excised liver samples at t=0 served as within-animal controls. Rat Gene 2.0 ST (Affymetrix, Santa Clara, CA) arrayswere used to obtain global gene expression data from pooled liver samples (pools of 3 or 4 biological replicates/array, total 8 arrays).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27634014" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67274" }, "primaryId" : "GEO:GSE67274", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67274" } ] }, "title" : "Impact of Vitamine D depletion and repletion on rat skeletal muscle", "dateAssigned" : "2015-03-25T00:00:00.000-05:00", "summary" : "15 months Old Wistar Rat were submitted to 3 differents diets: control, without vitamin D and without vitamin D followed by a supplementation in vitamin D. At sacrifice, skeletal muscle were recovered, quickly frozen in liquid nitrogen. RNA profiling by microarrays was performed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67429" }, "primaryId" : "GEO:GSE67429", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67429" } ] }, "title" : "Gene expression analysis in the adult carotid body stem cell niche", "dateAssigned" : "2015-03-30T00:00:00.000-05:00", "summary" : "We have previously described a subpopulation of neural crest-derived stem cells residing in the organ. These cells are responsible for hypoxia-induced neurogenesis. Little is known about the molecular mechanisms underlying this neurogenic process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67499" }, "primaryId" : "GEO:GSE67499", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67499" } ] }, "title" : "Unraveling the rat blood genome-wide transcriptome after oral administration of Lavender oil by a two-color dye-swap DNA microarray approach", "dateAssigned" : "2015-04-01T00:00:00.000-05:00", "summary" : "Lavender oil (LO) is commonly used oil in aromatherapy, with well-defined volatile components linalool and linalyl acetate, in non-traditional medicine. To understand and demonstrate the potential positive effects of LO on the body, we have established an animal model for investigating the orally administered LO effects genome-wide in the rat tissues. In this data submission, we investigate the effect of LO ingestion in the blood. These results are the first such inventory of genes that are affected by lavender essential oil (LO) in the blood of an animal model, forming the basis for further functional analysis and investigation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27330992" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67659" }, "primaryId" : "GEO:GSE67659", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67659" } ] }, "title" : "Comparative transcriptomics of endometrial stromal fibroblasts", "dateAssigned" : "2015-04-08T00:00:00.000-05:00", "summary" : "We sequenced mRNA of endometrial stromal fibroblasts from six mammalian species.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27401177" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67782" }, "primaryId" : "GEO:GSE67782", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67782" } ] }, "title" : "The effect of dietary soybeans and their isoflavone content on the expression profiles of mRNAs in liver of rats", "dateAssigned" : "2015-04-12T00:00:00.000-05:00", "summary" : "The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18328687" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67787" }, "primaryId" : "GEO:GSE67787", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67787" } ] }, "title" : "Different exercise modalities have distinct effects on the transcriptome profile in the male rat femoral diaphysis", "dateAssigned" : "2015-04-13T00:00:00.000-05:00", "summary" : "Mechanical loading is a key determinant of bone mass, geometry and strength and is essential to maintain optimal skeletal health. We hypothesized that spontaneous low-impact exercise would affect global gene transcript levels in cortical bone of growing rats. We used RNA-Seq to analyse the transcriptome of the femoral mid-diaphysis in pre-pubertal male rats that were assigned to one of three exercise groups for 15 days: control (CON); bipedal stance (BPS); and wheel exercise (WEX). RNA-seq analysis identified 808 and 324 differentially expressed transcripts in the BPS and WEX animals, respectively. In WEX animals, the up-regulated transcripts were enriched for gene ontology terms associated with bone metabolism. Both BPS and WEX animals showed changes in transcripts that were enriched for muscle-related processes. However, in WEX these transcripts were down-regulated while in BPS such transcripts were up-regulated. Importantly, we observed that the exercise mode had diametrically opposite effects on transcripts for multiple genes within the integrin-linked kinase (ILK) and Ca2+ signalling pathways such that they were up-regulated in BPS and down-regulated in WEX. The findings are important for our understanding of possible ways in which different exercise regimens might affect bone when normal activities apply mechanical stimuli during post-natal growth and development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26471755" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67788" }, "primaryId" : "GEO:GSE67788", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67788" } ] }, "title" : "Transcriptional analysis of apoptotic cerebellar granule neurons following rescue by Gip, Sp, Pacap and Igf1", "dateAssigned" : "2015-04-13T00:00:00.000-05:00", "summary" : "Primary cultures of Cerebellar Granule Neurons (CGNs) have been extensively utilized to examine the signal transduction mechanisms underlying neuronal apoptosis. We conducted whole-genome expression profiling to decipher the transcriptional program controlling the apoptotic/survival switch in cerebellar granule neurons (CGNs) following the induction of apoptosis by serum and potassium deprivation and their rescue by gastric inhibitory polypeptide (Gip), substance p (Sp), insulin-like growth factor-1 (Igf1) or pituitary adenylyl cyclase-activating polypeptide (Pacap). Our results reveal the transcriptional changes intersecting neuronal apoptosis and survival and form the basis for further functional analyses and pharmacological exploitation to identify neuroprotective drugs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67830" }, "primaryId" : "GEO:GSE67830", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67830" } ] }, "title" : "Spinal gene expression signature in male wistar rats exposed to repeated psychological stress", "dateAssigned" : "2015-04-13T00:00:00.000-05:00", "summary" : "To test the effect of chronic water avoidance stress on spinal gene expression profile in male wistar rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26222740" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67831" }, "primaryId" : "GEO:GSE67831", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67831" } ] }, "title" : "Spinal microRNA expression signature in male wistar rats exposed to repeated psychological stress", "dateAssigned" : "2015-04-13T00:00:00.000-05:00", "summary" : "To test the effect of chronic water avoidance stress on spinal microRNA expression profile in male wistar rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26222740" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67836" }, "primaryId" : "GEO:GSE67836", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67836" } ] }, "title" : "Gene expression profile in rat frontal cortex during the secondary phase of trauma injury", "dateAssigned" : "2015-04-14T00:00:00.000-05:00", "summary" : "The pathophysiology of TBI is complex and can be divided into primary damage resulting from mechanical impact and secondary damage, which comprises complex interconnecting structural, functional, cellular and molecular changes. The current study was performed to evaluate gene expression profiles in the frontal cortex at 1 month, a time at which secondary damaged can be detected, following lateral fluid percussion induced TBI (lfp-TBI) and rotational acceleration induced TBI (rot-TBI) in rats. After lfp-TBI, genes significantly expressed belong to metabolic process, immune system, cellular process, and morphogenesis. After rot-TBI, genes were related to apoptosis response, morphogenesis, angiogenesis, extracellular matrix, metabolic process, and transport and localization. Interestingly, we found that the molecular signature of secondary TBI share similar alterations to pathologies related to ischemia stroke and depression. Overlapped genes belong to immune/inflammation processes, extracellular organization, and intracellular trafficking. Their biological implications in multiple brain pathologies remain to be further examined. Nonetheless, these genes homologies may indicate that therapeutic strategies following stroke and depression may also be beneficial after trauma.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67874" }, "primaryId" : "GEO:GSE67874", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67874" } ] }, "title" : "Altered neurotrophin expression profiles in the nucleus of the solitary tract of spontaneously hypertensive rats", "dateAssigned" : "2015-04-14T00:00:00.000-05:00", "summary" : "To unveil the characteristics of the neurodevelopmental environment in the NTS of hypertensive rats, we investigated the gene expression profile of neurotrophins and their receptors in SHRs compared to that of normotensive rat WKY.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26485190" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67880" }, "primaryId" : "GEO:GSE67880", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE67880" } ] }, "title" : "Gene expression profile of liver tissue in low-dose, repeated diethylnitrosamine (DEN)-treated rat treated with epigallocatechin gallate (EGCG)", "dateAssigned" : "2015-04-14T00:00:00.000-05:00", "summary" : "Background: Hepatocellular carcinoma (HCC) is increasing in incidence and treatment is often unsuccessful. Thus, prevention in high-risk patients with established cirrhosis has been proposed as an alternative strategy. It has been suggested that the increased inflammation and fibrogenesis observed during cirrhosis predisposes the liver to future malignant transformation to HCC through a “field effect”. A growing body of evidence indicates that the green tea polyphenol, (-)-epigallocatechin gallate (EGCG), can reduce inflammation and fibrogenesis during chronic liver injury. Here, we test the hypothesis that EGCG administered in the setting of cirrhosis can prevent future HCC development. Methods: A rat model of diethylnitrosamine (DEN)-induced cirrhosis was used to examine the efficacy of EGCG for inhibition of HCC formation in these cirrhotic livers. DEN (50 mg/kg) was administered weekly throughout the study while 0.02% EGCG was given in drinking water beginning at the onset of cirrhosis. At the end of the study, rats were sacrificed, livers were sectioned and stained to analyze disease progression and tumor nodules were counted. Liver function tests were performed to determine liver injury and overall liver function. Finally, genome-wide gene expression profiling on the surrounding, non-tumoral liver tissue was used to monitor the “field effect” in response to EGCG. Results: EGCG significantly (p < 0.01) prevented the development of HCC tumor nodules from on average 18.8 in vehicle controls to on average 9.1 in EGCG-treated animals. EGCG also reduced liver injury and improved liver function as assessed by serum chemistry tests. Finally, a gene expression signature predictive of poor survival and HCC development in human cirrhosis patients was reversed in response to EGCG. Conclusions: Our data are consistent with the growing body of evidence suggesting that EGCG has protective effects in liver disease. Further, our results suggest that EGCG is a potentially effective HCC prevention strategy that can be monitored using gene expression signatures.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32253266" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68010" }, "primaryId" : "GEO:GSE68010", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68010" } ] }, "title" : "Gene expression change in the liver by luteolin treatment in rats with nonalcoholic steatohepatitis", "dateAssigned" : "2015-04-17T00:00:00.000-05:00", "summary" : "Gene expression change in the liver of connexin dominant negative transgenic (Tg) and wild-type (Wt) rats fed methionine-choline deficient diet (MCDD) or MCDD with luteolin for 12 weeks.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26494227" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68065" }, "primaryId" : "GEO:GSE68065", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68065" } ] }, "title" : "Expression data from predose and postdose rat blood after acetaminophen treatment", "dateAssigned" : "2015-04-20T00:00:00.000-05:00", "summary" : "Four out of ten selected genes were found to be reproducibly in real-time PCR with independent set animals to predict the susceptible individuals to acetaminophen-induced hapatotoxicity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26512990" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68110" }, "primaryId" : "GEO:GSE68110", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68110" } ] }, "title" : "Trancriptional profiling of rat liver after short-term (up tp 14 days) administration of carcinogenic and non-carcinogenic chemicals", "dateAssigned" : "2015-04-21T00:00:00.000-05:00", "summary" : "The carcinogenic potential of chemicals is currently evaluated with rodent life-time bioassays, which are time consuming, and expensive with respect to cost, number of animals and amount of compound required. Since the results of these 2-year bioassays are not known until quite late during development of new chemical entities, and since the short-term test battery to test for genotoxicity, a characteristic of genotoxic carcinogens, is hampered by low specificity, the identification of early biomarkers for carcinogenicity would be a big step forward. Using gene expression profiles from the livers of rats treated up to 14 days with genotoxic and non-genotoxic carcinogens we previously identified characteristic gene expression profiles for these two groups of carcinogens. We have now added expression profiles from further hepatocarcinogens and from non-carcinogens the latter serving as control profiles. We used these profiles to extract biomarkers discriminating genotoxic from non-genotoxic carcinogens and to calculate classifiers based on the support vector machine (SVM) algorithm. These classifiers then predicted a set of independent validation compound profiles with up to 88% accuracy, depending on the marker gene set. We would like to present this study as proof of the concept that a classification of carcinogens based on short-term studies may be feasible.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24830643" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68112" }, "primaryId" : "GEO:GSE68112", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68112" } ] }, "title" : "Hepatitis B virus-mediated alterations to the primary hepatocyte transcriptome [Full Set]", "dateAssigned" : "2015-04-21T00:00:00.000-05:00", "summary" : "Results: Following this pipeline, we were able to identify a number of HBV-mediated differentially expressed transcripts at 48hr and 72hr. In addition, we noted considerable change to the hepatocyte transcriptome as a direct result of the isolation/plating procedure, regardless of the presence of HBV. Further pathway analysis of these differentially expressed transcripts identified many important cellular pathways, including those involved with cell cycle regulation and metabolism, as being differentially regulated by HBV in primary hepatocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26891448" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68120" }, "primaryId" : "GEO:GSE68120", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68120" } ] }, "title" : "Trancriptomic profiling of hepatocytes and mesenchymal cells of rats treated with nongenotoxic carcinogens for up to 2 weeks", "dateAssigned" : "2015-04-21T00:00:00.000-05:00", "summary" : "Conventional notion regards the action of non-genotoxic carcinogens (NGC) an autonomous process largely confined to parenchymal cells. Here we aim to elucidate the role of the hepatic mesenchyme for the action of two prototypical NGC, phenobarbital (PB), an anti-epileptic drug, and cyproterone acetate (CPA) a gestagen used in contraceptive pills.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68121" }, "primaryId" : "GEO:GSE68121", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68121" } ] }, "title" : "Trancriptomic profiling of liver tumors in rats after chronical phenobarbital treatment", "dateAssigned" : "2015-04-21T00:00:00.000-05:00", "summary" : "Here we investigate the difference in global gene expression in different tumor types found in the liver of rats after NNM-initiation/PB-promotion of tumor growth. We aim to identify tumor characteristic expression in nodules, focii, adenomas and carcinomas.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68128" }, "primaryId" : "GEO:GSE68128", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68128" } ] }, "title" : "Chronic subacute (incl. one subchronic study) exposure of Wistar rats to (non-)carcinogenic compound", "dateAssigned" : "2015-04-21T00:00:00.000-05:00", "summary" : "The carcinogenic potential of chemicals is currently evaluated with rodent life-time bioassays, which are time consuming, and expensive with respect to cost, number of animals and amount of compound required. For insight into early mechanisms of non-genotoxoc carcinogenesis and for identification of potential early biomarkers of non-genotoxic carcinogenesis, groups of rats were treated with a range of known non-genotoxic carcinogens for a period of 14, 28, or 90 days, and liver tissue was harvested for expression profiling. Control groups were treated with appropriate vehicles.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24690595" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68207" }, "primaryId" : "GEO:GSE68207", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68207" } ] }, "title" : "Gene expression profile for male SD Rats with and without traumatic brain injury (TBI) by RNA-Seq (CA1 and WBC)", "dateAssigned" : "2015-04-23T00:00:00.000-05:00", "summary" : "To investigate the effects of TBI on affecting the gene expressions in the hippocampus of male SD rats by RNA-Seq", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28174132" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68225" }, "primaryId" : "GEO:GSE68225", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68225" } ] }, "title" : "MicroRNA signature in skeletal muscle in insulin resistant rats", "dateAssigned" : "2015-04-23T00:00:00.000-05:00", "summary" : "The current study aimed to address the hypothesis that programmed expression of key miRNAs in skeletal muscle mediates the development of insulin resistance, and consequently long-term health. We thus examined microRNA signatures in skeletal muscle of programmed insulin resistant rats offspring from high fat-fed dams vs control offspring from chow fed dams.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27163678" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68243" }, "primaryId" : "GEO:GSE68243", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68243" } ] }, "title" : "Expression data from rat lung-resident mesenchymal stem cells and bone marrow-derived mesenchymal stem cells", "dateAssigned" : "2015-04-24T00:00:00.000-05:00", "summary" : "In this dataset, we include the expression data obtained from LR-MSCs and BM-MSCs cultured under similar conditions at passage 5. These data are used to obtain genes that are differentially expressed by these two types of cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68272" }, "primaryId" : "GEO:GSE68272", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68272" } ] }, "title" : "Transcriptome profiling of control and FOSL1 knockdown Rcho-1 trophoblast stem (TS) cells", "dateAssigned" : "2015-04-26T00:00:00.000-05:00", "summary" : "In hemochorial placentation, trophoblast stem cells differentiate into multiple lineages to aquire specific functions, such as invasive and endocrine phenotype. FOSL1 has been identified as a key regulator for trophoblast differentiation. We used microarray to detail mechanisms underlying FOSL1 signaling pathway in trophoblast differentiation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26149388" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68278" }, "primaryId" : "GEO:GSE68278", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68278" } ] }, "title" : "Alcohol-induced anxiolysis is mediated through inhibition of microRNA-494 expression in the amygdala", "dateAssigned" : "2015-04-27T00:00:00.000-05:00", "summary" : "MicroRNA profiling of adult rat amygdala following acute ethanol (1g/kg IP) exposure", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26786313" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68411" }, "primaryId" : "GEO:GSE68411", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68411" } ] }, "title" : "Identification and Differential Expression of MicroRNAs Associated with Fat Deposition in Wistar Rat Liver Using Solexa Sequencing", "dateAssigned" : "2015-04-29T00:00:00.000-05:00", "summary" : "we analyzed the miRNAs expression in Wistar rat liver tissues, High glucose (HG)-induced NAFLD Wistar rats (NAFLD group, n=3) and normal Wistar rats (normal group, n=3). Results provided the first global miRNAs in the NAFLD Wistar rat livers, and expanded the miRNAs repertoire in normal Wistar rat livers, which should be useful for further investigation into the biological functions and evolution of miRNAs in rats and other species. These findings suggest an important role of miRNAs in liver fat deposition, and implicate the participation of miRNAs in the NAFLD pathophysiological processes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27331102" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68430" }, "primaryId" : "GEO:GSE68430", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68430" } ] }, "title" : "Molecular alterations in areas generating fast ripples in an animal model of temporal lobe epilepsy", "dateAssigned" : "2015-04-30T00:00:00.000-05:00", "summary" : "The molecular basis of epileptogenesis is poorly characterized. Studies in humans and animal models have identified an electrophysiological signature that precedes the onset of epilepsy, which has been termed fast ripples (FRs) based on its frequency. Multiple lines of evidence implicate regions generating FRs in epileptogenesis, and FRs appear to demarcate the seizure onset zone, suggesting a role in ictogenesis as well. We performed gene expression analysis comparing areas of the dentate gyrus that generate FRs to those that do not generate FRs in a well-characterized rat model of epilepsy. We identified a small cohort of genes that are differentially expressed in FR versus non-FR brain tissue and used quantitative PCR to validate some of those that modulate neuronal excitability. Gene expression network analysis demonstrated conservation of gene co-expression between non-FR and FR samples, but examination of gene connectivity revealed changes that were most pronounced in the cm-40 module, which contains several genes associated with synaptic function and the differentially expressed genes Kcna4, Kcnv1, and Npy1r that are down-regulated in FRs. We then demonstrate that the genes within the cm-40 module are regulated by seizure activity and enriched for the targets of the RNA binding protein Elavl4. Our data suggest that seizure activity induces co-expression of genes associated with synaptic transmission and that this pattern is attenuated in areas displaying FRs, implicating the failure of this mechanism in the generation of FRs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25818007" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68485" }, "primaryId" : "GEO:GSE68485", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68485" } ] }, "title" : "Expression data from rat Achilles tendon-derived stem cells during development", "dateAssigned" : "2015-05-03T00:00:00.000-05:00", "summary" : "We have compared the gene expression profile of rat Achilles tendon-derived stem cells in post-natal tendon development. Rat tendon stem/progenitor cells (TSPCs) were isolated at different stages of post-natal development: TSPCs-1d, TSPCs-7d and TSPCs-56d.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26972579" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68542" }, "primaryId" : "GEO:GSE68542", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68542" } ] }, "title" : "Progesterone responsive uterine transcriptome in rat", "dateAssigned" : "2015-05-05T00:00:00.000-05:00", "summary" : "We have previously shown that Brown Norway (BN) rats are progesterone resistant. Thus this experiment was designed to compare the transcriptomes in uterus that are altered by progesterone challenge between this strain of rat with Holtzman Sprague Dawley (HSD) rats", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68592" }, "primaryId" : "GEO:GSE68592", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68592" } ] }, "title" : "Trancriptional profiling of rat bladder after daily administration of Pioglitazone and Rosiglitazone in vivo (mRNA)", "dateAssigned" : "2015-05-06T00:00:00.000-05:00", "summary" : "The purpose of the study was to investigate the nongenotoxic carcinogenic effect of Pioglitazone. Pioglitazone is a PPARgamma agonist and is known to cause bladder tumours in male rats and an increase in the incidence of bladder cancer in humans has been observed in patients treated with Pioglitazone. Pioglitazone is not considered genotoxic or carcinogenic in mice and tumours are only observed in male rats suggesting a nongenotoxic mechanism of tumorigenesis. A suggested hypothesis is urinary calculi formation and subsequent irritation, hyperplasia and metaplasia. Rosiglitazone was used as reference compound as this PPARgamma agonist does not cause changes in the bladder but cause lipoma/liposarcoma in rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68604" }, "primaryId" : "GEO:GSE68604", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68604" } ] }, "title" : "Trancriptional profiling of rat bladder after daily administration of Pioglitazone and Rosiglitazone in vivo (miRNA)", "dateAssigned" : "2015-05-06T00:00:00.000-05:00", "summary" : "The purpose of the study was to investigate the nongenotoxic carcinogenic effect of Pioglitazone. Pioglitazone is a PPARgamma agonist and is known to cause bladder tumours in male rats and an increase in the incidence of bladder cancer in humans has been observed in patients treated with Pioglitazone. Pioglitazone is not considered genotoxic or carcinogenic in mice and tumours are only observed in male rats suggesting a nongenotoxic mechanism of tumorigenesis. A suggested hypothesis is urinary calculi formation and subsequent irritation, hyperplasia and metaplasia. Rosiglitazone was used as reference compound as this PPARgamma agonist does not cause changes in the bladder but cause lipoma/liposarcoma in rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68625" }, "primaryId" : "GEO:GSE68625", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68625" } ] }, "title" : "Human beta cell proliferation induced by inhibition of Dyrk1a and GSK3b", "dateAssigned" : "2015-05-06T00:00:00.000-05:00", "summary" : "Conclusions: Since only a small subset of islet cells proliferate when stimulated with GNF4877, single-cell transcriptome sequencing allowed us to examine expression of genes co-regulated with known proliferation markers and will hopefully allow us to characterize beta cell subsets which are responsive to proliferation-associated therapies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26496802" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68653" }, "primaryId" : "GEO:GSE68653", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68653" } ] }, "title" : "Gene expression profiling in IBD rat treat with MSC transplantation", "dateAssigned" : "2015-05-07T00:00:00.000-05:00", "summary" : "Investigation of whole genome gene expression level changes in Inflammatory bowel disease rats after MSC transplantation, compared to IBD control rats, and to explore the mechanism of MSC transplantation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25998108" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68676" }, "primaryId" : "GEO:GSE68676", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68676" } ] }, "title" : "Gene expression profiling of ovaries collected from rat treated with pregnant mare serum gonadotropins (PMSG) and without PMSG", "dateAssigned" : "2015-05-08T00:00:00.000-05:00", "summary" : "PMSG acts like LH in horses and mares but works like FSH in heterologous animals under certain circumstances.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68687" }, "primaryId" : "GEO:GSE68687", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68687" } ] }, "title" : "Expression data from NRK-52E cells treated with aristolochic acids for 6h, 24h and 72h", "dateAssigned" : "2015-05-08T00:00:00.000-05:00", "summary" : "We used microarrays to detail the mechanism of toxicity and possibly carcinogenicity of aristolochic acids in rat renal proximal cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26484264" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68738" }, "primaryId" : "GEO:GSE68738", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68738" } ] }, "title" : "Space environmental factor impacts upon murine colon microbiota and mucosal homeostasis", "dateAssigned" : "2015-05-11T00:00:00.000-05:00", "summary" : "We report how high and low linear energy transfer (LET) radiation, microgravity, and elevated dietary iron affect colon microbiota (determined by 16S rDNA pyrosequencing) and colon function. Three independent experiments were conducted: 1) fractionated low LET ¿ radiation (137Cs, 3 Gy, RAD), high Fe diet (IRON) (650 mg/kg diet), and a combination of low LET ¿ radiation and high Fe diet (IRON+RAD) in male Sprague-Dawley rats; 2) high LET 38Si particle exposure (0.050 Gy), 1/6 G partial weight bearing (PWB), and a combination of high LET38Si particle exposure and PWB in female BalbC/ByJ mice; and 3) 13 d spaceflight in female C57BL/6 mice. For each experiment, the colon was resected and feces removed for microbial sequencing analysis on a Roche 454 Genome Sequencer FLX Titanium instrument (Microbiome Core Facility, Chapel Hill NC) using the GS FLX Titanium XLR70 sequencing reagents and protocols. Analysis of amplicon sequencing data was carried out using the QIIME pipeline. Low LET radiation, high iron diet, and spaceflight increased Bacteroidetes and decreased Firmicutes. Low LET radiation, high Fe diet, and spaceflight did not significantly affect diversity or richness, or elevate pathogenic genera. Spaceflight increased Clostridiales and decreased Lactobacillales, and similar trends were observed in the experiment using a ground-based model of microgravity, suggesting altered gravity may affect colonic microbiota. Microbiota characteriztion in these models is a first step in understanding the impact of the space environment on intestinal health.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26083373" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68785" }, "primaryId" : "GEO:GSE68785", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68785" } ] }, "title" : "Expression data of sandwich cultured primary rat hepatocytes incubated to piperazine designer drugs", "dateAssigned" : "2015-05-12T00:00:00.000-05:00", "summary" : "We performed a gene array study with rat hepatocytes incubated with the four designer drugs for 24 h in order to detail the global programme of gene expression", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68913" }, "primaryId" : "GEO:GSE68913", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68913" } ] }, "title" : "Differential miRNA expression in Cells and Matrix Vesicles in Vascular Smooth Muscle Cells from Rats with Kidney Disease", "dateAssigned" : "2015-05-14T00:00:00.000-05:00", "summary" : "Vascular calcification is a complex process and has been associated with aging, diabetes, chronic kidney disease (CKD). Although there have been several studies studying the role of miRNAs (miRs) in bone osteogenesis, little is known about the role of miRs in vascular calcification and their role in the pathogenesis of vascular abnormalities. Matrix vesicles (MV) are known to play an important role in initiating vascular smooth muscle cell (VSMC) calcification. In the present study, we performed miRNA microarray analysis to identify the dysregulated miRs between MV and VSMC derived from CKD rats to understand the role of post-transcriptional regulatory networks governed by these miRNAs in vascular calcification and to uncover the differential miRNA content of MV. The percentage of miRNA to total RNA was increased in MV compared to VSMC. Comparison of expression profiles of miRNA by microarray demonstrated 33 miRs to be differentially expressed with the majority (~ 57%) of them down-regulated. Target genes controlled by differentially expressed miRNAs were identified utilizing two different complementary computational approaches Miranda and Targetscan to understand the functions and pathways that may be affected due to the production of MV from calcifying VSMC thereby contributing to the regulation of genes by miRs. We found several processes including vascular smooth muscle contraction, response to hypoxia and regulation of muscle cell differentiation to be enriched. Signaling pathways identified included MAP-kinase and wnt signaling that have previously been shown to be important in vascular calcification. In conclusion, our results demonstrate that miRs are concentrated in MV from calcifying VSMC, and that important functions and pathways are affected by the miRs dysregulation between calcifying VSMC and the MV they produce. This suggests that miRs may play a very important regulatory role in vascular calcification in CKD by controlling an extensive network of post-transcriptional targets.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68960" }, "primaryId" : "GEO:GSE68960", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68960" } ] }, "title" : "Histone methylation by the Kleefstra Syndrome protein EHMT1 mediates homeostatic synaptic scaling.", "dateAssigned" : "2015-05-15T00:00:00.000-05:00", "summary" : "Homeostatic plasticity, a form of synaptic plasticity, maintains the fine balance between overall excitation and inhibition in developing and mature neuronal networks. Although the synaptic mechanisms of homeostatic plasticity are well characterized, the associated transcriptional program remains poorly understood. We show that the Kleefstra syndrome-associated protein, EHMT1, plays a critical and cell-autonomous role in synaptic scaling by responding to attenuated neuronal firing or sensory drive. Chronic activity deprivation increased the amount of neuronal dimethylated H3 at lysine 9 (H3K9me2), the catalytic product of EHMT1 and an epigenetic marker for gene repression. Genetic knockdown and pharmacological blockade of EHMT1 or EHMT2 prevented the increase of H3K9me2 and synaptic scaling up. Furthermore, BDNF repression was preceded by EHMT1/2-mediated H3K9me2 deposition at the Bdnf promoter during synaptic scaling up, both in vivo or in vivo. These findings suggest that changes in chromatin state through H3K9me2 governs a repressive program to achieve synaptic scaling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27373831" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68967" }, "primaryId" : "GEO:GSE68967", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68967" } ] }, "title" : "The rat lncRNA microarray analysis of the 8 samples from control and NNK treatment group", "dateAssigned" : "2015-05-18T00:00:00.000-05:00", "summary" : "In order to assess the alteration in lncRNA expression in rat lung carcinogenesis induced by NNK, we determined the lncRNA expression profiles in 3 rat lung tumor samples and matched normal lung tissues and 2 blood samples from the control and NNK treatment group in the 95th week using Arraystar Rat lncRNA Microarray.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26908441" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68973" }, "primaryId" : "GEO:GSE68973", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE68973" } ] }, "title" : "Prenatal exposure to bisphenol A, genistein and indole-3-carbinol on early mammary gland development and carcinogenesis in female Sprague-Dawley offspring", "dateAssigned" : "2015-05-18T00:00:00.000-05:00", "summary" : "Rodent studies have indicated that gestational and perinatal bisphenol A (BPA) exposure increase the risk of developing breast cancer during adulthood. In contrast, some dietary compounds such as genistein (GEN) and indole 3-carbinol (I3C) present potential protective effects against inducing hormone-dependent cancers, including that of the mammary gland. Thus, we aimed to evaluate the role of these dietary compounds on early mammary gland development and carcinogenesis in female Sprague-Dawley offspring. Pregnant Sprague-Dawley (SD) rats were treated with BPA at 25 or 250µg/kg b.w./day by gavage from gestational day (GD) 10 to 21 with or without dietary GEN (250 mg/kg chow, ~5.5 mg/kg b.w./day) or I3C (2000 mg/kg chow, ~45.0 mg/kg b.w./day). At post-natal day (PND) 21, some female offspring from different litters were euthanized for mammary gland development and gene expression analyses while other female offspring received a single dose of N-methyl-N-nitrosourea (MNU) for mammary carcinogenesis initiation. The findings this study indicated the prenatal exposure to BPA, GEN and I3C did not significantly alter ductal elongation, number of terminal end buds (TEB) or cell proliferation, and estrogen receptor alpha (ER-a) immunostaining expression in epithelial mammary cells at PND 21. BPA treatment modulated the expression of several genes, but these changes were not associated with a dose dependent response. Dietary GEN and I3C treatment causally and consistent with the mammary gland structures outcomes. Besides, maternal BPA exposure associated with dietary GEN and I3C did not alter the susceptibility to the mammary cancer development in adulthood when the carcinogen was administered in a window of immature mammary gland development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27178563" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69131" }, "primaryId" : "GEO:GSE69131", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69131" } ] }, "title" : "Gene Expression of primary rat hippocampal neurons after Ncoa3 knockdown", "dateAssigned" : "2015-05-21T00:00:00.000-05:00", "summary" : "We identified Ncoa3 as a regulator of neuronal morphology and microRNA activity. In order to uncover target genes of this transcriptional coactivator we performed this microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26105073" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69194" }, "primaryId" : "GEO:GSE69194", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69194" } ] }, "title" : "Genome-wide maps of H3K9me3 and H3K4me3 state in failing heart with or without chaetocin in animal model", "dateAssigned" : "2015-05-23T00:00:00.000-05:00", "summary" : "Epigenetic status has been linked to cardiac hypertrophy and heart failure. Histone deacetylase inhibitors are promising drugs for preventing cardiac remodeling. We previously demonstrated very different patterns of histone H3 lysine 9 trimethylation (H3K9me3) and histone H3 lysine 4 trimethylation (H3K4me3) in failing hearts compared to control hearts in both animal models and clinical heart specimens. Here, we focused on a heart failure-specific histone modification, H3K9me3, and investigated the prognostic efficacy of administering a histone H3K9 methyltransferase inhibitor, chaetocin, to Dahl salt-sensitive rats, an animal model of heart failure. Chaetocin delayed the timing of transition from cardiac hypertrophy to heart failure, and prolonged survival in this animal model. Mitochondrial dysfunction was improved with inhibitor use in the failing heart. ChIP-seq analysis demonstrated that heart failure caused an increase in H3K9me3 alignments in thousands of repetitive elements, including regions neighboring mitochondrial genes, and a corresponding reduction of this effect with inhibitor use. However, at 35 loci, heart failure was conversely associated with a reduction in H3K9me3 alignments, and inhibitor use reversed this effect. These data suggest that excessive heterochromatinization of repetitive elements in the failing heart might impair pumping function with mitochondrial gene silencing. H3K9 methyltransferase inhibitors may be a promising novel therapy for chronic heart failure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69267" }, "primaryId" : "GEO:GSE69267", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69267" } ] }, "title" : "Expression data from rat organotypic hippocampal slices lentivirally infected with shRNF10 or scramble construct", "dateAssigned" : "2015-05-27T00:00:00.000-05:00", "summary" : "In this dataset we included expression data from homogenates of DIV14 rat organotypic hippocampal slices lentivirally infected with shRNF10 or scramble construct", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69334" }, "primaryId" : "GEO:GSE69334", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69334" } ] }, "title" : "Expression data from adult wistar female rat 5mm spinal cord tissue", "dateAssigned" : "2015-05-28T00:00:00.000-05:00", "summary" : "We used microarray gene expression analyses to unveil the mechanisms underlying NT-3-chitosan-induced spinal cord regeneration.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26460053" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69337" }, "primaryId" : "GEO:GSE69337", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69337" } ] }, "title" : "Differential expression produced by Pdrg1 gene silencing in rat hepatoma H35 cells", "dateAssigned" : "2015-05-28T00:00:00.000-05:00", "summary" : "RTqPCR results suggested a relevant role for Pdrg1 in rat hepatoma H35 cells, where its expression was dramatically enhanced. Hence, these cells were chosen as a suitable model for stable Pdrg1 silencing. For this purpose, H35 cells were transfected with appropriate shRNA plasmids against Pdrg1 and stable clones isolated. Among those exhibiting reproducible behavior, clones CN-10 (negative control), 3-44 (shRNA3) and 4-18 (shRNA4) were selected for further analysis. Pdrg1 expression analyzed by RT-qPCR was reduced by 50% and 70% in 3-44 and 4-18 clones, respectively, as compared to CN-10. RNAs of CN-10, 3-44 and 4-18 clones, as well as, RNA of an enriched pool of shRNA3 transiently transfected cells (shRNA3T) were used for expression analysis using Agilent one-color microarrays. Genes exhibiting changes =2-fold with FDR<0.05, according to LIMMA analysis, were identified. Pathway analysis was performed with BioProfiling using data of 114 genes (74 upregulated and 40 downregulated) exhibiting similar behavior in the three silenced samples. Selected genes, at least two of pathways with p=0.02, were used for verification of expression changes by RT-qPCR, together with Pdrg1.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27548429" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69338" }, "primaryId" : "GEO:GSE69338", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69338" } ] }, "title" : "Different Vitamin D Receptor Agonists Exhibit Differential Effects on Endothelial Function and Aortic Gene Expression in 5/6 Nephrectomized (NX) Rats", "dateAssigned" : "2015-05-28T00:00:00.000-05:00", "summary" : "Vitamin D analogs alfacalcidol, paricalcitol, and VS-105 exhibit different effects on endothelial function and aortic gene expression in 5/6 NX uremic rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25500070" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69466" }, "primaryId" : "GEO:GSE69466", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69466" } ] }, "title" : "Conditioning lesion rat DRG time course", "dateAssigned" : "2015-06-02T00:00:00.000-05:00", "summary" : "To identify potential regeneration-associated genes, rat dorsal root ganglia (DRG) were lesioned and then sampled at 4, 8, 12, 24, 48, 148, or 296 hrs", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26236189" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69467" }, "primaryId" : "GEO:GSE69467", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69467" } ] }, "title" : "cAMP treated rat DRGs", "dateAssigned" : "2015-06-02T00:00:00.000-05:00", "summary" : "To identify potential regeneration-associated genes, rat cultures of dissociated dorsal root ganglia (DRG) cells were treated with dbcAMP for 0,3,6,12, or 18 hours.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26236189" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69520" }, "primaryId" : "GEO:GSE69520", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69520" } ] }, "title" : "Hepatic miRNA profiles and thyroid hormone homeostasis in rats exposed to dietary potassium perfluorooctanesulfonate (PFOS) [mRNA]", "dateAssigned" : "2015-06-03T00:00:00.000-05:00", "summary" : "Perfluorooctanesulfonate (PFOS) has been widely used in a variety of industrial and commercial applications as a surfactant and stain repellent. PFOS causes liver damage (including liver tumors) in experimental animals, primarily via interaction with PPARa and CAR/PXR. We investigated the involvement of microRNAs (miRNAs) in PFOS-induced hepatotoxicity, and mechanisms involved in abnormal TH homeostasis, in the livers of adult male rats exposed in feed to 50 mg PFOS/kg diet for 28 days. PFOS-treated rats exhibited expected histopathological and clinical chemistry changes. Global gene expression changes were consistent with the involvement of PPARa and CAR/PXR in PFOS-induced effects. Thirty-eight miRNAs were significantly altered. Three members of the miR-200 family were the most increased, while miR-122 and miR-21 were the most decreased, in PFOS-treated relative to control rats. Expression of the miR-23b/27b/24 cluster also decreased in PFOS-treated animals. Pathway analysis of miRNAs and associated gene expression changes demonstrated enrichment of transcripts involved in epithelial to mesenchymal transition (EMT), which is a primary process involved in tumor cell motility and cancer metastasis. Liver expression analysis revealed transcripts that may mediate PFOS effects on thyroid hormone (TH) homeostasis including: activation of the CAR/PXR pathway, phase II/III enzymes, and deiodinase. These changes are consistent with low serum TH due to enhanced metabolic clearance of TH. However, most TH hepatic target genes were not altered in a manner consistent with reduced TH signalling; suggesting that PFOS exposure did not induce functional hypothyroidism. Collectively, PFOS-induced miRNA perturbations were strongly associated with EMT suggesting an important role for miRNAs in PFOS-induced hepatotoxicity. The work also provides novel insights into the effects of PFOS on TH homeostasis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69521" }, "primaryId" : "GEO:GSE69521", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69521" } ] }, "title" : "Hepatic miRNA profiles and thyroid hormone homeostasis in rats exposed to dietary potassium perfluorooctanesulfonate (PFOS) [miRNA]", "dateAssigned" : "2015-06-03T00:00:00.000-05:00", "summary" : "Perfluorooctanesulfonate (PFOS) has been widely used in a variety of industrial and commercial applications as a surfactant and stain repellent. PFOS causes liver damage (including liver tumors) in experimental animals, primarily via interaction with PPARa and CAR/PXR. We investigated the involvement of microRNAs (miRNAs) in PFOS-induced hepatotoxicity, and mechanisms involved in abnormal TH homeostasis, in the livers of adult male rats exposed in feed to 50 mg PFOS/kg diet for 28 days. PFOS-treated rats exhibited expected histopathological and clinical chemistry changes. Global gene expression changes were consistent with the involvement of PPARa and CAR/PXR in PFOS-induced effects. Thirty-eight miRNAs were significantly altered. Three members of the miR-200 family were the most increased, while miR-122 and miR-21 were the most decreased, in PFOS-treated relative to control rats. Expression of the miR-23b/27b/24 cluster also decreased in PFOS-treated animals. Pathway analysis of miRNAs and associated gene expression changes demonstrated enrichment of transcripts involved in epithelial to mesenchymal transition (EMT), which is a primary process involved in tumor cell motility and cancer metastasis. Liver expression analysis revealed transcripts that may mediate PFOS effects on thyroid hormone (TH) homeostasis including: activation of the CAR/PXR pathway, phase II/III enzymes, and deiodinase. These changes are consistent with low serum TH due to enhanced metabolic clearance of TH. However, most TH hepatic target genes were not altered in a manner consistent with reduced TH signalling; suggesting that PFOS exposure did not induce functional hypothyroidism. Collectively, PFOS-induced miRNA perturbations were strongly associated with EMT suggesting an important role for miRNAs in PFOS-induced hepatotoxicity. The work also provides novel insights into the effects of PFOS on TH homeostasis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69548" }, "primaryId" : "GEO:GSE69548", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69548" } ] }, "title" : "RNA-Seq analysis of glycosylation related gene expression in STZ-induced diabetic rat kidney inner medulla", "dateAssigned" : "2015-06-03T00:00:00.000-05:00", "summary" : "The UT-A1 urea transporter is crucial to the kidney’s ability to generate concentrated urine. Native UT-A1 from kidney inner medulla (IM) is a heavily glycosylated protein with two glycosylation forms of 97 and 117 kDa. In diabetes, UT-A1 protein abundance, particularly the 117 kD isoform, is significantly increased corresponding to an increased urea permeability in perfused IM collecting ducts, which plays an important role in preventing the osmotic diuresis caused by glucosuria. In this study, using sugar-specific binding lectins, we found that the carbohydrate structure of UT-A1 is also changed under diabetic conditions with increased amounts of sialic acid, fucose, and increased glycan branching. These changes were accompanied by altered UT-A1 association with the galectin proteins, a-galactoside glycan binding proteins. To explore the molecular basis of the alterations of glycan structures, the highly sensitive next generation sequencing (NGS) technology, Illumina RNA-seq, was employed to analyze genes involved in the process of UT-A1 glycosylation using streptozotocin (STZ) - induced diabetic rat kidney as the tissue source. Differential expression analysis combining quantitative PCR revealed that a number of important glycosylation related genes were changed under diabetic conditions. These genes include the glycosyltransferase genes Mgat4a, the sialylation enzymes St3gal1 and St3gal4and glycan binding protein galectin-3, -5, -8 and -9. In contrast, although highly expressed in kidney IM, the glycosyltransferase genes Mgat1, Mgat2, and fucosyltransferase Fut8, did not show any changes. We conclude that the alteration of these glycosylation related genes may contribute to changing the UT-A1 glycan structure, and therefore modulate kidney urea transport activity under diabetic conditions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26483702" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69765" }, "primaryId" : "GEO:GSE69765", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69765" } ] }, "title" : "The influence of the estrous cycle on sex differences in the rat adult medial prefrontal cortex transcriptome [RNA-Seq]", "dateAssigned" : "2015-06-11T00:00:00.000-05:00", "summary" : "Hormonal fluctuations throughout the ovarian cycle contribute to females’ higher vulnerability to anxiety disorders when compared to males. Notably, such sex differences are controlled by regulation of genes in the medial prefrontal cortex (mPFC) including the transcription factor early growth response 1 (Egr1) in rats, which highlights a control of anxiety-like behaviors by sexually-biased gene expression. We therefore undertook a large-scale characterization of sex differences and their interaction with the estrous cycle in the adult mPFC transcriptome and report that proestrus and diestrus females (with high and low ovarian hormones levels, respectively) exhibited a partly-opposed sexually-biased transcriptome. Surprisingly, the extent of regulations within females vastly exceeded sex differences, and support a multi-level reorganization of synaptic function across the estrous cycle. Furthermore, genome-wide analysis of Egr1 binding highlighted its role in controlling the synapse-related genes varying within females, and the sex- and estrous cycle-dependent transcriptomic reorganization in the rat mPFC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26628058" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69772" }, "primaryId" : "GEO:GSE69772", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69772" } ] }, "title" : "The influence of the estrous cycle on sex differences in the rat adult medial prefrontal cortex transcriptome [ChIP-Seq]", "dateAssigned" : "2015-06-11T00:00:00.000-05:00", "summary" : "Hormonal fluctuations throughout the ovarian cycle contribute to females’ higher vulnerability to anxiety disorders when compared to males. Notably, such sex differences are controlled by regulation of genes in the medial prefrontal cortex (mPFC) including the transcription factor early growth response 1 (Egr1) in rats, which highlights a control of anxiety-like behaviors by sexually-biased gene expression. We therefore undertook a large-scale characterization of sex differences and their interaction with the estrous cycle in the adult mPFC transcriptome and report that proestrus and diestrus females (with high and low ovarian hormones levels, respectively) exhibited a partly-opposed sexually-biased transcriptome. Surprisingly, the extent of regulations within females vastly exceeded sex differences, and support a multi-level reorganization of synaptic function across the estrous cycle. Furthermore, genome-wide analysis of Egr1 binding highlighted its role in controlling the synapse-related genes varying within females, and the sex- and estrous cycle-dependent transcriptomic reorganization in the rat mPFC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26628058" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69779" }, "primaryId" : "GEO:GSE69779", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69779" } ] }, "title" : "RNA-seq profiling of cortical collecting ducts in rats undergoing vasopressin escape", "dateAssigned" : "2015-06-11T00:00:00.000-05:00", "summary" : "We sequenced mRNAs in cortical collecting ducts microdissected from rats undergoing vasopressin escape.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28843412" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69783" }, "primaryId" : "GEO:GSE69783", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69783" } ] }, "title" : "RNA-Seq analysis facilitates quantitative analysis to identify genes in hepatic tissue of partially hepatectomized rats regulated by ASCs-miR27b introduction in comparison with ASCs-siRNC or saline controls", "dateAssigned" : "2015-06-11T00:00:00.000-05:00", "summary" : "Results: The sequencing runs yielded a total of 22.67 M reads with an average length of 100 bp. The high-throughput sequencing performed for liver samples with different treatments showed similar numbers of yielded reads ranged from 5.57 to 5.74 M and the same average length. The Strand NGS software (version 2.1) was used using default parameters for pre-alignment and post-alignment quality control analysis and 100% of the raw reads remained in the dataset. Of these, 19.02 M reads (84%) were mapped into contigs of the rat genome (rn5) and identified 31457 transcripts in liver samples.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26836372" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69803" }, "primaryId" : "GEO:GSE69803", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69803" } ] }, "title" : "miR-182 inhibition in AKI", "dateAssigned" : "2015-06-12T00:00:00.000-05:00", "summary" : "gene expression modification after miR-182 inhibition, day 2 and day 7 after ischemic reperfusion injury", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69819" }, "primaryId" : "GEO:GSE69819", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69819" } ] }, "title" : "Transcriptomic analysis of the estrogenic effect of soy protein isolate in rat uterus", "dateAssigned" : "2015-06-12T00:00:00.000-05:00", "summary" : "There are concerns regarding possible reproductive toxicity from consumption of soy including an increased risk of endometriosis and endometrial cancer. We used global uterine gene expression profiles in adult ovariectomized (OVX) female rats assessed by RNAseq to examine the estrogenicity of soy protein isolate (SPI) and the potential for feeding SPI to alter estrogen signaling in the uterus. Rats were fed AIN93G diets made with casein (CAS) or SPI from postnatal day (PND) 30. Rats were OVX on PND 50 and infused with 17 beta-estradiol (E2) or vehicle. E2 increased uterine wet weight (P<0.05) and significantly altered expression of 2084 uterine genes. In contrast, SPI feeding had no effect on uterine weight and only altered expression of 177 genes. Overlap between E2 and SPI genes was limited to 69 genes (3%). GO analysis indicated significant differences in uterine biological processes affected by E2 and SPI and little evidence for recruitment of ER alpha to the promoters of ER-responsive genes after SPI feeding. The major E2 up-regulated uterine pathways were cancer pathways and extracellular organization. SPI feeding up-regulated uterine PPAR signaling and fatty acid metabolism. The combination of E2 and SPI feeding resulted in significant regulation of 715 fewer genes relative to E2 alone. In a separate experiment, the combination of E2 and SPI reversed the ability of E2 to induce uterine proliferation in response to the carcinogen dimethybenz(a)anthracene (DMBA). These data suggest SPI does not act as a weak estrogen in the uterus but appears to be a selective estrogen receptor modulator (SERM) interacting with a small sub-set of E2-regulated genes and to be anti-estrogenic in the presence of endogenous estrogens.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27182546" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69866" }, "primaryId" : "GEO:GSE69866", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69866" } ] }, "title" : "IL-22 impedes the proliferation of Schwann cells and influence nerve regeneration", "dateAssigned" : "2015-06-15T00:00:00.000-05:00", "summary" : "Schwann cells (SCs) proliferation is crucial for axonal guidance and nerve regeneration following nerve injury. This study aims to investigate the in vitro effects of interleukin-22 (IL-22) on SCs and the corresponding mechanism.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69984" }, "primaryId" : "GEO:GSE69984", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE69984" } ] }, "title" : "Genome-wide DNA methylation profiling reveals epigenetic changes in the rat nucleus accumbens associated with cross-generational effects of adolescent THC exposure", "dateAssigned" : "2015-06-18T00:00:00.000-05:00", "summary" : "Drug exposure during critical periods of development is known to have lasting effects, increasing one’s risk for developing mental health disorders. Emerging evidence has also indicated the possibility for drug exposure to even impact subsequent generations. Our previous work demonstrated that adolescent exposure to ¿9-tetrahydrocannabinol (THC), the main psychoactive component of marijuana (Cannabis sativa), in a Long-Evans rat model affects reward-related behavior and gene regulation in the subsequent (F1) generation unexposed to the drug. Questions, however, remained regarding potential epigenetic consequences. In the current study, using the same rat model, we employed Enhanced Reduced Representation Bisulfite Sequencing to interrogate the epigenome of the nucleus accumbens, a key brain area involved in reward processing. This analysis compared 16 animals with parental-THC exposure and 16 without to characterize relevant systems-level changes in DNA methylation. We identified 1,027 differentially methylated regions (DMRs) associated with parental THC exposure in F1 adults, each represented by multiple CpGs. These DMRs fell predominantly within introns, exons, and intergenic intervals, while showing a significant depletion in gene promoters. From these, we identified a network of DMR-associated genes involved in glutamatergic synaptic regulation, which also exhibited altered mRNA expression in the nucleus accumbens. These data provide novel insight into drug-related cross-generational epigenetic effects, and serve as a useful resource for investigators to explore novel neurobiological systems underlying drug abuse vulnerability.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26044905" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70006" }, "primaryId" : "GEO:GSE70006", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70006" } ] }, "title" : "rat PFC: Sham vs. SNI", "dateAssigned" : "2015-06-18T00:00:00.000-05:00", "summary" : "DNA methylation profiles of prefrontal cortec (PFC) comparing 9 months post Spared Nerve Injury (SNI) rats with Sham rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70007" }, "primaryId" : "GEO:GSE70007", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70007" } ] }, "title" : "rat T Cells: Sham vs. SNI", "dateAssigned" : "2015-06-18T00:00:00.000-05:00", "summary" : "DNA methylation profiles of T cells comparing 9 months post Spared Nerve Injury (SNI) rats with Sham rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70012" }, "primaryId" : "GEO:GSE70012", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70012" } ] }, "title" : "RNA-seq profiling of glomeruli, S1 proximal tubule, and the whole kidney of uninephrecomized rats", "dateAssigned" : "2015-06-18T00:00:00.000-05:00", "summary" : "We sequenced mRNAs in microdissected glomeruli and S1 proximal tubule segments and the whole remnant kidney of uninephrectomized rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70097" }, "primaryId" : "GEO:GSE70097", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70097" } ] }, "title" : "Transcriptome analysis of aflatoxin B1 (AFB1) induced hepatocellular carcinoma (HCC) and AFB1 resistant liver sample from rats", "dateAssigned" : "2015-06-22T00:00:00.000-05:00", "summary" : "Applied de novo assembly, both protein coding and non-coding RNAs were profiled in AFB1 induced HCC and AFB1 resistant liver sample. Compared with normal liver, the perturbation on transcriptome was revealed in multiple aspects, implying the potential mechanism of toxic resistance.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70142" }, "primaryId" : "GEO:GSE70142", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70142" } ] }, "title" : "The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis (RNA-Seq)", "dateAssigned" : "2015-06-22T00:00:00.000-05:00", "summary" : "SOX9 is a transcriptional activator required for chondrogenesis, and SOX5 and SOX6 are closely related DNA-binding proteins that critically enhance its function. We used RNA-seq to charatierize a rat chondrosarcoma (RCS) cells as a faithful model for proliferating/early prehypertrophic growth plate chondrocytes and ChIP-seq to gain novel insights into the full spectrum of the target genes and modes of action of this chondrogenic trio.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26150426" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70143" }, "primaryId" : "GEO:GSE70143", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70143" } ] }, "title" : "The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis (ChIP-Seq)", "dateAssigned" : "2015-06-22T00:00:00.000-05:00", "summary" : "SOX9 is a transcriptional activator required for chondrogenesis, and SOX5 and SOX6 are closely related DNA-binding proteins that critically enhance its function. We used RNA-seq to charatierize a rat chondrosarcoma (RCS) cells as a faithful model for proliferating/early prehypertrophic growth plate chondrocytes and ChIP-seq to gain novel insights into the full spectrum of the target genes and modes of action of this chondrogenic trio.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26150426" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70320" }, "primaryId" : "GEO:GSE70320", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70320" } ] }, "title" : "Cytokeratin-19 positivity is acquired along cancer progression and does not predict cell origin in rat hepatocarcinogenesis (I)", "dateAssigned" : "2015-06-26T00:00:00.000-05:00", "summary" : "Analysis of early changes in the R-H model of carcinogenesis in order to investigate the relationship between oval cell proliferation and preneoplastic foci", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26452031" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70321" }, "primaryId" : "GEO:GSE70321", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70321" } ] }, "title" : "Cytokeratin-19 positivity is acquired along cancer progression and does not predict cell origin in rat hepatocarcinogenesis (II)", "dateAssigned" : "2015-06-26T00:00:00.000-05:00", "summary" : "Analysis of early changes in the R-H model of carcinogenesis in order to investigate the relationship between oval cell proliferation and preneoplastic foci", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26452031" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70354" }, "primaryId" : "GEO:GSE70354", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70354" } ] }, "title" : "Genomic binding and regulation of gene expression by the thyroid carcinoma-associated PAX8-PPARG fusion protein", "dateAssigned" : "2015-06-28T00:00:00.000-05:00", "summary" : "A chromosomal translocation results in production of an oncogenic PAX8-PPARG fusion protein (PPFP) in a subset of thyroid carcinomas. PAX8 is an important thyroid transcription factor, and PPARG is a transcription factor that plays important roles in the biology of adipocytes and macrophages, but has no known function in the thyroid. PPFP retains the DNA binding domains of both proteins. However, the genomic DNA binding sites of PPFP have not been identified, and only limited data exist to characterize gene expression in PPFP thyroid carcinomas. Therefore, we expressed PPFP in PCCL3 rat thyroid cells and used ChIP-seq to identify PPFP genomic binding sites (PPFP peaks) and RNA-seq to characterize PPFP-dependent gene expression. The genome contains ~20 000 PPFP peaks, including known PAX8 and PPARG binding sites, indicating that both DNA binding domains are functional. PPFP binds to and regulates many genes involved in cancer-related processes such as development and cell division. PPFP also binds to and regulates many genes related to mitochondria and lipid metabolism that are regulated by PPARG in adipocytes. Our data highlight the complexity of PPFP as a transcription factor and the numerous ways that it regulates thyroid oncogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26595524" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70459" }, "primaryId" : "GEO:GSE70459", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70459" } ] }, "title" : "Expression data from post-natal rat Achilles tendons", "dateAssigned" : "2015-07-01T00:00:00.000-05:00", "summary" : "We have compared the gene expression profile of post-natal 1 day and 7 day rat Achilles tendons.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70473" }, "primaryId" : "GEO:GSE70473", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70473" } ] }, "title" : "tRNA-Derived Small Non-Coding RNAs in Response to Ischemia Inhibit Angiogenesis", "dateAssigned" : "2015-07-02T00:00:00.000-05:00", "summary" : "Ischemic injuries will lead to necrotic tissue damage, and post-ischemia angiogenesis plays critical roles in blood flow restoration and tissue recovery. Recently, several types of small RNAs have been reported to be involved in this process. In this study, we first generated a rat brain ischemic model to investigate the involvement of new types of small RNAs in ischemia. We utilized deep sequencing and bioinformatics analyses to demonstrate that the level of small RNA fragments derived from tRNAs was strikingly up-regulated in the ischemic rat brain. Among these sequences, tRNAVal- and tRNAGly-derived small RNAs account for the most abundant segments. The up-regulation of tRNAVal- and tRNAGly-derived fragments was verified through northern blot and quantitative PCR analyses. The levels of these two fragments also increased in a mouse hindlimb ischemia model and cellular hypoxia model. Importantly, the overexpression of tRNAVal- and tRNAGly-derived fragments in endothelial cells inhibited cell proliferation, migration and tube formation. Our results indicate that tRNA-derived fragments are involved in tissue ischemia, and we demonstrate for the first time that tRNAVal- and tRNAGly-derived fragments inhibit angiogenesis by modulating the function of endothelial cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26865164" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70522" }, "primaryId" : "GEO:GSE70522", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70522" } ] }, "title" : "A Novel, Dynamic Pattern-based Analysis of NF-kappaB Binding During the Priming Phase of Liver Regeneration Reveals Switch-Like Functional Regulation", "dateAssigned" : "2015-07-06T00:00:00.000-05:00", "summary" : "Following partial hepatectomy, a coordinated series of molecular events occurs to regulate hepatocyte entry into the cell cycle to recover lost mass. In rats during the first six hours following resection, hepatocytes are primed by a tightly controlled cytokine response to prepare hepatocytes to begin replication. Although it appears to be a critical element driving regeneration, the cytokine response to resection has not yet been fully characterized. Specifically, the role of one of the key response elements to cytokine signaling (NF-¿B) remains incompletely characterized. In this study, we present a novel, genome-wide, pattern-based analysis characterizing NF-¿B binding during the priming phase of liver regeneration. We interrogated the dynamic regulation of priming by NF-¿B through categorizing NF-¿B binding in different temporal profiles: immediate sustained response, early transient response, and delayed response to partial hepatectomy. We then identified functional regulation of NF-¿B binding by relating the temporal response profile to differential gene expression. We found that NF-¿B bound genes govern negative regulation of cell growth and inflammatory response immediately following hepatectomy. NF-¿B also transiently regulates genes responsible for lipid biosynthesis and transport as well as induction of apoptosis following hepatectomy. By the end of the priming phase, NF-¿B regulation of genes involved in inflammatory response, negative regulation of cell death, and extracellular structure organization became prominent. These results suggest that the immediate, transient, and delayed NF-¿B signaling serve different functional transitions that drive the onset of regeneration.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26217230" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70559" }, "primaryId" : "GEO:GSE70559", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70559" } ] }, "title" : "Gene expression patterns associated with histopathology in toxic liver injury", "dateAssigned" : "2015-07-06T00:00:00.000-05:00", "summary" : "Predicting liver injury after exposure to toxic industrial chemicals is complicated by the large number of potential environmental contaminants, mixtures, and exposure dose and route scenarios. Identifying indicators of end organ injury can complement exposure-based assays and improve predictive power. A multiplexed approach was used to experimentally evaluate a panel of 67 genes predicted to be fibrogenic by computationally mining DrugMatrix, a publicly available repository of gene microarray data. Five-day oral gavage studies in male Sprague-Dawley rats dosed with varying concentrations of three fibrogenic compounds (allyl alcohol, carbon tetrachloride, and 4,4’-methylenedianiline) and two non-fibrogenic compounds (bromobenzene and dexamethasone) were conducted. Fibrosis was definitively diagnosed by histopathology. Transcriptomics data matched the predictions made using the DrugMatrix data with greater than 90% accuracy. Microarray data were verified using a 67-plex panel Bioplex® assay, confirming that the 67-plex panel constituted a biomolecular signature of hepatic fibrosis (Figure). Necrosis and inflammatory infiltration were comorbid with fibrosis. Interaction analysis identified 24 genes specific for the fibrosis phenotype. The protein product of the gene most strongly correlated with the fibrosis phenotype (Pcolce) was dose-dependently elevated in plasma from animals administered fibrogenic chemicals (p<0.05). PCOLCE is a novel biomarker candidate of fibrotic injury. These results support the development of gene panels for liver injury and may suggest bridging biomarkers for molecular mediators linked to histopathology.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26396155" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70583" }, "primaryId" : "GEO:GSE70583", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70583" } ] }, "title" : "Response of rat liver to GW7647", "dateAssigned" : "2015-07-07T00:00:00.000-05:00", "summary" : "Activation of PPARa pathways by some environmental chemicals causes hepatocyte proliferation and cancer in rodents. While these responses do not seem to occur in humans, the biological basis of these species differences remains uncertain. We systematically evaluated multiple readouts in rat and human hepatocytes and gene expression in intact rat livers using a PPARa-selective agonist, GW7467. In vitro rat hepatocytes had more genes significantly altered by GW7647 than did human (2320 versus 192). There were common pathways of fatty acid metabolism, amino acid metabolism and lipid transport, mostly represented by upregulated genes, shared between species. In rat hepatocytes, there were many downregulated genes enriched for processes including apoptosis, inflammation, response to hormones and chemical stimuli. In vivo, gene expression signatures for proliferation were present at high doses. In both species, a third of the genes with altered expression had direct binding of PPARa to a nearby peroxisome proliferator response element (PPRE). While the PPRE associated with upregulated genes in both species, was similar, the downregulated genes in the rat had altered flanking region conservation of nucleotides. Among the down regulated genes with direct PPARa binding in the rat were two key transcription factors – Hnf6 (onecut1) and Ets. Our results support a qualitative difference in biology of PPARa activation between human and rats. The secondary downregulated pathways, in the rat, appear to be reversion to an earlier lineage more responsive to proliferative signals that likely arise from interactions between the PPARa activated hepatocytes and other cell types in the intact liver.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70585" }, "primaryId" : "GEO:GSE70585", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70585" } ] }, "title" : "Response of primary hepatocytes to GW7647", "dateAssigned" : "2015-07-07T00:00:00.000-05:00", "summary" : "Activation of PPARa pathways by some environmental chemicals causes hepatocyte proliferation and cancer in rodents. While these responses do not seem to occur in humans, the biological basis of these species differences remains uncertain. We systematically evaluated multiple readouts in rat and human hepatocytes and gene expression in intact rat livers using a PPARa-selective agonist, GW7467. In vitro rat hepatocytes had more genes significantly altered by GW7647 than did human (2320 versus 192). There were common pathways of fatty acid metabolism, amino acid metabolism and lipid transport, mostly represented by upregulated genes, shared between species. In rat hepatocytes, there were many downregulated genes enriched for processes including apoptosis, inflammation, response to hormones and chemical stimuli. In vivo, gene expression signatures for proliferation were present at high doses. In both species, a third of the genes with altered expression had direct binding of PPARa to a nearby peroxisome proliferator response element (PPRE). While the PPRE associated with upregulated genes in both species, was similar, the downregulated genes in the rat had altered flanking region conservation of nucleotides. Among the down regulated genes with direct PPARa binding in the rat were two key transcription factors – Hnf6 (onecut1) and Ets. Our results support a qualitative difference in biology of PPARa activation between human and rats. The secondary downregulated pathways, in the rat, appear to be reversion to an earlier lineage more responsive to proliferative signals that likely arise from interactions between the PPARa activated hepatocytes and other cell types in the intact liver.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70587" }, "primaryId" : "GEO:GSE70587", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70587" } ] }, "title" : "Targeting biliary cancer desmoplasia in culture", "dateAssigned" : "2015-07-07T00:00:00.000-05:00", "summary" : "To more closely reproduce key cellular and stromal features of the desmoplastic reaction of cholangiocarcinoma in vitro, we developed a novel 3-dimensional culture modeling of cancer and stromal cells as a strategy for targeted therapies", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28315313" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70600" }, "primaryId" : "GEO:GSE70600", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70600" } ] }, "title" : "Gene expression changes in the retina following human neural progenitor cell injection into a rodent model for retinal degeneration", "dateAssigned" : "2015-07-07T00:00:00.000-05:00", "summary" : "The goal of this study is to compare gene expression changes in retinal degenerate Royal College of Surgeons (RCS) rats following an injection of human neural progenitor cells (hNPCs) using RNA-seq, as compared to RCS rats receiving a sham surgery and wild-type Long Evans rats. These changes may lead to understanding of the therapeutic potential of hNPCs in inducing photoreceptor survival and visual function preservation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27217715" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70662" }, "primaryId" : "GEO:GSE70662", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70662" } ] }, "title" : "Gene expression in response to low-intensity pulsed ultrasound treatment of bone marrow cells under osteogenic conditions in vitro", "dateAssigned" : "2015-07-09T00:00:00.000-05:00", "summary" : "Bone marrow cells were obtained from the femora of rats and were suspended in an osteogenic medium to make a cell culture. After cultures were established, test cultures were exposed to LIPUS via the base of the cell culture plates for 15 min/day on days 3–9 (LIPUS group). Control cultures (without LIPUS exposure) were otherwise treated identically to the LIPUS group. On day 10, total RNA was extracted from both sets of cultures and hybridized to microarray slides, the data sets were analysed. Markers for differentiated osteoblasts and osteocytes, as well as collagen-related genes, cell adhesion factors were up-regulated in LIPUS group on day 10.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70695" }, "primaryId" : "GEO:GSE70695", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70695" } ] }, "title" : "Genome-wide sequencing of REST binding (ChIP-seq) in adult hippocampal neural stem cells in vitro a.k.a. HCN cells in quiescent (iQNP) and proliferative (TAP) conditions", "dateAssigned" : "2015-07-09T00:00:00.000-05:00", "summary" : "We report the high-throughput profiling of REST binding in mammalian adult hippocampal stem cells in culture (HCN cells). By obtaining 33 to 38 million single-end reads of sequence from chromatin immunoprecipitated DNA, we generated genome-wide REST binding state of HCN cells in induced quiescent (iQNP) and proliferating (TAP) conditions. Thereafter, we annotated the peaks to genomic regions and associated genes. We find that with +/-10kb of transcription start site of genes, REST efficiently binds neuronal genes and represses them in HCN cells in both iQNP and TAP conditions. Moreover, only in the iQNP REST also binds non-neuronal genes like DNA replication genes. This study reveals that in addition to its well known function as a neuronal repressor in non-neuronal tissue, REST can also play other diverse roles in non-neuronal tissues.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27819263" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70696" }, "primaryId" : "GEO:GSE70696", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70696" } ] }, "title" : "Genome wide transcriptome analysis (RNA-seq) of adult hippocampal neural stem cells in vitro a.k.a. HCN cells in quiescent and proliferative conditions in non-electroporated or electroporated with control empty vector or REST knock-down shRNA vector", "dateAssigned" : "2015-07-09T00:00:00.000-05:00", "summary" : "We report the high-throughput transcriptome profiling of induced quiescent (iQNP) and proliferative (TAP) conditions in mammalian adult hippocampal stem cells in culture (HCN cells). By obtaining 145 to 78 million pair-end reads of sequence from isolated RNA from HCN cells in iQNP and TAP conditions. Thereafter, we intersected this gene expression data with REST bound ChIP-seq peaks within +/-10kb of transcription start site of genes also from HCN cells in iQNP and TAP conditions. We find that with +/-10kb of transcription start site of genes, REST efficiently binds neuronal genes and represses them in HCN cells in both iQNP and TAP conditions. Moreover, only in the iQNP REST also binds non-neuronal genes like DNA replication genes. We also report the high-throughput transcriptome profiling of iQNP and TAP condition HCN cells electroporated with a control empty vector or REST knock-down shRNA vector. By obtaining 145 to 78 million pair-end reads of sequence from isolated RNA from HCN cells in electroporated control empty vector or REST knock-down vector in iQNP and TAP conditions. In REST knockdown in iQNP and TAP conditions we found that predominantly non-neuronal genes and neuronal genes were derepressed. This study reveals that in addition to its well known function as a neuronal repressor in non-neuronal tissue, REST can also play other diverse roles in non-neuronal tissues.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27819263" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70747" }, "primaryId" : "GEO:GSE70747", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70747" } ] }, "title" : "Comparison of C3 or C3156-181-peptide treated Isolated primary rat neonatal Schwann Cells after 12 h", "dateAssigned" : "2015-07-10T00:00:00.000-05:00", "summary" : "Results from two loops of two different treatment times are summarized in this study. The samples were taken from two C3 or C3156-181-peptide treated Isolated primary rat neonatal Schwann Cell cultures. Microarrays were hybridized in a loop approach.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26417907" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70748" }, "primaryId" : "GEO:GSE70748", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70748" } ] }, "title" : "Comparison of C3 or C3156-181-peptide treated Isolated primary rat neonatal Sschwann Cells after 72 h", "dateAssigned" : "2015-07-10T00:00:00.000-05:00", "summary" : "Results from two loops of two different treatment times are summarized in this study. The samples were taken from two C3 or C3156-181-peptide treated Isolated primary rat neonatal Schwann Cell cultures. Microarrays were hybriszed in a loop approach.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26417907" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70860" }, "primaryId" : "GEO:GSE70860", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70860" } ] }, "title" : "Changes of axonal transcriptomes in response to local Abeta", "dateAssigned" : "2015-07-13T00:00:00.000-05:00", "summary" : "We report that local application of Abeta(1-42) for 24h triggers changes in the localized transcriptome, while the transcriptome in cell bodies remains largely unchanged.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25171414" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70918" }, "primaryId" : "GEO:GSE70918", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70918" } ] }, "title" : "Expression data from rat tendon fibroblasts treated with PRP and PPP.", "dateAssigned" : "2015-07-14T00:00:00.000-05:00", "summary" : "Tendon is a hypocellular tissue that contains functional cable-like units of type I collagen responsible for the transmission of force from muscle to bone. In the setting of injury or disease, patients can develop chronic tendinopathies that are characterized by pain, loss of function and persistent inflammatory changes that are often difficult to treat. Platelet-rich plasma (PRP) has shown promise in the treatment of chronic tendinopathy, but little is known about the mechanisms by which PRP can improve tendon healing. PRP contains many different growth factors and cytokines, and since these proteins can both activate and inhibit various signaling pathways it has been challenging to determine precisely which signaling pathways and cellular responses are most important. Using state-of-the-art bioinformatics tools and genome wide-expression profiling, the purpose of this study was to determine the signaling pathways activated within cultured tendon fibroblasts in response to PRP treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27400714" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70950" }, "primaryId" : "GEO:GSE70950", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70950" } ] }, "title" : "Cocoa polyphenols and fiber modify colonic gene expression in rats", "dateAssigned" : "2015-07-15T00:00:00.000-05:00", "summary" : "Cocoa intake has been associated with health benefits, improving cardiovascular function and metabolism, as well as modulating intestinal immune function. The aim of this study was to take an in-depth look into the mechanisms affected by the cocoa intake by evaluating the colonic gene expression after nutritional intervention, and to ascertain the role of the fiber of cocoa in these effects. To achieve this, Wistar rats were fed for 3-weeks with either a reference diet, a diet containing 10% cocoa (C10), a diet based on cocoa fiber (CF) or a diet containing inulin (I). At the end of the study, colon was excised to obtain the RNA to evaluate the differential gene expression by microarray. Results were validated by RT-PCR. The C10 group was the group with most changes in colonic gene expression, most of them down-regulated but a few in common with the CF diet. The C10 diet significantly up-regulated the expression of Scgb1a1 and Scnn1g and down-regulated Tac4, Mcpt2, Fcer1a and Fabp1 by twofold, most of them related to lipid metabolism and immune function. The CF and I diets down-regulated the expression of Serpina10 and Apoa4 by twofold. Similar patterns of expression were found by PCR. Cocoa consumption down-regulated genes related to the immune system (B cell and mast cell functionality), lipid metabolism in the colon tissue. Most of the beneficial effects attributed to cocoa were due not only to its fiber content, but also to the possible contribution of polyphenols and other compounds.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70990" }, "primaryId" : "GEO:GSE70990", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE70990" } ] }, "title" : "MiRNA expression profiling of skeletal muscles in aged rodents", "dateAssigned" : "2015-07-16T00:00:00.000-05:00", "summary" : "Skeletal muscle atrophy is one of the critical issues which elderly people face. The precise mechanism underlying muscle atrophy during aging is not fully understood. In order to identify miRNA whose expression is changed in age-associated muscle atrophy, we performed miRNA expression profiling of skeletal muscles in young and aged rats. Microarray analysis revealed differential miRNA expression in EDL and soleus muscles of aged rats compared with those of young rats. We next investigated whether the age-associated changes of miRNA expression observed in rats were recapitulated in mice and found that the expression level of miR-206 in EDL muscle and that of miR-196a in EDL and soleus muscles were respectively higher and lower in aged rodents than in young rodents. In mouse C2C12 myoblasts and myotubes, introduction of miR-196a decreased the protein level of Forkhead-box transcription factor Foxo1, a known target of miR-196a, indicating that miR-196a may regulate Foxo1 expression also in skeletal muscles. Furthermore, miR-196a overexpression exacerbated cell death caused by an exposure to hydrogen peroxide. Lastly, we demonstrated that expression of Foxo1 was elevated in EDL and soleus muscles of aged mice compared with those of young mice. These results suggest that miRNAs are involved in skeletal muscle atrophy during aging and that decreased miR-196a expression may protect skeletal muscle cells from oxidative stress in part through induction of Foxo1.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71021" }, "primaryId" : "GEO:GSE71021", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71021" } ] }, "title" : "Endothelin-Mediated Changes in Gene Expression in Isolated Purified Rat Retinal Ganglion Cells", "dateAssigned" : "2015-07-16T00:00:00.000-05:00", "summary" : "Primary RGCs treated with 100nM of ET-1, ET-2 or ET-3 for 24 hours was used as cell model to investigation the role of endothelins in gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26397462" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71055" }, "primaryId" : "GEO:GSE71055", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71055" } ] }, "title" : "Effect of furan on transcriptomic and gene-specific DNA methylation changes in the livers of Fischer 344 rats in a two-year carcinogenicity study", "dateAssigned" : "2015-07-17T00:00:00.000-05:00", "summary" : "The carcinogenic effect of furan, a potent hepatotoxicant and rodent liver carcinogen, has been attributed to genotoxic and non-genotoxic, including epigenetic, changes in the liver; however, the mechanisms of the furan liver tumorigenicity are still unclear. The goal of the present study was to investigate the role of transcriptomic and epigenetic events in the development of hepatic lesions in Fischer (F344) rats induced by furan treatment in a classic two-year rodent tumorigenicity bioassay. Male F344 rats were distributed randomly into control and experimental groups. Rats from the experimental groups were treated by gavage 5 days/week with either 0.92 or 2.0 mg furan/kg body weight (bw) in corn oil for 104 weeks. Rats from control group received corn oil only. High-throughput whole genome microarray analyses demonstrated distinctive dose-dependent alterations in gene expression in the furan-induced liver lesions. A total of 2073 and 2422 genes was found to be differentially expressed in the furan-induced liver lesions in rats treated with 0.92 and 2.0 mg furan/kg bw, respectively, as compared to normal liver tissue. Approximately 60% (1340) of the differentially expressed genes were common to both treatment groups. In silico analysis of the common differentially expressed genes revealed the presence of CpG island in 51% (679) of the genes, suggesting that they may be epigenetically regulated. Promoter methylation analysis of individual differentially expressed CpG island-containing genes demonstrated dose-dependent gene-specific methylation changes that were highly correlated with gene expression. Our findings illustrate that gene-specific DNA methylation changes have functional consequences and may contribute to the development of furan-induced pathologic liver lesions.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71083" }, "primaryId" : "GEO:GSE71083", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71083" } ] }, "title" : "Fibrinogen promotes autoimmunity and demyelination via chemokine release and antigen presentation [Rn]", "dateAssigned" : "2015-07-20T00:00:00.000-05:00", "summary" : "We subjected fibrin-stimulated microglia to microarray to determine the genes involved in innate and adaptive immune responses by fibrinogen deposited in the CNS after blood-brain barrier disruption.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26353940" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71201" }, "primaryId" : "GEO:GSE71201", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71201" } ] }, "title" : "Effect of a High Phosphorus Diet on Hepatic Gene Expressions in Rat", "dateAssigned" : "2015-07-22T00:00:00.000-05:00", "summary" : "A high phosphorus (HP) diet causes disorders of renal function, bone metabolism, and vascular function. We previously demonstrated that DNA microarray analysis is an appropriate method to comprehensively evaluate the effects of a HP diet on kidney dysfunction such as calcification, fibrillization, and inflammation. We reported that type IIb sodium-dependent phosphate transporter is significantly up-regulated in this context. In the present study, we performed DNA microarray analysis to investigate the effects of a HP diet on the liver, which plays a pivotal role in energy metabolism. DNA microarray analysis was performed with total RNA isolated from the livers of rats fed a control diet (containing 0.3% phosphorus) or a HP diet (containing 1.2% phosphorus). Gene Ontology analysis of differentially expressed genes (DEGs) revealed that the HP diet induced down-regulation of genes involved in hepatic amino acid catabolism and lipogenesis, while genes related to fatty acid ß-oxidation process were up-regulated. Although genes related to fatty acid biosynthesis were down-regulated in HP diet-fed rats, genes important for the elongation and desaturation reactions of omega-3 and -6 fatty acids were up-regulated. Concentrations of hepatic arachidonic acid and eicosapentaenoic acid were increased in HP diet-fed rats. These essential fatty acids activate peroxisome proliferator-activated receptor alpha (PPARa), a transcription factor for fatty acid ß-oxidation. Evaluation of the upstream regulators of DEGs using Ingenuity Pathway Analysis indicated that PPARa was activated in the livers of HP diet-fed rats. Furthermore, the serum concentration of fibroblast growth factor 21, a hormone secreted from the liver that promotes fatty acid utilization in adipose tissue as a PPARa target gene, was higher (p = 0.054) in HP diet-fed rats than in control diet-fed rats. These data suggest that a HP diet enhances energy expenditure through the utilization of free fatty acids released via lipolysis of white adipose tissue.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27187182" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71259" }, "primaryId" : "GEO:GSE71259", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71259" } ] }, "title" : "FRT thyroid cells: 2D monolayers vs. 3D follicles", "dateAssigned" : "2015-07-23T00:00:00.000-05:00", "summary" : "Transcriptional profiling of the Fischer Rat Thyroid (FRT) cells comparing polarizing cells grown as a confluent two-dimensional monolayer (2D culture system) with cells grown in matrigel where they acquire a three-dimensional follicular structure (3D culture system).The goal was to identify regulators of 3D epithelial thyroid polarization and follicle formation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27780871" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71277" }, "primaryId" : "GEO:GSE71277", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71277" } ] }, "title" : "Gene expression profiles in liver of Sprague-Dawley rat using two types of anesthesia.", "dateAssigned" : "2015-07-23T00:00:00.000-05:00", "summary" : "To reveal influence of anesthesia in toxicogenomics study, gene expression analysis of liver of Sprague-Dawley rat after isoflurane anesthesia or CO2/O2 anesthesia was performed. The liver samples were excised from each rat after isoflurane anesthesia or CO2/O2 anesthesia. The gene expression profiles in liver were measureed by Agilent microarray.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71306" }, "primaryId" : "GEO:GSE71306", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71306" } ] }, "title" : "Scl-Ab: Exploratory 26-Week Subcutaneous Toxicology Study in the Aged Ovariectomized Female Sprague Dawley Rat with an 18-week Recovery [vertebrae]", "dateAssigned" : "2015-07-24T00:00:00.000-05:00", "summary" : "This study is designed to compare and contrast the temporal and spatial changes in bone formation rates and transcriptional profiles in cortical and cancellous bone cell populations enriched by laser capture microdissection (LCM) in ovariectomized rats administered Scl-Ab by subcutaneous injection for up to 26 consecutive weeks, followed by a recovery period of up to 18 weeks.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26721737" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71324" }, "primaryId" : "GEO:GSE71324", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71324" } ] }, "title" : "miRNA expression in kidney Thick Ascending Limb in Hypersodic diet treated rats (H samples) vs normal diet rats (N samples)", "dateAssigned" : "2015-07-24T00:00:00.000-05:00", "summary" : "3 H samples vs 3 N samples Each sample was made by 3 pooled animals", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71413" }, "primaryId" : "GEO:GSE71413", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71413" } ] }, "title" : "Expression data from the liver of rat treated by Piperonyl butoxide and Dammar resin", "dateAssigned" : "2015-07-28T00:00:00.000-05:00", "summary" : "Piperonyl butoxide (PBO) and Dammar resin (DAM) are NGTX hepatocarcinogens. Gene expression data in the liver treated by PBO and DAM was used for validation of constructed model.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71425" }, "primaryId" : "GEO:GSE71425", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71425" } ] }, "title" : "Gene expression of rat cerebellum in a new animal model of hepatic encephalopathy (HE)", "dateAssigned" : "2015-07-28T00:00:00.000-05:00", "summary" : "The animal model consists on the simulation of several bouts of HE in PCA rats, being the precipitant factors of the episodes ammonia (NH3) and/or lipopolisaccharide (LPS) or saline.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27154504" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71612" }, "primaryId" : "GEO:GSE71612", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71612" } ] }, "title" : "Comparative transcriptome analysis reveals naked mole rat liver adaptations to hypoxia", "dateAssigned" : "2015-07-31T00:00:00.000-05:00", "summary" : "This study compares the transcriptional response to hypoxia in liver of the hypoxia-tolerant naked mole rat (NMR) and the hypoxia-sensitive rat.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71653" }, "primaryId" : "GEO:GSE71653", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71653" } ] }, "title" : "Alterations in serum microRNA in humans with alcohol use disorders impact cell proliferation and cell death pathways and predict structural and functional changes in brain [rat miRNA 2.0]", "dateAssigned" : "2015-08-03T00:00:00.000-05:00", "summary" : "We performed a global analysis of extracellular miRNAs in the serum of human subjects diagnosed with Alcohol Use Disorder (AUD) to identify robust biomarkers of early brain damage or dysfunction. This was performed in a set of 20 AUD subjects and 10 age-matched controls. They were subjected to comprehensive medical, neuropsychological and neuroimaging tests, followed by comparison of miRNA levels found in peripheral blood serum. The levels of miRNAs were quantified using two independent high-throughput methods: Affymetrix microarray and Illumina next-generation RNA-sequencing. Cross-species validation was performed using rat drinking models and mouse neural stem cell culture models, with tissue specificity of the serum miRNAs examined using additional RNA-sequencing of serum and body tissues in untreated rats. This data series includes the rat miRNA 2.0 GeneChip data only but is part of a larger SuperSeries (GSE71579).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26341662" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71697" }, "primaryId" : "GEO:GSE71697", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE71697" } ] }, "title" : "Alterations in serum microRNA in humans with alcohol use disorders impact cell proliferation and cell death pathways and predict structural and functional changes in brain [rat miRNA-Seq]", "dateAssigned" : "2015-08-04T00:00:00.000-05:00", "summary" : "We performed a global analysis of extracellular miRNAs in the serum of human subjects diagnosed with Alcohol Use Disorder (AUD) to identify robust biomarkers of early brain damage or dysfunction. This was performed in a set of 20 AUD subjects and 10 age-matched controls. They were subjected to comprehensive medical, neuropsychological and neuroimaging tests, followed by comparison of miRNA levels found in peripheral blood serum. The levels of miRNAs were quantified using two independent high-throughput methods: Affymetrix microarray and Illumina next-generation RNA-sequencing. Cross-species validation was performed using rat drinking models and mouse neural stem cell culture models, with tissue specificity of the serum miRNAs examined using additional RNA-sequencing of serum and body tissues in untreated rats. This data series includes the rat brain and body tissue miRNA data obtained from RNA-sequencing only and is part of a larger SuperSeries (GSE71579) now being curated at GEO", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26341662" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72004" }, "primaryId" : "GEO:GSE72004", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72004" } ] }, "title" : "Comparison of radiation-induced rat mammary carcinomas from individuals with different sensitivity to diet-induced obesity", "dateAssigned" : "2015-08-12T00:00:00.000-05:00", "summary" : "Understanding the relationship between radiation-induced breast cancer and obesity, together with information on underlying mechanisms, are potentially useful in risk management and prevention of second cancer in patients receiving radiotherapy. The present study aims to develop a novel animal model to study the relationship by combining two Sprague-Dawley rat models of radiation carcinogenesis and diet-induced obesity. Mammary carcinomas were induced in female obese and lean rats by irradiation with 4 Gy of gamma rays. Gene expression of mammary carcinomas and normal mammary tissues were analyzed with Agilent Whole Rat Genome DNA microarray. The result indicated that genes related to translation and oxidative phosphorylation were upregulated in carcinomas of obese rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27135968" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72062" }, "primaryId" : "GEO:GSE72062", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72062" } ] }, "title" : "Whole genome microarray gene expression profiling of hippocampal genes from aged rats subjected to chronic unpredictable mild stress", "dateAssigned" : "2015-08-13T00:00:00.000-05:00", "summary" : "Psychological, psychosocial and physical stress are major risk factors, which enhance the development of sporadic late-onset Alzheimer`s disease. The chronic unpredictable mild stress model mimics those risk factors and triggers signs of neurodegeneration and neuropathological features of sporadic AD such as tau hyperphosphorylation and enhanced amyloid beta generation. The study investigated the impact of chronic unpredictable mild stress on signs of neurodegeneration by analyzing hippocampal gene expression with whole genome microarray gene expression profiling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26697495" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72076" }, "primaryId" : "GEO:GSE72076", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72076" } ] }, "title" : "Time course expression data from Brown Norway rat livers treated with nevirapine or galactosamine or both", "dateAssigned" : "2015-08-14T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying the sequential responses of nevirapine alone, galactosamine alone, and the identified distinct classes of up-regulated genes during this process.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26733602" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72135" }, "primaryId" : "GEO:GSE72135", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72135" } ] }, "title" : "Expression data from hyperoxaluric rats", "dateAssigned" : "2015-08-18T00:00:00.000-05:00", "summary" : "Calcium oxalate stones account for over 80% of urinary stones, while the molecular mechanism of its formation is still not completely elucidated. The incidence of hyperoxaluria in calcium oxalate stone formation ranks only second to hypercalciuria. It plays an important role in the pathophysiological process of stone formation. We analyzed miRNA expression profiles between experimental hyperoxaluric rats and normal rats in order to find out the target genes and signaling pathways in the pathogenesis of hyperoxaluria.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72157" }, "primaryId" : "GEO:GSE72157", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72157" } ] }, "title" : "Expression data from pooled biological replicates (n=6) from MEF2D knockdown in neonatal rat ventricular myocytes (NRVMs)", "dateAssigned" : "2015-08-18T00:00:00.000-05:00", "summary" : "We knocked down expression of MEF2D in NRVMs, and assessed global expression pattern changes in MEF2D knockdown against a negative control.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26294766" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72181" }, "primaryId" : "GEO:GSE72181", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72181" } ] }, "title" : "Differential Gene Expression Profiles of PASMCs Induced by Quercetin under Hypoxia", "dateAssigned" : "2015-08-19T00:00:00.000-05:00", "summary" : "As the critical step of pathogenesis during hypoxic pulmonary arterial hypertension (PAH) vascular remodeling is closely associated with pulmonary arterial smooth muscle cell (PASMC) alterations induced by hypoxia that include persistent vasoconstriction, abnormal proliferation and PASMC resistance to apoptosis. Quercetin is a flavonoid compound extracted from green plants that inhibits proliferation, induces apoptosis, arrests the cell cycle, and rescues the constriction of PASMCs, but the underlying mechanisms remain poorly understood. In this study, we used a commercial Agilent Whole Rat Genome Oligo Microarray to determine the overall transcriptional response of PASMCs in response to exposure to hypoxia and the optimal concentration of quercetin. Hypoxia induced the upregulation of 1694 genes and the downregulation of 2091 genes compared with the normoxia group. Quercetin treatment resulted in 1790 upregulated genes and 1450 downregulated genes. Quercetin is known to cause differential expression of several of these genes that are known to promote proliferation, induce apoptosis (Cycs, Ppp3ca, Prkar2b, Akt3, Ppp3cc, Il1rap, Ntrk1), arrest the cell cycle (Chek2, Cdkn1c, Gadd45b, Stag2, Anapc7, Orc1, Ccne1, Myc3, Skp1, Espl1, Cdc45, Mcm4), and rescue PASMC constriction (Ramp1, Ramp3, Adcy5, Gnas, Prkcd, Itpr3, Adra1d, Calm1, Npr1, Avpr1a, Ednra, Adcy8). Real-time quantitative RT-PCR was performed to verify the microarray results. In conclusion, quercetin altered the expression profile of many genes regulated by hypoxia in PASMCs, which helps to further explore the mechanism of the effects of quercetin treatment on hypoxic PAH.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72198" }, "primaryId" : "GEO:GSE72198", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72198" } ] }, "title" : "Differentially Expressed microRNAs in Bone Marrow Mesenchymal Stem Cell-derived Microvesicles in Young and Older Rats and Their Effect on Tumor Growth Factor-ß1-mediated Epithelial-Mesenchymal Transition in HK2 cells", "dateAssigned" : "2015-08-19T00:00:00.000-05:00", "summary" : "miRNA profiles of the Young-MSC-MVs and Old-MSC-MVs were analyzed with a quantitative PCR (qPCR)-based array of the whole rat genome. Further analysis revealed the expression of miR-344a, miR-133b-3p, miR-294, miR-423-3p, and miR-872-3p was significantly downregulated in Old-MSC-MVs than in Young-MSC-MVs (p<0.05).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26415502" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72276" }, "primaryId" : "GEO:GSE72276", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72276" } ] }, "title" : "Mammary transcriptome of rats treated with low-dose environmental chemicals at critical developmental windows", "dateAssigned" : "2015-08-21T00:00:00.000-05:00", "summary" : "Exposure to common environmental chemicals, including those found in personal care products has been linked to mammary cancer at high doses in animal models. Their effects at low doses at levels comparable to human exposure, especially during critical windows of development remain poorly understood. Using a Sprague-Dawley rat model, we investigated the effects of of three environmental chemicals – diethyl phthalate (DEP), methyl paraben (MPB) and triclosan (TCS) – on the transcriptome of normal developing mammary glands at low doses mimicking human exposure. Rats were exposed during three windows of early development – perinatal (gestation day (GD) 1 - 20 or postnatal day (PND) 1 - 20), prepubertal (PND 21 - 41) and pubertal (PND 42 - 62), as well as chronic exposure from birth to end of lactation (PND 1 - 146). Mammary gland whole-transcriptomes were profiled by Affymetrix rat gene 2.0 st arrays.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27810681" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72357" }, "primaryId" : "GEO:GSE72357", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72357" } ] }, "title" : "mRNA expression data for rat liver treated for 24h with RG3487 (180mg/kg po.) vs vehicle only (deionized water)", "dateAssigned" : "2015-08-25T00:00:00.000-05:00", "summary" : "No consistent gene expression changes related to nuclear receptor activation, in particular target genes of CAR, PXR or PPAR were observed at the 24h time point", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72361" }, "primaryId" : "GEO:GSE72361", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72361" } ] }, "title" : "Microarray Analysis Gene Expression Profiles in Laryngeal Muscle After Recurrent Laryngeal Nerve Injury", "dateAssigned" : "2015-08-25T00:00:00.000-05:00", "summary" : "The pathophysiology of recurrent laryngeal nerve (RLN) transection injury is rare in that it is characteristically followed by a high degree of spontaneous reinnervation, with reinnervation of the laryngeal adductor complex (AC) preceding that of the abducting posterior cricoarytenoid (PCA) muscle. Here, we aim to elucidate the differentially expressed myogenic factors following RLN injury that may be at least partially responsible for the spontaneous reinnervation. F344 male rats underwent RLN injury or sham surgery (n=12). One week after RLN injury, larynges were harvested following euthanasia. mRNA was extracted from PCA and AC muscles bilaterally, and microarray analysis was performed using a full rat genome array. Microarray analysis of denervated AC and PCA muscles demonstrated dramatic differences in gene expression profiles, with 205 individual probes that were differentially expressed between the denervated AC and PCA muscles, and only 14 genes with similar expression patterns. The differential expression patterns of the AC and PCA suggest different mechanisms of reinnervation. The PCA showed the gene patterns of Wallerian degeneration, while the AC expressed the gene patterns of reinnervation by adjacent axonal sprouting. This finding may reveal important therapeutic targets applicable to RLN and other peripheral nerve injuries.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26530091" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72387" }, "primaryId" : "GEO:GSE72387", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72387" } ] }, "title" : "mRNA Expression data from rats treated with ANIT or vehicle", "dateAssigned" : "2015-08-26T00:00:00.000-05:00", "summary" : "Livers were extracted from rats at 24h and 120 h post ANIT exposure. This study investigated differences in mRNA expression between the injury and repair phases in the context of ANIT exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26614776" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72401" }, "primaryId" : "GEO:GSE72401", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72401" } ] }, "title" : "Motivated cocaine seeking lead to transgenerational epigenetic inheritance of vulnerability to cocaine addiction", "dateAssigned" : "2015-08-26T00:00:00.000-05:00", "summary" : "Familial transmission and high heritability of liability for drug abuse has been demonstrated by large scale epidemiological and twin studies, but the role of pre-existing susceptibility to addiction is still not clear. Our data show that F1 and F2 offspring sired by rats with high motivation for drug reinforcement and drug intake during cocaine self-administration maintained their ancestor’s addict-like behavior. This paternal transmission of drug addiction is an acquired trait that is dependent on cocaine induced high motivation in F0. Reduced representation bisulfite sequencing of F0 and F1 sperm DNA reveal a few persistent epigenetic changes in genes that critically regulate early development and morphogenesis. These epigenetic traits may underlie alterations in the neurological basis that lead to the transmission of cocaine motivation. Our results reveal the epigenetic transgenerational inheritance of drug craving and provide a potential etiology in cocaine abuse vulnerability.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28556835" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72431" }, "primaryId" : "GEO:GSE72431", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72431" } ] }, "title" : "Self-maintenance of rat C6 glioma stem cells (GSCs) by their non-GSC progenies", "dateAssigned" : "2015-08-27T00:00:00.000-05:00", "summary" : "Analysis of Hoechst 33342 dye-effluxing side population cells (SP cells defined as glioma stem cells, GSCs) and dye-retaining main population cells (MP cells defined as non-GSCs) that were FACS-sorted from the C6 glioma cell line stably expressing EGFP (C6-eGFP). ECM-related genes, such as Col4a1 and Col4a2, and the iron carrier gene Tf are upregulated in MP cells. Results provide the insight into molecular basis underlying the maintenance of GSCs by non-GSCs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26822103" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72464" }, "primaryId" : "GEO:GSE72464", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72464" } ] }, "title" : "Islet mRNA changes in rat pancreatic islets during aging", "dateAssigned" : "2015-08-27T00:00:00.000-05:00", "summary" : "Aging is a risk factor for a majority of metabolic diseases including type 2 diabetes. During aging pancreatic beta-cell function decreases leading to impaired insulin secretion and proliferation and to an increase in apoptosis. Impairment of pancreatic beta cell functions and survival has been linked to gene expression changes. The aim of our study was to obtain a global expression profile of microRNAs and mRNAs of pancreatic islets of 3 and 12 month old male Wistar rats in order to identify the changes occurring during aging.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72465" }, "primaryId" : "GEO:GSE72465", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72465" } ] }, "title" : "Islet microRNA changes in the rat pancreatic islets during aging", "dateAssigned" : "2015-08-27T00:00:00.000-05:00", "summary" : "Aging is a risk factor for a majority of metabolic diseases including type 2 diabetes. During aging pancreatic beta-cell function decreases leading to impaired insulin secretion and proliferation and to an increase in apoptosis. Impairment of pancreatic beta cell functions and survival has been linked to gene expression changes. The aim of our study was to obtain a global expression profile of microRNAs and mRNAs of pancreatic islets of 3 and 12 month old male Wistar rats in order to identify the changes occurring during aging.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72469" }, "primaryId" : "GEO:GSE72469", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72469" } ] }, "title" : "Environmentally Induced Epigenetic Transgenerational Inheritance of Altered SRY Genomic Binding During Gonadal Sex Determination", "dateAssigned" : "2015-08-27T00:00:00.000-05:00", "summary" : "A critical transcription factor required for mammalian male sex determination is SRY (sex determining region on the Y chromosome). The expression of SRY in precursor Sertoli cells is one of the initial events in testis development. The current study was designed to determine the impact of environmentally induced epigenetic transgenerational inheritance on SRY during gonadal sex determination in the male. The agricultural fungicide vinclozolin and vehicle control (DMSO) exposed gestating females (F0 generation) during gonadal sex determination promoted the transgenerational inheritance of differential DNA methylation in sperm of the F3 generation (great grand-offspring). The fetal gonads in F3 generation males were used to identify potential alterations in SRY binding sites in the developing Sertoli cells. Chromatin immunoprecipitation with an SRY antibody followed by genome-wide promoter tiling array (ChIP-Chip) was used to identify alterations in SRY binding. A total of 81 adjacent oligonucleotide sites and 173 single oligo SRY binding sites were identified to be altered transgenerationally in the Sertoli cell vinclozolin lineage F3 generation males. Observations demonstrate the majority of the previously identified normal SRY binding sites were not altered and the altered SRY binding sites were novel and new additional sites. The chromosomal locations, gene associations and potentially modified cellular pathways were investigated. In summary, environmentally induces epigenetic transgenerational inheritance of germline epimutations appears to alter the cellular differentiation and development of the precursor Sertoli cell SRY binding during gonadal sex determination that influence the developmental origins of adult onset testis disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23555832" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72506" }, "primaryId" : "GEO:GSE72506", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72506" } ] }, "title" : "Zonal Gene Expression and Gene Regulatory Network Responses in Centrilobular and Periportal Hepatocytes Following Repeated Exposure to TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin)", "dateAssigned" : "2015-08-28T00:00:00.000-05:00", "summary" : "Persistent activation of the aryl hydrocarbon receptor (AHR) is believed to play a key role in the mode-of-action for TCDD induced rat liver tumorigenesis. It has been hypothesized that the cellular responses of hepatocytes to AHR activation may differ across regions of the liver lobule and that zone-specific effects of AHR agonists may play a role in the pathogenesis of rat liver tumorigenesis. Dose-dependent changes in gene expression were observed in both populations of hepatocytes collected from WT rats which were consistent with activation of AHR signaling. No significant or dose-dependent changes in gene expression were observed in samples from AHR-KO rats. In addition, evidence of inflammatory signaling pathway activation was observed only in centrilobular hepatocytes. Evidence of cell adhesion pathway enrichment was observed only in periportial hepatocytes. Benchmark dose analysis demonstrated that dose-dependent changes in gene expression occurred at lower doses in centrilobular as compared to periportal hepatocytes. These results indicate zone-specific differences in the sensitivity and response of hepatocytes to persistent AHR activation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72551" }, "primaryId" : "GEO:GSE72551", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72551" } ] }, "title" : "Transcriptional changes in sensory ganglion associated with primary afferent collateral sprouting in spared dermatome model", "dateAssigned" : "2015-08-31T00:00:00.000-05:00", "summary" : "In this study, we sought to identify gene expression changes in PACS using 20 Affymetrix Rat Genome 230 2.0 microarrays. The experiments were designed to discover global gene expression changes in non-injured DRG neurons undergoing PACS. T11 DRG neurons remained intact and undergo PACS after the cutaneous nerves of the adjacent segments (T9, T10, T12, and T13) were injured and regeneration of those injured nerves prevented by ligation. Thus, the T9, T10, T12, and T13 dermatomes were denervated, but the T11 dermatome remained intact. Axons of the T11dermatome (and thus housed in the T11 dorsal root ganglion (DRG)), extended new branches to innervate the T9, T10, T12, and T13 dermatomes. N.B.: This is NOT a spared root experiment. ALL spinal roots were non-injured. Peripheral nerves were used.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26697387" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72569" }, "primaryId" : "GEO:GSE72569", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72569" } ] }, "title" : "Effects of residual metals contained in single-wall carbon nanotubes on cellular response in rat alveolar macrophages and human alveolar epithelial cell line", "dateAssigned" : "2015-09-01T00:00:00.000-05:00", "summary" : "Gene expression profiling of the rat alveolar macrophages (NR8383) and human alveolar epithelial cell line (A549) exposure to iron-enriched pristine single-wall carbon nanotubes (SWCNTs) or their purified SWCNTs were employed to gain insights at the transcriptional level.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72701" }, "primaryId" : "GEO:GSE72701", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72701" } ] }, "title" : "Gene expression profiling in a rat model of monocrotaline-induced heart failure", "dateAssigned" : "2015-09-03T00:00:00.000-05:00", "summary" : "Cardiac cachexia is a common complication of heart failure in severe cases and is associated with a poor prognosis. Several skeletal muscle abnormalities have been described in patients and animals with cardiac cachexia; these include atrophy, fibrosis, altered myosin heavy chain composition, and decreased oxidative capacity. It is also well established that gene expression patterns are substantially altered in cardiac cachexia, but the reasons for such differences are not clear.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72707" }, "primaryId" : "GEO:GSE72707", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72707" } ] }, "title" : "Genomic alterations during the progress of pulmonary hypertension", "dateAssigned" : "2015-09-03T00:00:00.000-05:00", "summary" : "Pulmonary hypertension (PH), a rare disorder is a complication of a number of cardiopulmonary, unrelated systemic diseases, drug toxicity and genetic mutations. Major advances have been made in the field, but the pathogenesis of PH is not yet understood. Several experimental models such as monocrotaline (MCT) and hypoxia have been used to understand the mechanism underlying the pathogenesis of PH. We have recently shown that that the addition of hypoxia to MCT injected rats accelerates the disease process leading to neointima formation. We have profiled the lungs of adult male Sprague-Dawley rats kept for 4 weeks in normal atmospheric conditions or in hypobaric hypoxia (380 mmHg) w/o subcutaneous injection with 40 mg/kg MCT or just saline. While MCT and hypoxia altered expression of few genes when applied separately, together they induced a substantial alteration of the transcriptome. The most profoundly altered pathways by the combined effect of hypoxia and MCT were: endocytosis, apoptosis, HIF-1 signaling pathway and vascular smooth muscle contraction.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72725" }, "primaryId" : "GEO:GSE72725", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72725" } ] }, "title" : "Chromatin Remodeler CHD7 mutated in CHARGE Syndrome Interacts with Sox10 to Regulate Timing of CNS Myelination and Remyelination [ChIP-seq]", "dateAssigned" : "2015-09-04T00:00:00.000-05:00", "summary" : "Mutations in CHD7, encoding ATP-dependent chromodomain-helicase-DNA-binding protein 7, in CHARGE syndrome leads to multiple congenital anomalies including growth retardation, craniofacial malformations and neurological dysfunction. Currently, mechanisms underlying the CNS phenotypes remain poorly understood. Here, we show that Chd7 is a direct transcriptional target of oligodendrogenesis-promoting factors Olig2 and Brg1 and required for proper timing of CNS myelination and remyelination. Genome-occupancy analyses coupled with transcriptome profiling reveal that Chd7 cooperates with Sox10 to target the enhancers of key myelinogenic genes, and identify novel Chd7 target.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72739" }, "primaryId" : "GEO:GSE72739", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72739" } ] }, "title" : "Cross-species transcriptomic comparison of in vitro and in vivo mammalian neural cells", "dateAssigned" : "2015-09-04T00:00:00.000-05:00", "summary" : "We report the first RNA profiing of mammalian neural cells grown in vitro. About 50 million reads are generated by RNA-seq from rat astrocytes, neurons and oligodendrocyte precursor cells in primary culture. These data are compared with theose generated from the correponding mouse neural cells that are acutely purified from brains. Cross-species RNA-seq data analysis revealed hundreds of genes that are differentially expressed between cultured and acutely purified cells. Astrocytes have more such genes compared to neurons and oligodendrocyte precursor cells, indicating that signalling pathways are greatly perturbed in cultured astrocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26640375" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72787" }, "primaryId" : "GEO:GSE72787", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72787" } ] }, "title" : "Effects of eye opening on gene expression in the superficial layers of the rat superior colliculus", "dateAssigned" : "2015-09-08T00:00:00.000-05:00", "summary" : "We performed RNA-seq on six samples of P20 Sprague Dawley rat superior colliculus, three control rats that underwent eye opening at P14 until P20 and three deprived rats which had their eyes glued closed from P14 until P20. Each sample was created from two pooled colliculi.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72834" }, "primaryId" : "GEO:GSE72834", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72834" } ] }, "title" : "Skeletal muscle derived stem cell implantation therapy in a rat model of erectile dysfunction", "dateAssigned" : "2015-09-09T00:00:00.000-05:00", "summary" : "The skeletal muscle derived stem cells were grown in culture and analyzed by DNA microarray analysis for gene expression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72887" }, "primaryId" : "GEO:GSE72887", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72887" } ] }, "title" : "Novel RNA- and FMRP-binding protein TRF2-S regulates axonal mRNA transport and presynaptic plasticity", "dateAssigned" : "2015-09-10T00:00:00.000-05:00", "summary" : "Despite considerable evidence that RNA-binding proteins (RBPs) regulate mRNA transport and local translation in dendrites, roles for axonal RBPs are poorly understood. Here we demonstrate that a nontelomeric isoform of telomere repeat-binding factor 2 (TRF2-S) is a novel RBP that regulates axonal plasticity. TRF2-S interacts directly with target mRNAs to facilitate their axonal delivery. The process is antagonized by fragile X mental retardation protein (FMRP). Distinct from the current RNA-binding model of FMRP, we show that FMRP occupies the GAR domain of TRF2-S protein to block the assembly of TRF2-S-mRNA complexes. Overexpressing TRF2-S and silencing FMRP promotes mRNA entry to axons, and enhances axonal outgrowth and neurotransmitter release from presynaptic terminals. Our findings suggest a pivotal role for TRF2-S in an axonal mRNA localization pathway that enhances axon outgrowth and neurotransmitter release.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72907" }, "primaryId" : "GEO:GSE72907", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72907" } ] }, "title" : "Effects of dexamethasone on gene expression in rat pancreatic AR42J cell line", "dateAssigned" : "2015-09-10T00:00:00.000-05:00", "summary" : "The rat pancreatic cell line AR42J is relatively undifferentiated under normal culture conditions. When the glucocorticoid dexamethasone is added to the medium the cells display a dramatic decrease in proliferative rate and are induced to a more exocrine phenotype that includes increased expression of exocrine pancreas products (digestive enzymes) and more developed regulated secretion. We used microarray to determine changes in gene expression comparing control (without dexamethasone) vs induced (plus dexamethasone).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72960" }, "primaryId" : "GEO:GSE72960", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE72960" } ] }, "title" : "Transcriptome profiles of cirrhotic liver treated with lysophosphatidic acid pathway inhibitors", "dateAssigned" : "2015-09-11T00:00:00.000-05:00", "summary" : "Cirrhosis is a milieu that develops hepatocellular carcinoma (HCC), the second most lethal cancer worldwide. HCC prediction and prevention in cirrhosis are key unmet medical needs. Here we have established an HCC risk gene signature applicable to all major HCC etiologies: hepatitis B/C, alcohol, and non-alcoholic steatohepatitis. A transcriptome meta-analysis of >500 human cirrhotics revealed global regulatory gene modules driving HCC risk and lysophosphatidic acid pathway as a central chemoprevention target. Pharmacological inhibition of the pathway in vivo reduced tumors and reversed the gene signature, which was verified in organotypic ex vivo culture of patient-derived fibrotic liver tissues. These results demonstrate the utility of clinical organ transcriptome to enable a strategy, reverse-engineering precision cancer prevention. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27960085" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73039" }, "primaryId" : "GEO:GSE73039", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73039" } ] }, "title" : "Persistent Effect of mTOR Inhibition on Preneoplastic Foci Progression and Gene Expression in a Rat Model of Hepatocellular Carcinoma", "dateAssigned" : "2015-09-15T00:00:00.000-05:00", "summary" : "We previously identified the mTOR pathway as critical to progenitor cell proliferation in a model of liver injury, we investigated the temporal activation of mTOR signaling in a rat model of hepatic carcinogenesis. The model employed chemical carcinogens and partial hepatectomy to induce progenitor marker-positive HCC. Rats were administered the mTOR inhibitor rapamycin for a three week period and liver harvested one month following cessation of rapamycin treatment. Short-term rapamycin treatment resulted in a significant reduction of focal lesion burden. Microarray analysis was performed to characterize the gene expression signature of persistent focal lesions in the rapamcyin and placebo treated animals. This analysis revealed a persistent effect of short-term mTORC1 inhibition on gene expression that resulted in a genetic signature reminiscent of normal liver.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26905589" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73044" }, "primaryId" : "GEO:GSE73044", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73044" } ] }, "title" : "Expression data from prostate cancer and osteoblast co-cultures", "dateAssigned" : "2015-09-15T00:00:00.000-05:00", "summary" : "Dynamic interaction between prostate cancer and the bone microenvironment is a major contributor to metastasis of prostate cancer to bone. In this study we utilized an in-vitro co-culture model of PC3 prostate cancer cells and osteoblasts followed by microarray based gene expression profiling to identify previously unrecognized prostate cancer-bone microenvironment interactions. Factors secreted by PC3 cells resulted in the up-regulation of many genes in osteoblasts associated with bone metabolism and cancer metastasis, including Mmp13, Il-6 and Tgfb2, and down-regulation of Wnt inhibitor Sost. To determine whether altered Sost expression in the bone microenvironment has an effect on prostate cancer metastasis, we co-cultured PC3 cells with Sost knockout (SostKO) osteoblasts and wildtype (WT) osteoblasts and identified several genes differentially regulated between PC3-SostKO osteoblast co-cultures and PC3-WT osteoblast co-cultures. Co-culturing PC3 cells with WT osteoblasts up-regulated cancer-associated long noncoding RNA (lncRNA) MALAT1 in PC3 cells. MALAT1 expression was further enhanced when PC3 cells were co-cultured with SostKO osteoblasts and treatment with recombinant Sost down-regulated MALAT1 expression in these cells. Our results suggest that reduced Sost expression in the tumor microenvironment may promote bone metastasis by up-regulating MALAT1 in prostate cancer.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73116" }, "primaryId" : "GEO:GSE73116", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73116" } ] }, "title" : "Detecting metastatic tumors after ¿-irradiation using longitudinal molecular imaging and gene expression profiling of metastatic tumor nodules", "dateAssigned" : "2015-09-17T00:00:00.000-05:00", "summary" : "Metastatic tumors in C6-L (rat glioma cells ) xenografted mice were studied after local treatment with fractionated ¿-IR. To accurately detect the metastatic nodules after ¿-IR, we observed the effect of ¿-IR on distant metastatic tumor growth. Metastatic nodules after ¿-IR indicated extensive colonization of C6-L cells in the lungs within 6 weeks after ¿-IR. Identified and described the molecular events occurring after ¿-IR through gene expression profiling to elucidate genetic changes (differentially expressed genes between the ¿-IR primary tumors vs. non-¿-IR primary tumors and metastatic lung nodules vs. ¿-IR primary tumors).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73307" }, "primaryId" : "GEO:GSE73307", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73307" } ] }, "title" : "A transcriptomic study of maternal thyroid adaptation to pregnancy in rats", "dateAssigned" : "2015-09-22T00:00:00.000-05:00", "summary" : "To identify potential regulators of late pregnancy-dependent thyroid weight increase, thyroid gene expression profiles of non-pregnant (NP) and late pregnant (LP, day 18) rats was analyzed using the RNA-seq approach.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26580608" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73328" }, "primaryId" : "GEO:GSE73328", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73328" } ] }, "title" : "Identification of drugs that enhance skin repair using dermal stem cell-based screens [Rat]", "dateAssigned" : "2015-09-22T00:00:00.000-05:00", "summary" : "Here, we asked whether we could identify pharmacological agents that enhance endogenous stem cell function to promote skin repair, focusing on SKPs (skin-derived precursors) a dermal precursor cell population. Libraries of compounds already used in humans were screened for their ability to enhance the self-renewal of human and rodent SKPs. We identified and validated 5 such compounds, and showed that two of them, alprostadil and trimebutine maleate, enhanced the repair of full thickness skin wounds in middle-aged mice. Moreover, SKPs isolated from drug-treated skin displayed long-term increases in self-renewal when cultured in basal growth medium without drugs. Both alprostadil and trimebutine maleate likely mediated increases in SKPs self-renewal by moderate hyperactivation of the MEK-ERK pathway. These findings identify candidates for potential clinical use in human skin repair, and provide support for the idea that pharmacological activation of endogenous tissue precursors represents a viable therapeutic strategy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26724904" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73387" }, "primaryId" : "GEO:GSE73387", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73387" } ] }, "title" : "Alteration of Gene Expression Profile in Spontaneously Hypertensive Rats Treated with Protein Hydrolysate of Blue Mussel (Mytilus edulis) by DNA Microarray Analysis", "dateAssigned" : "2015-09-24T00:00:00.000-05:00", "summary" : "The aim of this study was to investigate the antihypertensive effect of enzymatic hydrolysis of blue mussel protein (HBMP) in rats. Spontaneously hypertensive rats (SHRs) were orally administration with high- or low-dose of HBMP for 28 days. Major components of the renin-angiotensin (RAS) system in serum of SHRs from different groups were analyzed, and gene expression profiling were performed in the kidney of SHRs, using the Whole Rat Genome Oligonucleotide Microarray. Results indicated although genes involved in RAS system were not significantly altered, those related to blood coagulation system, cytokine and growth factor, and fatty acids metabolism were remarkablely changed. Several genes which were seldom reported to be implicated in pathogenesis of hypertension also showed significant expression alterations after oral administration of HBMP.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73411" }, "primaryId" : "GEO:GSE73411", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73411" } ] }, "title" : "Gene expression signature of Lewis rats with experimental NMO and controls", "dateAssigned" : "2015-09-24T00:00:00.000-05:00", "summary" : "study was performed to reveal the extent to which NMO-IgG contributes to tissue damage in experimental NMO", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26990978" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73494" }, "primaryId" : "GEO:GSE73494", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73494" } ] }, "title" : "Gene expression profiles of rat liver tissues after carbon tetrachloride treatment", "dateAssigned" : "2015-09-28T00:00:00.000-05:00", "summary" : "We used Rat Genome 230 2.0 microarray to further highlight the rat liver tissues after carbon tetrachloride treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27659347" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73498" }, "primaryId" : "GEO:GSE73498", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73498" } ] }, "title" : "Gene expression profiles of rat liver tissues after diethylnitrosamine treatment", "dateAssigned" : "2015-09-28T00:00:00.000-05:00", "summary" : "We used HC Genome 230 2.0 microarray to further highlight the regulatory role of rat liver tissues after diethylnitrosamine treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:22194203" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73499" }, "primaryId" : "GEO:GSE73499", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73499" } ] }, "title" : "Gene expression profiles of rat liver tissues after carbon tetrachloride administration", "dateAssigned" : "2015-09-28T00:00:00.000-05:00", "summary" : "We used Rat Genome 230 2.0 microarray to further highlight the rat liver tissues after carbon tetrachloride administration", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27659347" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73500" }, "primaryId" : "GEO:GSE73500", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73500" } ] }, "title" : "Gene expression profiles of rat liver tissues after high-fat emulsion feeding", "dateAssigned" : "2015-09-28T00:00:00.000-05:00", "summary" : "We used Rat Genome 230 2.0 microarray to further highlight the rat liver tissues after high-fat emulsion feeding.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21327921" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73510" }, "primaryId" : "GEO:GSE73510", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73510" } ] }, "title" : "Transcriptome analysis of tenotomy immobilized rat soleus muscle", "dateAssigned" : "2015-09-28T00:00:00.000-05:00", "summary" : "The transcriptome provided clear-cut evidence for the upregulation of collagens and several extracellular matrix components that defined fibrotic remodeling of the skeletal muscle architecture as well as activation of the fibro-adipogenic precursors.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27113532" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73597" }, "primaryId" : "GEO:GSE73597", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73597" } ] }, "title" : "miRNA-99 family diverges physiological cardiac hypertrophy to pathological cardiac hypertrophy", "dateAssigned" : "2015-09-30T00:00:00.000-05:00", "summary" : "Conclusions: The results proved Egr-1 mediated regulation of miR-99 family determines the uniqueness of pathological and physiological hypertrophy. Upregulated miR-99 expression during pathological hypertrophy suggests that it can be a valuable diagnostic marker and potential therapeutic target for cardiac hypertrophy and heart failure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73598" }, "primaryId" : "GEO:GSE73598", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73598" } ] }, "title" : "Expression data from cardiac stem cells (CSCs) with or without MSC-exosomes treatment", "dateAssigned" : "2015-09-30T00:00:00.000-05:00", "summary" : "Cardiac resident c-kit+ cells aroused much interest among the cardiologists at the beginning of the century. These cells are selfrenewing, clonogenic, and multipotent and possess the potential to differentiate into all cardiovascular lineages. However, one of the critical problems faced by c-kit+ cells is the poor engraftment and survival after transplantation. Therefore, researchers are focusing on developing next generation CSC products that will enhance the engraftment, survival, and regenerative capabilities of these cells. Considering this, we made a proposal that cardiac stem cells preconditioned with exosomes derived from bone marrow mesenchymal stem cells could survive and function better in a myocardial infarction model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26811168" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73604" }, "primaryId" : "GEO:GSE73604", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73604" } ] }, "title" : "In utero exposure of rats to high-fat diets perturbs gene-expression profiles and cancer susceptibility of prepubertal mammary glands", "dateAssigned" : "2015-09-30T00:00:00.000-05:00", "summary" : "Human studies suggest that high-fat diets (HFD) increase the risk of breast cancer. The 7,12 dimethylbenz[a]anthracene (DMBA)-induced mammary carcinogenesis rat model is commonly used to evaluate the effects of lifestyle factors such as HFD on mammary-tumor risk. Past studies focused primarily on the effects of continuous maternal exposure on the risk of offspring at the end of puberty (PND50). We assessed the effects of prenatal HFD exposure on cancer susceptibility in prepubertal mammary glands and identified key gene networks associated with such disruption. During pregnancy, dams were fed AIN93G-based diets with high (39% Kcal) olive oil, butterfat, or safflower oil. The control group received AIN-93G with 10% Kcal soy oil. Female offspring were treated with DMBA on PND21. However, a significant increase in tumor volume and a trend of shortened tumor latency were observed in rates with HFD exposure against the controls (p=0.067 and 0.048 respectively). Large-volume tumors harbored carcinoma in situ. Transcriptome profiling identified 43 differentially expressed genes in the mammary glands of the HFD group as compared with control. Rapid hormone signaling was the most dysregulated pathway. The diet also induced aberrant expression of Dnmt3a, Mbd1, and Mbd3, suggesting potential epigenetic disruption. Collectively, these findings provide the first evidence supporting susceptibility of prepubertal mammary glands to DMBA-induced tumorigenesis that can be modulated by dietary fat that involves aberrant gene expression and epigenetic dysregulation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73605" }, "primaryId" : "GEO:GSE73605", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73605" } ] }, "title" : "Effects of low-doses of antiandrogenic substances on Wistar Rat testes [miRNome analysis]", "dateAssigned" : "2015-09-30T00:00:00.000-05:00", "summary" : "Three antiandrogenic substances (Flutamide, Prochloraz, Vinclozolin) were administered in aqueous preparations at 3 doses: i) Acceptable Daily Intake (ADI) ; ii) No Observed Adverse Effect Level (NOAEL) ; iii) Low Observed Adverse Effect Level (LOAEL) . Pregnant females (20/group) were treated by gavage from gestation day (GD) 6 until postnatal (PND) day 21. After weaning, the offspring received the same test-substance as their mothers by oral gavage. Twenty males were selected to be raised until the weaning (Subset 1, PND 21), the day of sexual maturation (Subset 2, puberty) or early adulthood (Subset 3, PND 83±2). At each subset, testes were used for transcriptome and miRNome analyses.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73606" }, "primaryId" : "GEO:GSE73606", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73606" } ] }, "title" : "Effects of low-doses of antiandrogenic substances on Wistar Rat testes [Transcriptome analysis]", "dateAssigned" : "2015-09-30T00:00:00.000-05:00", "summary" : "Three antiandrogenic substances (Flutamide, Prochloraz, Vinclozolin) were administered in aqueous preparations at 3 doses: i) Acceptable Daily Intake (ADI) ; ii) No Observed Adverse Effect Level (NOAEL) ; iii) Low Observed Adverse Effect Level (LOAEL) . Pregnant females (20/group) were treated by gavage from gestation day (GD) 6 until postnatal (PND) day 21. After weaning, the offspring received the same test-substance as their mothers by oral gavage. Twenty males were selected to be raised until the weaning (Subset 1, PND 21), the day of sexual maturation (Subset 2, puberty) or early adulthood (Subset 3, PND 83±2). At each subset, testes were used for transcriptome and miRNome analyses.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73627" }, "primaryId" : "GEO:GSE73627", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73627" } ] }, "title" : "Genome-wide analysis of nucleus accumbens gene expression after ethanol consumption in rat ", "dateAssigned" : "2015-09-30T00:00:00.000-05:00", "summary" : "Keywords: RNAseq, Gene expression profiles, Ethanol consumption, Rat.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73786" }, "primaryId" : "GEO:GSE73786", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73786" } ] }, "title" : "piRNA expression in rat ovary", "dateAssigned" : "2015-10-06T00:00:00.000-05:00", "summary" : "Conclusions: Large number of piRNAs are expressed in rat ovary", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73848" }, "primaryId" : "GEO:GSE73848", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73848" } ] }, "title" : "Expression data from intestinal mucosa of Zucker rats", "dateAssigned" : "2015-10-08T00:00:00.000-05:00", "summary" : "We used microarrays to investigate the global gene expression on intestinal mucosa after the treatment with probiotic strains.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28512356" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73884" }, "primaryId" : "GEO:GSE73884", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73884" } ] }, "title" : "Transcriptome analysis of liver and kidneys of rats chronically fed a NK603 Roundup-tolerant genetically modified maize [kidney]", "dateAssigned" : "2015-10-09T00:00:00.000-05:00", "summary" : "We used microarrays to detail the alterations in gene expression profiles associated with the consumption of a Roundup-tolerant genetically modified maize (NK603) sprayed or unsprayed with a Roundup herbicide from these same animals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73886" }, "primaryId" : "GEO:GSE73886", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73886" } ] }, "title" : "Transcriptome analysis of liver and kidneys of rats chronically fed a NK603 Roundup-tolerant genetically modified maize [liver]", "dateAssigned" : "2015-10-09T00:00:00.000-05:00", "summary" : "We used microarrays to detail the alterations in gene expression profiles associated with the consumption of a Roundup-tolerant genetically modified maize (NK603) sprayed or unsprayed with a Roundup herbicide from these same animals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73896" }, "primaryId" : "GEO:GSE73896", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73896" } ] }, "title" : "Hypertrophy induced KIF5B controls mitochondrial localization and function in neonatal rat cardiomyocytes", "dateAssigned" : "2015-10-09T00:00:00.000-05:00", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27094714" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73910" }, "primaryId" : "GEO:GSE73910", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73910" } ] }, "title" : "RNAome Modulation in Lung During Metabolic Syndrome in a Rat Model", "dateAssigned" : "2015-10-11T00:00:00.000-05:00", "summary" : "There is evidence that suggests that MetS is a condition that increases the risk of different lung diseases. It have been reported in some MetS patients a diminished lung function, as assessed by spirometry, in addition, there is an association with insulin resistance, increase in body mass index; abdominal obesity and systemic inflammation (high levels of C reactive protein) [4-6]. In other cases, like asthma, some components of MetS such as abdominal obesity, hypertension and pro-inflammatory cytokines have been with related with this disease [7-9]. Also, a few clinical studies reported that abdominal obesity, hyperglycemia and elevated levels of systemic inflammatory markers, which are components of MetS, were significantly more prevalent in patients with chronic obstructive pulmonary disease [10-13]. In the present work we evaluated the transcriptomic changes of lung tissue in an animal model of MetS induced by diet.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73955" }, "primaryId" : "GEO:GSE73955", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE73955" } ] }, "title" : "Comparison of Gene expression profiling of granulosa cells treated with follicle stimulating hormone or constitutively active protein kinase A", "dateAssigned" : "2015-10-13T00:00:00.000-05:00", "summary" : "PKA activation by FSH is essential to transduce FSH-mediated effects on granulosa cell proliferation, differentiation and steroidogenesis. However, It is unknown whether activation of PKA is sufficient to account for the entire program of granulosa cell responses to FSH. We addressed this question by conducting a comprehensive comparative analysis of signaling pathways and gene expression profiles of granulosa cells stimulated with FSH or expressing a constitutively active PKA mutant, PKA-CQR.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27324437" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74145" }, "primaryId" : "GEO:GSE74145", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74145" } ] }, "title" : "Intermittent neonatal hypoxia elicits the upregulation of inflammatory-related genes in the adult rat through long-lasting programming effects", "dateAssigned" : "2015-10-19T00:00:00.000-05:00", "summary" : "Apnea is the most common cause of neonatal hypoxia affecting about 50% of preterm births (30 – 31 weeks), usually due to immature respiratory development. Upregulation of inflammatory genes and pathways in children 7 – 10 years of age has been shown, and there is a known increased risk of insulin resistance in adulthood when the fetus is exposed to maternal hypoxia, but the mechanism is unclear. The long-term metabolic, endocrine, and immunological effects of neonatal intermittent hypoxia (IH) exposure, an accepted model of apnea-induced hypoxia, have not been thoroughly evaluated. Recent studies in rats have shown that perinatal IH exposure can result in oxidative stress, causing a permanent immune response subsequently resulting in features of diabetes mellitus. We have previously examined adult rats exposed to neonatal intermittent hypoxia and perinatal continuous hypoxia, and have found lasting “programming” effects on the HPA axis. We now assess the long term effects of an accepted model of apnea-induced hypoxia using a validated transcriptional bioassay to study the extracellular milieu of adult rats exposed to neonatal intermittent hypoxia. We hypothesize that exposure to neonatal intermittent hypoxia will result in an increased inflammatory state in the adult as a result of long-lasting programming.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26660555" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74150" }, "primaryId" : "GEO:GSE74150", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74150" } ] }, "title" : "Changes in the gene expression in the inferior colliculus of the sound stimulated rats both Wistar and the strain susceptible to audiogenic seizures WAR", "dateAssigned" : "2015-10-19T00:00:00.000-05:00", "summary" : "Genetic animal models of epilepsy are an important tool for further understanding the basic cellular mechanisms underlying epileptogenesis and for developing novel antiepileptic drugs. We conducted a comparative study of gene expression in the inferior colliculus, a nucleus that triggers audiogenic seizures, using two animal models, the Wistar audiogenic rat (WAR) and the genetic audiogenic seizure hamster (GASH:Sal). For this purpose, both models were subjected to auditory stimulation, and 60 minutes after stimulation, the inferior colliculi were collected. As a control, intact Wistar rats and Syrian hamsters were subjected to identical stimulation and tissue preparation protocols to those performed on the experimental animals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74185" }, "primaryId" : "GEO:GSE74185", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74185" } ] }, "title" : "MBNL1-mediated Regulation of Differentiation RNAs Promotes Myofibroblast Transformation and the Fibrotic Response", "dateAssigned" : "2015-10-20T00:00:00.000-05:00", "summary" : "The differentiation of fibroblasts into myofibroblasts mediates tissue wound healing and fibrotic remodeling. To better understand this process we performed a genome-wide screen in fibroblasts, which identified the RNA-binding protein muscleblind-like 1 (MBNL1) as a potent regulator of myofibroblast differentiation. MBNL1 promoted transformation of fibroblasts into myofibroblasts, while loss of Mbnl1 abrogated myofibroblast differentiation and impaired the fibrotic phase of wound healing in mouse models of myocardial infarction and dermal injury. Conditional fibroblast-specific MBNL1 transgenic mice showed a fibrotic phenotype in the absence of injury. Mechanistically, MBNL1 directly bound to and regulated the alternative splicing and stability of a network of myofibroblast differentiation specific genes, such as the nodal transcriptional regulator serum response factor (SRF). CRISPR-Cas9 mediated gene editing of the MBNL1 binding site in Srf impaired myofibroblast differentiation. These data establish a new RNA-dependent paradigm through MBNL1 that underlies global myofibroblast differentiation, the fibrotic response, and tissue wound healing.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74205" }, "primaryId" : "GEO:GSE74205", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74205" } ] }, "title" : "microRNA data in cardiomyocytes isolated from rat at 1 versus 10 day of age", "dateAssigned" : "2015-10-20T00:00:00.000-05:00", "summary" : "This study was to identify microRNAs responsible for postnatal cardiomyocyte proliferation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29053138" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74221" }, "primaryId" : "GEO:GSE74221", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74221" } ] }, "title" : "TGF-beta, COUP-TFII, and Gli1/Zic transcription factor dynamics revealed in Retinoic acid induced Neural Tube Defect", "dateAssigned" : "2015-10-20T00:00:00.000-05:00", "summary" : "The morphologic changes of neuroepithelial cells, and their interactions with surrounding cells, are fundamental to primary neurulation and are a function of several timed signaling gradients. Retinoic acid administration at fetal day E10 induces neural tube defects in 84.2% of rat pups. Negative selection using A2B5 and E-NCAM has been validated for isolation of neuroepithelial cells for culture. Here we report the isolation and analysis of the fundamental actors in primary neurulation by flow cytometry with CD147 positive selection followed by whole transcriptome analysis of this purified population via microarray enhanced with the ERCC RNA internal controls. Comparison of the gene expression in Retinoic acid exposed versus wild-type isolates shows excellent correspondence to known neural tube defect genes. Analysis of transcription factor binding sites in regulatory regions of differentially expressed genes, implicates a binding site “cross-roads” where improper signaling through a multitude of pathways could potentially elicit neural tube defects.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74273" }, "primaryId" : "GEO:GSE74273", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74273" } ] }, "title" : "Novel Comparative Pattern Count Analysis Reveals a Chronic Ethanol Induced Dynamic Shift In NF-¿B Genome-wide Promoter Binding During Liver Regeneration", "dateAssigned" : "2015-10-22T00:00:00.000-05:00", "summary" : "We analyzed the effect of chronic alcohol intake on the genome-wide binding activity of NF-¿B during the initial response phase following partial hepatectomy. We analyzed the data in the adapted state as well as in response to partial hepatectomy, using chromatin immunoprecipitation followed by promoter microarray analysis. We found several ethanol-specific NF-¿B binding target promoters in the chronic adapted state.. Partial hepatectomy induced a diet-independent shift in NF-¿B binding loci relative to the transcription start sites. We employed a novel pattern count analysis to exhaustively enumerate and compare the number of promoters corresponding to the temporal binding patterns between ethanol and isocaloric pair-fed control groups. We found that NF-¿B bound genes govern negative regulation of cell growth and inflammatory response immediately following hepatectomy. We, integrated the ChIP-chip results with a time series gene expression data set to identify the NF-¿B promoter binding targets that showed differential gene expression changes at the baseline-adapted condition as well as after PHx. We identified a set of differential patterns of NF-¿B binding that were specific to the ethanol and pair-fed control groups. We found the regulatory pathways and co-incident transcription factor binding motifs corresponding some of the key comparative-binding patterns.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74288" }, "primaryId" : "GEO:GSE74288", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74288" } ] }, "title" : "Gene expression in the mesenteric arteries of SHR and SHRSP compared with WKYs treated with 2K1C or 1K1C, or without operation for 3 weeks at 6 weeks of age", "dateAssigned" : "2015-10-22T00:00:00.000-05:00", "summary" : "We examined gene expression profiles in the rat mesenteric arteries using genome-wide microarray technology, and determined gene expression profiles in 3 rat strains and treated ones: spontaneously hypertensive rats (SHR), stroke-prone SHR (SHRSP), and normotensive WKYs treated with 2K1C or 1K1C, or without operation for 3 weeks at 6 weeks of age. To identify candidate genes involved in the genesis of hypertension in the SHR strains in comparison to renal hypertensive WKY, we compared the gene expression levels at 6 weeks of age, isolated genes showing a more than 4-fold increase or a less than 1/4-fold compared with WKY treated with 2K1C, 1K1C or none.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30882592" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74327" }, "primaryId" : "GEO:GSE74327", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74327" } ] }, "title" : "Boolean modeling reveals the necessity of transcriptional regulation for bistablity in PC12 Cell Differentiation", "dateAssigned" : "2015-10-23T00:00:00.000-05:00", "summary" : "The nerve growth factor NGF has been shown to cause cell fate decisions towards either differentiation or proliferation depending on the relative activity of downstream pERK, pAKT or pJNK signaling. However, how these protein signals are translated into and fed back from transcriptional activity to complete cellular differentiation over a time span of hours to days is still an open question. Using dynamic proteome and transcriptome data from NGF-stimulated PC12 cells over a time span of 24 hours we inferred a dynamic Boolean model capturing the temporal sequence of protein signaling, transcriptional response and subsequent autocrine feedback. Optimal model topology was achieved by introducing multiple time scales for fast cellular signaling and slower gene response and subsequent fitting to the experimental data. The integrated model confirmed the parallel use of MEK/ERK, AKT/PI3K and JNK/JUN for PC12 cell differentiation. Redundancy of cell signaling is demonstrated from the inhibition of the different MAPK pathways. As suggested in silico and confirmed in vitro, differentiation was substantially suppressed under JNK/JUN inhibition, yet delayed only under MEK/ERK inhibition. Most importantly, we found that sustained transcriptional feedback is necessary to induce bistability in the cell fate switch. De novo Gene expression was necessary to activate autocrine feedback that caused integrin signaling to perpetuate the MAPK activity, finally resulting in the expression of late, differentiation related genes. Thus, the cellular decision towards differentiation depends on the establishment of a transcriptome-induced positive feedback between protein signaling and gene expression thereby constituting a robust control between proliferation and differentiation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27148350" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74382" }, "primaryId" : "GEO:GSE74382", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74382" } ] }, "title" : "Pramipexole induced place preference promoted after L-dopa therapy and nigral dopaminergic loss: linking behavior to transcriptional modifications", "dateAssigned" : "2015-10-27T00:00:00.000-05:00", "summary" : "To this end, the reinforcing properties of the D2/D3 agonist pramipexole (PPX) were assessed after chronic exposure to L-dopa in an alpha-synuclein PD rat model.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74424" }, "primaryId" : "GEO:GSE74424", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74424" } ] }, "title" : "Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models", "dateAssigned" : "2015-10-28T00:00:00.000-05:00", "summary" : "In this study, genome-wide gene expression profiles of primary hepatocytes and liver sinusoidal endothelial cells (LSECs) were measured at day 12 for each cell culture system using Affymetrix GeneChips and analyzed via Gene Set Enrichment Analysis (GSEA). The culture systems analyzed include the commonly used collagen sandwich and monolayers of hepatocytes, as well as 3-dimensional (3D) engineered liver models that contain hepatocytes and LSECs (3DHL) and hepatocytes, LSECs, and Kupffer cells (3DHLK). Our results highlight the up-regulation of several hepatocyte specific functions in hepatocytes and a novel interplay between Ppara signaling and bile acid biosynthesis in LSECs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30054499" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74532" }, "primaryId" : "GEO:GSE74532", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74532" } ] }, "title" : "CGH analysis of allodiploid embryonic stem cells", "dateAssigned" : "2015-10-30T00:00:00.000-05:00", "summary" : "We performed array comparative genomic hybridization (aCGH) for our hybrid cells. All two analyzed hybrid ES cell liness were chromosomally stable.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26771496" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74533" }, "primaryId" : "GEO:GSE74533", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74533" } ] }, "title" : "Gene expression data of allodiploid embryonic stem cells.", "dateAssigned" : "2015-10-30T00:00:00.000-05:00", "summary" : "RNA-Seq was used to assess the gene expression profiles of 4 allodiploid embryonic stem cell lines and 4 control embryonic stem cell lines. Moreover, single-cell RNA-Seq was used to quantify the transcriptomes of 87 allodiploid single cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26771496" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74546" }, "primaryId" : "GEO:GSE74546", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74546" } ] }, "title" : "Expression data of genes from the gustatory cortex follwing novel taste learning", "dateAssigned" : "2015-10-30T00:00:00.000-05:00", "summary" : "We used microarray for identification of genes involved in novel taste learning at two time points- 1 and 3 hours following memory formation for novel taste", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26856319" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74676" }, "primaryId" : "GEO:GSE74676", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74676" } ] }, "title" : "Toxicogenomic Characterization of Molecular Mechanisms Contributing to Chlorpyrifos Neurotoxicity in Adult Male Rats [microarray]", "dateAssigned" : "2015-11-04T00:00:00.000-06:00", "summary" : "Chlorpyrifos (CPF) is an organophosphorus pesticide (OP), and one of the most widely used pesticides in the world. Metabolites of CPF and other OPs continue to be identified in the majority of human samples, even in countries such as the United States where OP use is declining (Arcury et al., 2010). The effects of repeated occupational and environmental exposures to OPs are poorly understood, although human and animal studies consistently identify neurotoxicity as the primary endpoint of concern. Thus, occupational exposures to sublethal doses of CPF are consistently associated with problems in cognitive abilities, such as learning and memory but the biological mechanism(s) underlying this association remain speculative. To identify potential mechanisms of CPF neurotoxicity, we employed a rat model that simulated documented CPF exposures in Egyptian agricultural workers. We quantified mRNA expression profiles in the CA1 region of the hippocampus of adult male Long Evans (LE) rats administered CPF at 3 or 10 mg/kg/d (s.c.) for 21 days. Despite significant inhibition of cholinesterase activity by the end of the 21 d exposure period, the CPF-exposed rats displayed minimal signs of cholinergic toxicity. Distinct hippocampal mRNA and miRNA signatures were associated with CPF exposure. Toxicogenomics-based evidence identified increased expression of neuropeptide genes in the hippocampi of CPF-exposed rats, which have been shown to activate receptor-mediated signaling pathways involved in cell survival. The analysis of small non-coding RNA profiles suggested the possibility that miR132/212-mediated homeostatic regulatory pathways may also be activated by repeated exposures to CPF. These findings identify potential molecular effects that may contribute to neurobehavioral deficits.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74726" }, "primaryId" : "GEO:GSE74726", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74726" } ] }, "title" : "Toxicogenomic Characterization of Molecular Mechanisms Contributing to Chlorpyrifos Neurotoxicity in Adult Male Rats [RNA-seq]", "dateAssigned" : "2015-11-05T00:00:00.000-06:00", "summary" : "Chlorpyrifos (CPF) is an organophosphorus pesticide (OP), and one of the most widely used pesticides in the world. Metabolites of CPF and other OPs continue to be identified in the majority of human samples, even in countries such as the United States where OP use is declining (Arcury et al., 2010). The effects of repeated occupational and environmental exposures to OPs are poorly understood, although human and animal studies consistently identify neurotoxicity as the primary endpoint of concern. Thus, occupational exposures to sublethal doses of CPF are consistently associated with problems in cognitive abilities, such as learning and memory but the biological mechanism(s) underlying this association remain speculative. To identify potential mechanisms of CPF neurotoxicity, we employed a rat model that simulated documented CPF exposures in Egyptian agricultural workers. We quantified mRNA expression profiles in the CA1 region of the hippocampus of adult male Long Evans (LE) rats administered CPF at 3 or 10 mg/kg/d (s.c.) for 21 days. Despite significant inhibition of cholinesterase activity by the end of the 21 d exposure period, the CPF-exposed rats displayed minimal signs of cholinergic toxicity. Distinct hippocampal mRNA and miRNA signatures were associated with CPF exposure. Toxicogenomics-based evidence identified increased expression of neuropeptide genes in the hippocampi of CPF-exposed rats, which have been shown to activate receptor-mediated signaling pathways involved in cell survival. The analysis of small non-coding RNA profiles suggested the possibility that miR132/212-mediated homeostatic regulatory pathways may also be activated by repeated exposures to CPF. These findings identify potential molecular effects that may contribute to neurobehavioral deficits.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74727" }, "primaryId" : "GEO:GSE74727", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74727" } ] }, "title" : "Toxicogenomic Characterization of Molecular Mechanisms Contributing to Chlorpyrifos Neurotoxicity in Adult Male Rats [smallRNA-seq]", "dateAssigned" : "2015-11-05T00:00:00.000-06:00", "summary" : "Chlorpyrifos (CPF) is an organophosphorus pesticide (OP), and one of the most widely used pesticides in the world. Metabolites of CPF and other OPs continue to be identified in the majority of human samples, even in countries such as the United States where OP use is declining (Arcury et al., 2010). The effects of repeated occupational and environmental exposures to OPs are poorly understood, although human and animal studies consistently identify neurotoxicity as the primary endpoint of concern. Thus, occupational exposures to sublethal doses of CPF are consistently associated with problems in cognitive abilities, such as learning and memory but the biological mechanism(s) underlying this association remain speculative. To identify potential mechanisms of CPF neurotoxicity, we employed a rat model that simulated documented CPF exposures in Egyptian agricultural workers. We quantified mRNA expression profiles in the CA1 region of the hippocampus of adult male Long Evans (LE) rats administered CPF at 3 or 10 mg/kg/d (s.c.) for 21 days. Despite significant inhibition of cholinesterase activity by the end of the 21 d exposure period, the CPF-exposed rats displayed minimal signs of cholinergic toxicity. Distinct hippocampal mRNA and miRNA signatures were associated with CPF exposure. Toxicogenomics-based evidence identified increased expression of neuropeptide genes in the hippocampi of CPF-exposed rats, which have been shown to activate receptor-mediated signaling pathways involved in cell survival. The analysis of small non-coding RNA profiles suggested the possibility that miR132/212-mediated homeostatic regulatory pathways may also be activated by repeated exposures to CPF. These findings identify potential molecular effects that may contribute to neurobehavioral deficits.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74748" }, "primaryId" : "GEO:GSE74748", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74748" } ] }, "title" : "Effect of Cited2 knockdown on global transcript expression in Rcho-1 cell differentiation", "dateAssigned" : "2015-11-06T00:00:00.000-06:00", "summary" : "We had previously discovered that the transcription factor Cited2 was highly induced during trophoblast differentiation. In this study, we used an lentiviral shRNA strategy to decrease Cited2 expression in Rcho-1 trophoblast cells. A RNA-seq approach was used to determine global transcript differences inRcho-1 knockdown cells compared to control cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26917451" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74755" }, "primaryId" : "GEO:GSE74755", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74755" } ] }, "title" : "mRNA expression profile in vascular smooth muscle cells (VSMCs) after inducing calcification", "dateAssigned" : "2015-11-06T00:00:00.000-06:00", "summary" : "Vascular calcification (VC) is often associated with cardiovascular and metabolic diseases. However, the molecular mechanisms linking VC to these diseases have yet to be elucidated. Here we report that MDM2-induced polyubiquitination of histone deacetylase 1 (HDAC1) mediates VC. Loss of HDAC1 activity via either chemical inhibitor or genetic ablation enhanced VC. HDAC1 protein, but not mRNA, was reduced in cell and animal calcification models and in human calcified coronary artery. In the calcification-provoking condition, proteasomal degradation of HDAC1 preceded VC. The calcification-provoking condition induced MDM2 E3 ligase, which then resulted in HDAC1 K74 polyubiquitination. Overexpression of MDM2 enhanced VC, whereas loss of MDM2 blunted it. Decoy peptides spanning HDAC1 K74 and RG 7112, an MDM2 inhibitor, prevented VC in vivo and in vitro. These results demonstrate a previously unknown ubiquitination pathway and suggest MDM2-mediated HDAC1 polyubiquitination as a new therapeutic target in VC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26832969" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74898" }, "primaryId" : "GEO:GSE74898", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74898" } ] }, "title" : "Exercise dependent gene regulation in cartilage", "dateAssigned" : "2015-11-10T00:00:00.000-06:00", "summary" : "Conclusions. Our findings highlight that exercise is a robust transcriptional regulator of a wide array of genes in the healthy cartilage. The actions of exercise collectively regulate metabolic pathways that are critical for strengthening cartilage while attenuating detrimental effects of proteolytic enzymes and inflammatory pathways to provide prophylaxis against inflammatory joint diseases.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74903" }, "primaryId" : "GEO:GSE74903", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74903" } ] }, "title" : "Assessing concordance of drug-induced transcriptional response in rodent liver and cultured hepatocytes", "dateAssigned" : "2015-11-11T00:00:00.000-06:00", "summary" : "Gene expression studies in model systems are widely used for understanding the mechanism of drugs and other perturbations in biological systems. Other researchers have examined the reproducibility of microarray studies between laboratories, or comparing microarrays and/or RNA sequencing. However, no large scale studies have compared results from protocols which differ in minor details, or results generated in vivo vs. in vitro culture system thought to serve as useful models. The rat liver is by far the most extensively studied model evaluating effects of drugs and other perturbations, and existing data allowed us to assess the level of concordance between rat liver and rat primary hepatocytes cultured in collagen-coated plates (i.e. “flat” culture) for hundreds of drugs. We found that the mouse liver serves as a better model of the rat liver than do rat primary hepatocytes, even after allowing for differences due to pharmacokinetics. The low concordance observed between rat liver and rat hepatocytes suggests that validating the utility of ‘omics data generated on emerging cell culture approaches (e.g. “organ-on-a-chip”, 3D-printed tissues) using rat cells and comparison to the rat liver may be necessary in order to gain confidence these approaches substantially improve on traditional culture models of human cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27028627" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74976" }, "primaryId" : "GEO:GSE74976", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE74976" } ] }, "title" : "E16/E19 rat fetus microarray", "dateAssigned" : "2015-11-13T00:00:00.000-06:00", "summary" : "E19 samples were renamed as E18 samples in the relative manuscript", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75020" }, "primaryId" : "GEO:GSE75020", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75020" } ] }, "title" : "miRNA expression data of rat prostate cancer tissue treated with OBP-801, novel HDAC inhibitor", "dateAssigned" : "2015-11-15T00:00:00.000-06:00", "summary" : "miRNA expression was obtained from non-treated or OBP-801 treated TRAP rats which develop prostate cancer. The primary aim was to identify miRNAs which regulate prostate carcinogenesis induced by OBP-801.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27216188" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75021" }, "primaryId" : "GEO:GSE75021", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75021" } ] }, "title" : "Gene expression data of rat prostate cancer tissue treated with OBP-801, novel HDAC inhibitor", "dateAssigned" : "2015-11-15T00:00:00.000-06:00", "summary" : "Genome-wide gene expression was obtained from non-treated or OBP-801 treated TRAP rats which develop prostate cancer. The primary aim was to identify genes which regulate prostate carcinogenesis induced by OBP-801.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75079" }, "primaryId" : "GEO:GSE75079", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75079" } ] }, "title" : "Expression data from 3 week old Rat liver (F1)", "dateAssigned" : "2015-11-17T00:00:00.000-06:00", "summary" : "We used microarrays to detail the global program of gene expression underlying fatty acid liver and identified distinc distinct classes of up-regulated and down-regulated genes during this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75119" }, "primaryId" : "GEO:GSE75119", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75119" } ] }, "title" : "Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (TBI – MBD-seq)", "dateAssigned" : "2015-11-17T00:00:00.000-06:00", "summary" : "Explore DNA methylation in traumatic brain injury model of epilepsy and its relationship to gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27157830" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75120" }, "primaryId" : "GEO:GSE75120", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75120" } ] }, "title" : "Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (TBI – mRNA-seq)", "dateAssigned" : "2015-11-17T00:00:00.000-06:00", "summary" : "Explore DNA methylation in traumatic brain injury model of epilepsy and its relationship to gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27157830" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75148" }, "primaryId" : "GEO:GSE75148", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75148" } ] }, "title" : "Gene expression profiles in rat lung following intratracheal instillation with short size single-wall and multi-wall carbon nanotubes", "dateAssigned" : "2015-11-18T00:00:00.000-06:00", "summary" : "To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the transcriptional level, we have employed whole genome microarray expression profiling to discuss the differences of the pulmonary and pleural", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27259835" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75213" }, "primaryId" : "GEO:GSE75213", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75213" } ] }, "title" : "Cardiac Transcriptome Dynamics and MEF2 Function in Response to Chronic ß-Adrenergic Blockade During Heart Failure", "dateAssigned" : "2015-11-19T00:00:00.000-06:00", "summary" : "1) Profiling RNA expression in mice with surgically induced pressure overload (Transverase aortic contriction aka TAC) and/or Atenolol (AT) treated mice. 2)Profiling RNA expression in MEF2A depleted cardiomyocytes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75275" }, "primaryId" : "GEO:GSE75275", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75275" } ] }, "title" : "Effect of fipronil on the thyroid gland transcriptome in the rat", "dateAssigned" : "2015-11-20T00:00:00.000-06:00", "summary" : "Fipronil is a widely-used broad-spectrum phenylpyrazole insecticide. It has been shown that fipronil increases the hepatic metabolism of thyroid hormone in the rat, which may induce compensatory mechanisms at the level of the thyroid gland itself. Here, we studied the effect of fipronil on the transcriptome of the thyroid gland in the rat. Adult (2- to 3-month-old) female Wistar rats were treated per os with fipronil (3 mg/kg) or the vehicle alone for 14 days. The transcriptome of their thyroid gland was analyzed using Agilent 4x44K microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75280" }, "primaryId" : "GEO:GSE75280", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75280" } ] }, "title" : "Azoxymethane-induced colorectal tumorigenesis in hypertensive rat models", "dateAssigned" : "2015-11-21T00:00:00.000-06:00", "summary" : "To compare the tumor susceptibility between the hypertensive Dahl salt-sensitive rats (S) rat and S.LEW(10)x12x2x3x5 (S.LEW) congenic strain, one of the S.LEW congenic strains our laboratory previously constructed on rat chromosome 10 [Hypertension. 2007 Nov;50(5):891-8], Azoxymethane (AOM)-induced colon tumorigenesis in rats was assessed. At six weeks of age, both S and S.LEW congenic rats received intraperitoneal (IP) injection of AOM in sterial saline at a dose of 15mg/kg body weight once a week for two consecutive weeks. At 30 weeks of age, all the rats were euthanized through carbon dioxide inhalation. The colon tissue was harvested, dissected longitudinally, and washed with saline. The number and size of the colon tumors were recorded. We found that the total number of colon tumors was significantly higher in the S.LEW congenic strain compared with the S rat. To further study the genetic and molecular mechanisms causing the higher tumor susceptibility in the S.LEW congenic strain, we have employed the whole genome microarray expression profiling to identify genes and signaling pathways that are differential between the S and S.LEW congenic strain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27073989" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75400" }, "primaryId" : "GEO:GSE75400", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75400" } ] }, "title" : "Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (Amygdala stimulation – MBD-seq)", "dateAssigned" : "2015-11-25T00:00:00.000-06:00", "summary" : "Explore DNA methylation in focal amygdala stimulation model of epilepsy and its relationship to gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27157830" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75402" }, "primaryId" : "GEO:GSE75402", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75402" } ] }, "title" : "Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (Amygdala stimulation – mRNA-seq)", "dateAssigned" : "2015-11-25T00:00:00.000-06:00", "summary" : "Explore DNA methylation in focal amygdala stimulation model of epilepsy and its relationship to gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27157830" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75446" }, "primaryId" : "GEO:GSE75446", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75446" } ] }, "title" : "Testicular toxicity induced by carbendazim, iprodione, alone or in combination", "dateAssigned" : "2015-11-27T00:00:00.000-06:00", "summary" : "Using an ex-vivo testicular culture from rats, we carried out transcriptomic experiments to identify the pathway of toxicity ellicited by the fungicides carbendazim, iprodione alone or in combination. we used commercial Agilent Microarray GE 4x44K Rat (V3) Gene Expression Microarray (G2514F) AMADID : 028282", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27155993" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75458" }, "primaryId" : "GEO:GSE75458", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75458" } ] }, "title" : "MBD3 expression and DNA binding patterns are altered in a rat model of temporal lobe epilepsy", "dateAssigned" : "2015-11-29T00:00:00.000-06:00", "summary" : "Examine involvement of MBD3 (methyl-CpG-binding domain protein 3), a protein involved in reading DNA methylation patterns, in epileptogenesis and epilepsy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75488" }, "primaryId" : "GEO:GSE75488", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75488" } ] }, "title" : "Gene expression profiles of MBP-specific T cells during experimental autoimmune encephalomyelitis", "dateAssigned" : "2015-11-30T00:00:00.000-06:00", "summary" : "2nd generation sequencing was used to compare expression profiles of MBP-specific T cells retrieved from blood, CSF, spinal cord meninges and parenchyma. The overall expression profiles were found to be very similar.However, genes regulated during T cell activation were found to be upregulated in T cells from spinal cord meninges and parenchyma compared to blood and CSF.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26863192" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75541" }, "primaryId" : "GEO:GSE75541", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75541" } ] }, "title" : "Analysis of altered miRNA expression profiles in the genetic hypercalciuric stone-forming (GHS) rat compared to normal SD rat", "dateAssigned" : "2015-12-01T00:00:00.000-06:00", "summary" : "Urolithiasis is a common disease to human beings, and idiopathic hypercalciuria (IH) is an important risk factor of calcium urolithiasis, previous studies strongly suggested that the decreased tubular Ca2+ reabsorption played a key role of hypercalciuria. However,the molecular mechanism of IH-urolithiasis formation is still not completely elucidated. GHS rat is regarded as an ideal animal model of calcium urolithiasis, reveals many identical pathophysiologic characteristics with IH patients . We analyzed miRNA expression profiles of the kidney of GHS rat in order to find out the target genes and signaling pathways in the pathogenesis of IH.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27069814" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75542" }, "primaryId" : "GEO:GSE75542", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75542" } ] }, "title" : "Analysis of altered mRNA expression profiles in the genetic hypercalciuric stone-forming (GHS) rat compared to normal SD rat", "dateAssigned" : "2015-12-01T00:00:00.000-06:00", "summary" : "Urolithiasis is a common desease to human beings, and idiopathic hypercalciuria (IH) is an important risk factor of calcium urolithiasis, previous studies strongly suggested that the decreased tubular Ca2+ reabsorption played a key role of hypercalciuria. However,the molecular mechanism of IH-urolithiasis formation is still not completely elucidated. GHS rat is regarded as an ideal animal model of calcium urolithiasis, reveals many identical pathophysiologic characteristics with IH patients . We analyzed mRNA expression profiles of the kidney of GHS rat in order to find out the target genes and signaling pathways in the pathogenesis of IH.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27069814" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75578" }, "primaryId" : "GEO:GSE75578", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75578" } ] }, "title" : "Expression data from the kidney tissue of Han:SPRD rats", "dateAssigned" : "2015-12-01T00:00:00.000-06:00", "summary" : "We used microarrays to examine alterations in the renal gene expression in a rodent model of PKD, namely the Han:SPRD rat.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75629" }, "primaryId" : "GEO:GSE75629", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75629" } ] }, "title" : "Expression data from rat skeletal muscle", "dateAssigned" : "2015-12-02T00:00:00.000-06:00", "summary" : "We extracted skeletal muscle RNA from a total of 48 female animals (n=6 in each of the 8 group). Skeletal muscle tissue was obtained from theExtensor digitorum longus(EDL). All rats were dissected immediately after sacrificing, and all tissue samples were immediately weighed and snap frozen in liquid nitrogen, and stored at -80 ºC. Total RNA was extracted from frozen tissue with Trizol reagent (Invitrogen, Carlsbad, CA), treated with DNase-free (Invitrogen, Carlsbad, CA) and cleaned up with RNeasy columns (Qiagen, Hilden, Germany)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27637250" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75655" }, "primaryId" : "GEO:GSE75655", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75655" } ] }, "title" : "5-Day Gavage Study of Crude 4-Methylcyclohexanemethanol in Male Harlan Sprague Dawley Rats", "dateAssigned" : "2015-12-03T00:00:00.000-06:00", "summary" : "The goal of this study was to characterize the potential toxicity and genomic benchmark dose of crude 4-methylcyclohexylmethanol in liver and kidney of male Harlan Sprague Dawley rats using a 5 day dose-response toxicogenomics study design. The 5 day study is used to quickly identify the dose levels where changes in molecular pathways occur. These dose level where pathway level effects begin to occur have been shown to provide a close approximation of a no effect dose level from more resource intensive guideline toxicological assessments.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75656" }, "primaryId" : "GEO:GSE75656", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75656" } ] }, "title" : "5-Day Gavage Study of Propylene glycol phenyl ether (PPH; CASRN 770-35-4) in Male Harlan Sprague Dawley Rats", "dateAssigned" : "2015-12-03T00:00:00.000-06:00", "summary" : "The goal of this study was to characterize the potential toxicity and genomic benchmark dose of propylene glycol phenyl etherl in liver and kidney of male Harlan Sprague Dawley rats using a 5 day dose-response toxicogenomics study design. The 5 day study is used to quickly identify the dose levels where changes in molecular pathways occur. These dose level where pathway level effects begin to occur have been shown to provide a close approximation of a no effect dose level from more resource intensive guideline toxicological assessments.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75657" }, "primaryId" : "GEO:GSE75657", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75657" } ] }, "title" : "5-Day Gavage Study of 4-Methylcyclohexanemethanol (CASRN: 34885-03-5) in Male Harlan Sprague Dawley Rats", "dateAssigned" : "2015-12-03T00:00:00.000-06:00", "summary" : "The goal of this study was to characterize the potential toxicity and genomic benchmark dose of 4-methylcyclohexylmethanol in liver and kidney of male Harlan Sprague Dawley rats using a 5 day dose-response toxicogenomics study design. The 5 day study is used to quickly identify the dose levels where changes in molecular pathways occur. These dose level where pathway level effects begin to occur have been shown to provide a close approximation of a no effect dose level from more resource intensive guideline toxicological assessments.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75677" }, "primaryId" : "GEO:GSE75677", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75677" } ] }, "title" : "Comparison of Liver Tumor Models to Regenerating Liver Tissues", "dateAssigned" : "2015-12-03T00:00:00.000-06:00", "summary" : "To identify genes and pathways sepcific to tumorigenesis, we harvested tissues from two different liver tumor models as well as regenerating tissues. Genes significantly different in the two tumor models, but not in regenerating tissues, were used for further investigation", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75772" }, "primaryId" : "GEO:GSE75772", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75772" } ] }, "title" : "Transcription Profile of Aging and Cognition-Related Genes in the Medial Prefrontal Cortex.", "dateAssigned" : "2015-12-07T00:00:00.000-06:00", "summary" : "The results indicate regional differences in vulnerability to aging associated with increased expression of immune and defense response genes and a decline in synaptic and neural activity genes. Importantly, we provide evidence for region specific transcription related to behavior. In particular, expression of transcriptional regulators and neural activity-related immediate-early genes (IEGs) are increased in the mPFC of aged animals that exhibit delayed set shift behavior; relative to age-matched animals that exhibit set shift behavior similar to younger animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27242522" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75781" }, "primaryId" : "GEO:GSE75781", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75781" } ] }, "title" : "Endurance training in early life results in long-term programming of heart mass in rats", "dateAssigned" : "2015-12-08T00:00:00.000-06:00", "summary" : "We investigated the molecular pathways using microarray analysis to explain how endurance exercise in early life might be regulating the sustained increase in heart mass we have observed in these rats in adulthood. At 5 weeks of age, male WKY rats were allocated to one of the following exercise treatments: remained sedentary with post mortem (PM) at 9 or 24 weeks, early exercise training (from 5-9 weeks of age) with PM at 9 or 24 weeks, or later exercise training (from 20-24 weeks of age) with PM at 24 weeks (n=8 males/group). Exercise training involved treadmill running 5 days/ week for 4 weeks. Running duration progressively increased from 20 up to 60 minutes per day, with the treadmill speed set at 15 m/min for the first week and 20 m/min thereafter. At 9 or 24 weeks of age rats were killed with an intraperitoneal injection of Ilium Xylazil-20 (30 mg/kg) and Ketamine (225 mg/kg). The rats in the 9 week old early exercise and 24 week old later exercise groups were killed 72 hours following the last bout of treadmill running. Total RNA was obtained from the whole-hearts for analysis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75806" }, "primaryId" : "GEO:GSE75806", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE75806" } ] }, "title" : "miRNA expression data from neonatal rat ventricular myocytes (NRVM) silenced for KChIP2", "dateAssigned" : "2015-12-08T00:00:00.000-06:00", "summary" : "Loss of KChIP2 during cardiac stress has been suggested to have a transcriptional impact on cardiac ion channels through altered miRNA activity, contributing to maladaptive electrical remodeling. Therefore, we tested the consequence of KChIP2 loss, in the absence of cardiac stress, by treating cultured neonatal rat ventricular myocytes with siRNA for KChIP2 and subsequently performed miRNA microarray analysis to identify up-regulation of potential miRNA targets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28263709" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76002" }, "primaryId" : "GEO:GSE76002", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76002" } ] }, "title" : "Maternal Obesity is Associated with Ovarian Inflammation and Up-regulation of Early Growth Response Factor (Egr)-1", "dateAssigned" : "2015-12-14T00:00:00.000-06:00", "summary" : "Maternal obesity during the pre-implantation period leads to a pro-inflammatory milieu in the ovaries. We conducted a global transcriptomic profiling in ovaries from TEN fed rats during the pre-implantation period. Microarray analysis revealed that obesity lead to increased expression of genes related to inflammation, decreased glucose transporters, and dysregulation of ovarian function-related genes in the ovaries. Our results suggest maternal obesity led to an up-regulation of inflammatory genes and Egr-1 protien expression in peri-implantation ovarian tissue, and a concurrent down-regulation of glucose transporters mRNA and AKT and PI3K protein levels.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27279249" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76012" }, "primaryId" : "GEO:GSE76012", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76012" } ] }, "title" : "5-HT2A and 5-HT2C receptors as hypothalamic targets of developmental programming in male rats", "dateAssigned" : "2015-12-15T00:00:00.000-06:00", "summary" : "Though obesity is a global epidemic, the physiological mechanisms involved are little understood. Recent advances reveal that susceptibility to obesity can be programmed by maternal and neonatal nutrition. Specifically, a maternal low protein diet during pregnancy causes decreased intrauterine growth, rapid postnatal catch-up growth and increased risk for diet-induced obesity. Given that the synthesis of the neurotransmitter 5-hydroxytryptamine (5-HT) is nutritionally regulated and 5-HT is a trophic factor, we hypothesized that maternal diet influences fetal 5-HT exposure, which then influences central appetite network development and the subsequent efficacy of 5-HT to control energy balance in later life. Consistent with our hypothesis, pregnant low protein fed rat mothers exhibited elevated serum 5-HT, which was also evident in the placenta and fetal brains at E16.5. This increase was associated with reduced hypothalamic expression of 5-HT2CR - the primary 5-HT receptor influencing appetite. As expected, reduced 5-HT2CR expression was associated with impaired sensitivity to 5-HT-mediated appetite suppression. 5-HT primarily achieves effects on appetite via 5-HT2CR stimulation of pro-opiomelanocortin (POMC) peptides within the arcuate nucleus of the hypothalamus (ARC). We reveal that 5-HT2ARs are also anatomically positioned to influence the activity of ARC POMC and that 5-HT2AR mRNA is increased in the hypothalamus of in utero growth restricted offspring that underwent rapid postnatal catch-up growth. Furthermore, these animals are more sensitive to 5-HT2AR agonist-induced appetite suppression. These findings may not only reveal a 5-HT-mediated mechanism underlying programming of obesity susceptibility but also provide a promising means to correct it, via a 5-HT2AR agonist treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26769798" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76175" }, "primaryId" : "GEO:GSE76175", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76175" } ] }, "title" : "microRNA sequencing in rat cardiac fibroblasts and fibroblast-derived exosomes", "dateAssigned" : "2015-12-18T00:00:00.000-06:00", "summary" : "We found that cardiac fibroblasts produce and secrete exosomes. miRNA profiling and TaqMan qRT-PCR experiments identified miR-21 expression to be higher in cardiac fibroblasts compared to those of miR-21*, whereas in exosomes miR-21* expression was higher compared to miR-21. The purpose of the study was to validate these findings by miRNA sequencing in cardiac fibroblasts and fibroblasts-derived exosomes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76331" }, "primaryId" : "GEO:GSE76331", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76331" } ] }, "title" : "a-linolenic acid and long-chain n-3 polyunsaturated fatty acids modulate colitis operating with a different gene set", "dateAssigned" : "2015-12-24T00:00:00.000-06:00", "summary" : "Adult Wistar rats were fed diet enriched with either a-linolenic acid (ALA) or fish oil for 8 (n=10) weeks. Colitis was induced in rats using 5% dextran sulfate sodium for 7 days. The rats were dissected and RNA was isolated from the colon tissues of rats, the samples from 6 rats were pooled and used for the microarray experiments. Global gene expression analysis was done in duplicates in each group and the results were compared to n-6 fatty acid group. a-linolenic acid (ALA) and fish oil rich in eicosapentaenoic acid and docosahexaenoic acid significantly attenuated the symptoms of colitis, compared to n-6 fatty acid group. Gene expression analysis has revealed that there is no common gene signature in the two groups.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76354" }, "primaryId" : "GEO:GSE76354", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76354" } ] }, "title" : "Recurrent rearrangements of the Myb/SANT-like DNA-binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma", "dateAssigned" : "2015-12-28T00:00:00.000-06:00", "summary" : "By transcriptome (RNAseq) analysis of 3 human acinic cell carcimoma (AcCC) cases, we discovered two novel gene fusions, and further validated recurrent rearrangement of the MSANTD3 gene. By RNAseq of engineered MSANTD3 overexpression in rat salivary epithelial cells (compared to vector control), we identifed elevated expression of genes involved in protein synthesis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76364" }, "primaryId" : "GEO:GSE76364", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76364" } ] }, "title" : "mRNA expression during fracture healing in diabetic rats", "dateAssigned" : "2015-12-28T00:00:00.000-06:00", "summary" : "The association between DM and impaired fracture healing including delayed union and nonunion has been documented in clinical and experimental settings. We examine mRNA expression specific for impaired fracture healing in diabetic rat.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76365" }, "primaryId" : "GEO:GSE76365", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76365" } ] }, "title" : "miRNA expression during fracture healing in diabetic rats", "dateAssigned" : "2015-12-28T00:00:00.000-06:00", "summary" : "The association between DM and impaired fracture healing including delayed union and nonunion has been documented in clinical and experimental settings. We examine miRNA expression specific for impaired fracture healing in diabetic rat.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76411" }, "primaryId" : "GEO:GSE76411", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76411" } ] }, "title" : "Hdac3 Interaction with p300 Histone Acetyltransferase Regulates the Oligodendrocyte and Astrocyte Lineage Fate Switch (ChIP-Seq)", "dateAssigned" : "2015-12-29T00:00:00.000-06:00", "summary" : "Our data suggest that Hdac3 cooperates with p300 to prime and maintain oligodendrogenic programs while inhibiting Stat3-mediated astrogliogenesis, and thereby regulate phenotypic commitment at the point of oligodendrocyte-astrocytic fate decision.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26859354" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76448" }, "primaryId" : "GEO:GSE76448", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76448" } ] }, "title" : "Expression data from 9-day-old and 21-day-old rat Sertoli cell.", "dateAssigned" : "2015-12-31T00:00:00.000-06:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated and down-regulated genes during this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76632" }, "primaryId" : "GEO:GSE76632", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76632" } ] }, "title" : "Tonicity induced changes in Gene expression in IMCD cells", "dateAssigned" : "2016-01-07T00:00:00.000-06:00", "summary" : "The overall differences in gene expression were hightes between cells cultivated at 300 compared to cells cultivated at 900 mosmol/kg", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76679" }, "primaryId" : "GEO:GSE76679", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76679" } ] }, "title" : "Motor cortex after C3 lesion", "dateAssigned" : "2016-01-08T00:00:00.000-06:00", "summary" : "Gene expression analysis of motor cortex after spinal C3 lesion", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26898779" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76694" }, "primaryId" : "GEO:GSE76694", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76694" } ] }, "title" : "Transcriptomic effects of prenatal exposure to corticosteroids on synaptic transmission", "dateAssigned" : "2016-01-08T00:00:00.000-06:00", "summary" : "Prenatal exposure to synthetic corticosteroids can significantly alter postnatal development through changes in neurotransmitters and their receptors, and thus having long-lasting behavioral effects. Some of these changes have been observed in animal experiments, others also in humans prenatally exposed to synthetic corticosteroids. Here, we focused on transcriptomic changes within the prefrontal cortex of female rats prenatally exposed to either betamethasone or saline. The transcriptome has been assessed by novel computational tools to determine complex changes that may have life-long effects on phenotype, i.e., behavior. We analyzed how composition, topology and modulatory networks of the genomic fabric of the dopaminergic, GABAergic, and glutamatergic synapse (the transcriptome of the most interconnected and stably expressed gene network responsible for specific transmission) are affected by prenatal exposure to corticosteroids and postnatal ketamine/saline treated NMDA-induced seizures.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76702" }, "primaryId" : "GEO:GSE76702", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76702" } ] }, "title" : "Expression data from rat orthotopic bladder cancer", "dateAssigned" : "2016-01-11T00:00:00.000-06:00", "summary" : "We used microarrays to analysis the gene expression changes among these rat bladder carcinoma, adjacent normal tissues and bladder tissues of normal rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76704" }, "primaryId" : "GEO:GSE76704", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76704" } ] }, "title" : "Expression data from SHP specific siRNA or nonspecefic siRNA transfected rat astrocytes", "dateAssigned" : "2016-01-11T00:00:00.000-06:00", "summary" : "To clarify the effect of SHP in LXRs-mediated signaling pathway, we performed global gene expression analysis of SHP siRNA transfected- or control siRNA transfected- astrocytes after IFN-¿ and LXRs agonist. Microarray analysis revealed that expression of several genes encoding inflammatory mediators were reversed in SHP siRNA transfected-astrocytes, when compared with control siRNA transfected-astrocytes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76817" }, "primaryId" : "GEO:GSE76817", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76817" } ] }, "title" : "Identification of candidate targets for Haizao Yuhu Decoction acting on goiter rats", "dateAssigned" : "2016-01-13T00:00:00.000-06:00", "summary" : "To predict the different genes, this study compared the gene expression level among the control group, the model group and the treatment groups.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76969" }, "primaryId" : "GEO:GSE76969", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE76969" } ] }, "title" : "Functional maturation of rat beta cells", "dateAssigned" : "2016-01-19T00:00:00.000-06:00", "summary" : "The weaning period consist of a critical postnatal window for structural and physiologic maturation of rat beta cells. To investigate transcriptome changes involved in the maturation of beta cells neighboring this period we performed microarray analysis in FACS beta cell enriched populations to detail the global programme of gene expression to identify its changes during this process.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27220619" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77012" }, "primaryId" : "GEO:GSE77012", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77012" } ] }, "title" : "Real-time quantitative PCR analysis of male rat fed either Lard based or Corn Oil based high fat diet and their female offspring", "dateAssigned" : "2016-01-20T00:00:00.000-06:00", "summary" : "Sperm cells from Sprague Dawley male rats fed different high fat diets (lard or corn oil based) and their 50-days-old female offspring mammary gland were used to perfom this array", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77022" }, "primaryId" : "GEO:GSE77022", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77022" } ] }, "title" : "Transcription profiling of 8 months and 24 months old rat radial and sciatic nerves", "dateAssigned" : "2016-01-20T00:00:00.000-06:00", "summary" : "We find a strong signature of the cholesterol biosynthesis pathway being downregulated with age in both nerves, however, this effect is significantly milder in the radial nerve.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27019136" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77092" }, "primaryId" : "GEO:GSE77092", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77092" } ] }, "title" : "Hyperglycaemia-induced over-expression of miR-301a promotes the proliferation of prostate cancer cells by repressing Smad4 and p21.", "dateAssigned" : "2016-01-21T00:00:00.000-06:00", "summary" : "We found a novel molecular link between hyperglycaemia and the increased frequency of aggressive prostate cancer. High glucose was demonstrated to increase the expression of miR-301a which targeted Smad4 and p21, resulted in promoting the proliferation of prostate cancer cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77112" }, "primaryId" : "GEO:GSE77112", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77112" } ] }, "title" : "Regulation of Fetal Liver Growth in a Model of Diet Restriction in the Pregnant Rat", "dateAssigned" : "2016-01-21T00:00:00.000-06:00", "summary" : "The present study was designed to test the hypothesis that limited growth of the fetal liver in the model of maternal fasting is independent of well-characterized signaling mechanisms that are known to regulate somatic growth in adult animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27357801" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77121" }, "primaryId" : "GEO:GSE77121", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77121" } ] }, "title" : "Dietary Genistein Prevents Denervation-Induced Muscle Atrophy in Male Rodents via Effects on Estrogen Receptor-a.", "dateAssigned" : "2016-01-22T00:00:00.000-06:00", "summary" : "Genistein intake significantly suppressed the loss of soleus muscle weight and the denervation-induced up-regulations of FOXO1 protein. The results of a DNA microarray showed that the estrogen receptor (ER) target genes are changed by genistein intake. Genistein suppressed the soleus muscle atrophy, and it was attenuated under the ER antagonist treatment. The administration of an ERa agonist suppressed the denervation-induced muscle atrophy and up-regulation of Atrogin1 gene expression, but the ERß agonist had no effect.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27146914" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77231" }, "primaryId" : "GEO:GSE77231", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77231" } ] }, "title" : "Matrix-dependent cardiac progenitor cell fate is instructed by the early regulation of YAP and Plk2", "dateAssigned" : "2016-01-26T00:00:00.000-06:00", "summary" : "Although recent studies support regenerative potential based on cardiac progenitor cells (CPCs), it remains unclear what cues regulate CPC fate. Using 2- and 3D-culture models, we demonstrate that the two most abundantly expressed matrix proteins in the heart, laminin and fibronectin, have opposite roles in CPC fate decision. CPCs on fibronectin showed predominantly nuclear localization of the transcriptional co-activator YAP and maintained proliferation. In contrast, seeding on laminin induced cytosolic retention and degradation of YAP and altered gene expression, which preceded decreased proliferation and enhanced lineage commitment. RNA-sequencing identified Plk2 as candidate target gene of YAP. Plk2 expression depended on YAP stability, was rapidly downregulated on laminin, and its regulation was sufficient to rescue and/or mimic the CPC response to laminin and fibronectin, respectively. These findings propose a novel role of Plk2 and identify an early molecular mechanism in matrix-instructed CPC fate with potential implications for therapeutic cardiac regeneration.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29066438" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77377" }, "primaryId" : "GEO:GSE77377", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77377" } ] }, "title" : "Comparison of gene expression profiles of wildtype and two lines of Nrf2 knockout rat livers with or without CDDO-Im treatment", "dateAssigned" : "2016-01-29T00:00:00.000-06:00", "summary" : "Whole livers were collected from rats treated with or without CDDO-Im. Total RNA was purified using Sepazol-RNA I Super G.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27071940" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77384" }, "primaryId" : "GEO:GSE77384", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77384" } ] }, "title" : "Genome-wide RNA expression analysis of rat dorsal root ganglion tissue after local absorbable collagen sponge implantation and BMP-2 exposure", "dateAssigned" : "2016-01-29T00:00:00.000-06:00", "summary" : "Analysis of whole dorsal root ganglion tissue expression signatures in responses to absorbable collagen sponge implantation with and without BMP-2 exposure. The hypothesis is that inflammatory macrophage-associated responses to ACS implantation contributes to nociception in the DRG and spinal nerve.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77450" }, "primaryId" : "GEO:GSE77450", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77450" } ] }, "title" : "BET bromodomain proteins Brd2, Brd3 and Brd4 selectively regulate metabolic pathways in the pancreatic ß-cell", "dateAssigned" : "2016-02-01T00:00:00.000-06:00", "summary" : "Displacement of Bromodomain and Extra-Terminal (BET) proteins from chromatin has promise for cancer and inflammatory disease treatments, but roles of BET proteins in metabolic disease remain unexplored. Small molecule BET inhibitors, such as JQ1, block BET protein binding to acetylated lysines, but lack selectivity within the BET family (Brd2, Brd3, Brd4, Brdt), making it difficult to disentangle contributions of each family member to transcriptional and cellular outcomes. Here, we demonstrate multiple improvements in pancreatic ß-cells upon BET inhibition with JQ1 or BET-specific siRNAs. JQ1 (50-400 nM) increases insulin secretion from INS-1 cells in a concentration dependent manner. JQ1 increases insulin content in INS-1 cells, accounting for increased secretion, in both rat and human islets. Higher concentrations of JQ1 decrease intracellular triglyceride stores in INS-1 cells, a result of increased fatty acid oxidation. Specific inhibition of both Brd2 and Brd4 enhances insulin transcription, leading to increased insulin content. Inhibition of Brd2 alone increases fatty acid oxidation. Overlapping yet discrete roles for individual BET proteins in metabolic regulation suggest new isoform-selective BET inhibitors may be useful to treat insulin resistant/diabetic patients. Results imply that cancer and diseases of chronic inflammation or disordered metabolism are related through shared chromatin regulatory mechanisms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27008626" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77572" }, "primaryId" : "GEO:GSE77572", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77572" } ] }, "title" : "Bi-directional regulation between circadian rhythm and neurodegeneration-associated FUS", "dateAssigned" : "2016-02-04T00:00:00.000-06:00", "summary" : "Circadian rhythms are daily physiological and behavioral changes governed by an internal molecular clock, and dysfunctions in circadian rhythms have long been associated with various neurodegenerative diseases. Abnormal sleep-wake cycle often precedes the onset of cognitive and motor symptoms in patients, while the pathological changes may further exacerbate the disturbance in circadian cycle. It is unclear whether dysregulated circadian rhythm is a consequence of, or a contributing factor for, neurodegeneration. In addition, the evidence directly connecting the neurodegeneration-associated proteins to core circadian clock gene expression remains sparse. Here we show that FUS, a RNA-binding protein implicated in the pathogenesis of ALS and frontotemporal dementia, exhibits a bi-directional regulation with circadian rhythm. Our meta-analysis of RNAseq datasets and subsequent biochemical analysis revealed FUS as a gene regulated by circadian oscillation. Furthermore, NR1D1 binds the FUS promoter and regulates the amplitude of FUS oscillation. Meanwhile, FUS is recruited by transcriptional co-repressor PSF, and is found in the same complex as Bmal-Clock to repress Per2 expression. More strikingly, in cells and brain tissues from homozygous knock-in rats, the pathogenic R521C mutant FUS significantly alters the oscillation patterns of core circadian genes even at young age. Therefore, our results have revealed a novel bi-directional mechanism whereby dysregulated circadian clock and FUS expression may exacerbate neurodegeneration via mutual influence.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28335007" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77591" }, "primaryId" : "GEO:GSE77591", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77591" } ] }, "title" : "Rat cardiomyocyte; control vs celecoxib treatment", "dateAssigned" : "2016-02-04T00:00:00.000-06:00", "summary" : "Goal of study is to identify changes on genes expression induced by celecoxib. The data analysis focused on genes that might be related to cardiotoxicity; genes expression ion channels and pathways.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77698" }, "primaryId" : "GEO:GSE77698", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77698" } ] }, "title" : "Intralipid protects the heart in late pregnancy against ischemia/reperfusion injury", "dateAssigned" : "2016-02-08T00:00:00.000-06:00", "summary" : "We hypothesized that Intralipid (ITLD) protects the heart in LP rodents against I/R injury. We performed genome-wide expression profiling to identify the underlying mechanisms.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77765" }, "primaryId" : "GEO:GSE77765", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77765" } ] }, "title" : "Detection of a Yersinia pestis homologue in rodent samples", "dateAssigned" : "2016-02-10T00:00:00.000-06:00", "summary" : "In the work described here, a homologue to Yersinia pestis was found in rodent samples after screening with the microarray", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77880" }, "primaryId" : "GEO:GSE77880", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77880" } ] }, "title" : "Rat cardiomyocyte: control vs diclofenac treatment", "dateAssigned" : "2016-02-12T00:00:00.000-06:00", "summary" : "Goal of study is to identify changes on genes expression induced by diclofenac. The data analysis focused on genes that might be related to cardiotoxicity; genes expression ion channels and pathways.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77888" }, "primaryId" : "GEO:GSE77888", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE77888" } ] }, "title" : "Regulation of liver regeneration by interference with TNF alpha mediated inflammation", "dateAssigned" : "2016-02-12T00:00:00.000-06:00", "summary" : "Liver regeneration responses were then examined in conjunction with gene expression analysis at the peak of partial hepatectomy induced DNA synthesis. Substantive differences were identified in multiple gene ontology groups and cellular events and processes to indicate that TNF alpha was deleterious for partial hepatectomy induced liver regeneration.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78008" }, "primaryId" : "GEO:GSE78008", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78008" } ] }, "title" : "Mechanisms of variable ventilation in experimental lung injury", "dateAssigned" : "2016-02-17T00:00:00.000-06:00", "summary" : "In the present study we seek to identify changes in lung gene expression under mechanical ventilation in uninjured as well as acutely and chronically injured lungs. A standard volume-controlled lung-protective ventilatory protocol is compared to a concept of mechanical ventilation using variable tidal volumes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78031" }, "primaryId" : "GEO:GSE78031", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78031" } ] }, "title" : "microRNA profiling of Sprague Dawley organs", "dateAssigned" : "2016-02-17T00:00:00.000-06:00", "summary" : "We performed deep sequencing of the miRNAs present in ~20 toxicologically relevant tissues in Sprague Dawley rats and used three independent analysis of the data to determine which miRNAs are tissue specific and tissue enriched.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27576563" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78038" }, "primaryId" : "GEO:GSE78038", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78038" } ] }, "title" : "To determine whether interference with mechanisms of vasoconstriction or inflammation would improve outcomes in ischemia reperfusion injury of the liver", "dateAssigned" : "2016-02-17T00:00:00.000-06:00", "summary" : "Study was performed in groups of animals including healthy controls, ischemia reperfusion alone, and administration of drug followed by ischemia reperfusion. Samples from liver and isolated hepatocytes intact and one day after reperfusion were analyzed for gene expression in conjunction with other biological variables. Results indicated substantive alteration after drug intervention in multiple gene ontology groups and cellular events and processes after ischemia reperfusion.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78200" }, "primaryId" : "GEO:GSE78200", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78200" } ] }, "title" : "Transcriptome analyses of cerebral ischemia reveal functional lncRNAs in ischemia stroke", "dateAssigned" : "2016-02-23T00:00:00.000-06:00", "summary" : "Conclusions: This study reports the genome-wide lncRNA profiles in ischemia stroke using high throughput sequencing and constructs a systematic lncRNA-miRNA-mRNA network which reveals a complex functional noncoding RNA regulatory network in ischemia stroke.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78525" }, "primaryId" : "GEO:GSE78525", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78525" } ] }, "title" : "Effect of tail domain and kinase domain mutations in BMPR2 on gene expression in rat Hc92 cells studied by RNA-Seq", "dateAssigned" : "2016-02-25T00:00:00.000-06:00", "summary" : "We sequenced RNA from rat Hc92 cells transformed with empty vector, tail domain BMPR2 and kinase domain BMPR2 knockout vectors", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78688" }, "primaryId" : "GEO:GSE78688", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78688" } ] }, "title" : "Activity-dependent transcriptional changes in human neurons", "dateAssigned" : "2016-02-25T00:00:00.000-06:00", "summary" : "We used genome-wide sequencing methods to identify activity-regulated gene expression and regulatory elements in human neurons. Sensory stimuli drive the maturation and function of the mammalian nervous system in part through the activation of gene expression networks that regulate synapse development and plasticity. These programs of gene transcription have primarily been studied in mice, and it is not known if there are neuronal activity-regulated genes that control features of brain development and function that are unique to humans. In this study, we used genome-wide sequencing methods to identify activity-regulated gene expression and regulatory elements in human neurons.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27830782" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78702" }, "primaryId" : "GEO:GSE78702", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78702" } ] }, "title" : "Comparison of age-related changes in gene expression of 2 rat skeletal muscles", "dateAssigned" : "2016-02-26T00:00:00.000-06:00", "summary" : "In this study we compared Gastrocnemius and Triceps gene expression with age. Our results show that gene expression is massively modulated with age in Gastroc but on the contrary very stable in Triceps, suggesting that Triceps is resistant to age-related defects.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27019136" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78712" }, "primaryId" : "GEO:GSE78712", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78712" } ] }, "title" : "Direct conversion of rodent fibroblasts into myelinating induced Schwann cells", "dateAssigned" : "2016-02-26T00:00:00.000-06:00", "summary" : "Transcriptome analysis of rodent fibroblast-derived induced Schwann cells", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78731" }, "primaryId" : "GEO:GSE78731", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78731" } ] }, "title" : "mRNA microarray in MCAo rat model with IV-hUMSC", "dateAssigned" : "2016-02-26T00:00:00.000-06:00", "summary" : "At 72 h post-MCAo, the ipsilateral hemisphere subjected to MCAo was used for mRNA microarray. RNA was isolated from the ipsilateral hemisphere to MCAo in rats without MCAo (control group, n=5), rats treated with 1x106 IV-hUMSC (hUMSC group, n=6) and saline (saline group, n=5) at 24h post-MCAo.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78869" }, "primaryId" : "GEO:GSE78869", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78869" } ] }, "title" : "Radiation effects on lung carcinogenesis in neonatal, juvenile, and adult Wistar rats after thoracic X-ray irradiation", "dateAssigned" : "2016-03-03T00:00:00.000-06:00", "summary" : "Studies of radiation exposed populations have shown that children are at greater overall risk of radiation-induced cancer, although there is considerable debate relating to heterogeneity of the effect in different tissues. Given public concern around increasing radiation doses received by children from advanced diagnostic imaging, and the use of radiotherapy to treat childhood cancers, understanding the relationship between age-at-exposure and radiation-induced cancer risk is a priority of radiation protection research. Although tobacco smoking accounts for up to 90% of lung cancers in some countries, epidemiological studies and animal experiments show that exposure to ionizing radiation is also a risk factor for developing cancers of the lung. Female Wistar rats are susceptible to lung cancer upon thoracic X-ray irradiation, developing adenocarcinomas (AC) and squamous cell carcinomas (SCC) similar to those seen in humans, and have been used previously to evaluate the interaction of radiation and a chemical carcinogen in neonatal, juvenile and young adult rats. In the present study, the induction of lung tumors was analyzed in female Wistar rats exposed to increasing doses of thoracic X-rays as neonates, juveniles or adults, to allow the effect of age-at-exposure to be observed in the absence of interaction with smoking. Histology was used to compare tumor subtypes between groups, and genomic DNA copy number alterations in a number of tumors arising after exposure to radiation at different ages were examined.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78934" }, "primaryId" : "GEO:GSE78934", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE78934" } ] }, "title" : "Binding Profiles of Myc and RNA Polymerase II in Rat Neonatal Cardiomyocytes", "dateAssigned" : "2016-03-07T00:00:00.000-06:00", "summary" : "During the progression of cardiac hypertrophy, cardiomyocytes accelerate RNA biogenesis to meet increasing metabolic demands under exogenous hypertrophic stimuli. We have elucidated the quantitative kinetics of RNA in c-Myc (Myc)-mediated hypermetabolic analytical model using cultured neonatal rat cardiomyocytes. Chromatin immunoprecipitation and high-throughput sequencing demonstrate that overexpressed Myc binds to a specific set of genes directly in cardiomyocytes and recruits RNA polymerase II to these genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27346836" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79017" }, "primaryId" : "GEO:GSE79017", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79017" } ] }, "title" : "MicroRNA-SEQ analysis of kidney and liver damage in rat", "dateAssigned" : "2016-03-08T00:00:00.000-06:00", "summary" : "Purpose : Identification of novel microRNA biomarkers in urine and plasma from rats with kidney or liver damage", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27397436" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79063" }, "primaryId" : "GEO:GSE79063", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79063" } ] }, "title" : "Plasma-specific microRNA responses in rats treated with acute toxicity doses of aristolochic acid I", "dateAssigned" : "2016-03-10T00:00:00.000-06:00", "summary" : "In the present study, goal was to scan the potential biomarker for acute kidney injury induced by aristolochic acid I (AAI).We utilized the microarry analysis to investigate the microRNA (miRNA) expression profile in kidneys from rat treated by 40mg/kg AA I for 2-6 days. miRNAs with significantly different expression of global miRNA expression profile were validated by qRT-PCR. For miRNAs still significantly disregulation, we further examined the expression in plasma of rats treated with AAI dosed at 10, 20 and 40mg/kg AAI for 2-6 days by qRT-PCR. miRNAs with significantly dysregulation in plasma, their expressionin brain, liver and heart was examined for kicking out the non-specific disregulation in AAI induced acute kidney injury, so that the significant dysregulation miRNAs with specificity in kidney and plasma was found as potential biomarkers for AAI induced acute kidney injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79114" }, "primaryId" : "GEO:GSE79114", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79114" } ] }, "title" : "Effects of muscle regeneration after injury on overloading-induced hypertrophy", "dateAssigned" : "2016-03-11T00:00:00.000-06:00", "summary" : "After 8 weeks of regeneration period, both left and right soleus muscles were overloaded by the transection of synergists' tendons for 2 weeks.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79176" }, "primaryId" : "GEO:GSE79176", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79176" } ] }, "title" : "Effect of polyphosphates on osteoblast mineralization", "dateAssigned" : "2016-03-14T00:00:00.000-05:00", "summary" : "Rat osteoblasts ROB17/2.8 cells were cultured in the presence of high (1mg/ml) or low (0.01mg/ml) concentration of polyphosphates.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79224" }, "primaryId" : "GEO:GSE79224", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79224" } ] }, "title" : "C4b-binding protein protects beta-cells from islet amyloid polypeptide induced cytotoxicity.", "dateAssigned" : "2016-03-15T00:00:00.000-05:00", "summary" : "Complement inhibitor C4b-binding protein (C4BP) is synthesized in liver and pancreas and composed of 7 identical alpha chains and one unique beta chain. We showed previously that C4BP binds islet amyloid polypeptide (IAPP) and affects fibril formation in vitro. Now we found that polymeric C4BP inhibited lysis of human erythrocytes incubated with monomeric IAPP while no erythrocyte lysis was observed after incubation with preformed IAPP fibrils. In contrast, monomeric alpha chain of C4BP had significantly reduced activity. Further, addition of monomeric IAPP to a rat insulinoma cell line (INS-1) resulted in decreased cell viability, which was restored in the presence of physiological concentrations of C4BP. Accordingly, addition of C4BP rescued the ability of INS-1 cells and isolated rat islets to respond to glucose stimulation with insulin secretion, which was impaired in the presence of IAPP alone. C4BP was internalized together with IAPP into INS-1 cells and therefore we aimed to study its effect on gene expression. Pathway analyses of mRNA expression microarray data indicated that cells exposed to C4BP and IAPP in comparison to IAPP alone increased expression of genes involved in cholesterol synthesis. Depletion of cholesterol through methyl-ß-cyclodextrin or cholesterol oxidase abolished the protective effect of C4BP on IAPP cytotoxicity of INS-1 cells. Also, inhibition of phosphoinositide 3-kinase but not NF-¿B had a similar effect. Taken together, one of the mechanisms by which C4BP protects beta-cells from IAPP cytotoxicity is by enhancing cholesterol synthesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27566545" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79270" }, "primaryId" : "GEO:GSE79270", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79270" } ] }, "title" : "DNA Methylation profile for male SD Rats with and without traumatic brain injury (TBI) by RRBS-Seq", "dateAssigned" : "2016-03-16T00:00:00.000-05:00", "summary" : "To investigate the effects of TBI on affecting DNA methylations in the WBC of male SD rats by RRBS.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28174132" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79349" }, "primaryId" : "GEO:GSE79349", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79349" } ] }, "title" : "Expression data from dorsolateral prostates of ACI rats fed corn oil diets", "dateAssigned" : "2016-03-17T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global alterations of gene expression in the prostate of ACI rats fed high and low corn oil for 18 months", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79350" }, "primaryId" : "GEO:GSE79350", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79350" } ] }, "title" : "Title: Aging-associated changes in microRNA expression profile of internal anal sphincter smooth muscle: Role of microRNA-133a", "dateAssigned" : "2016-03-17T00:00:00.000-05:00", "summary" : "A comprehensive –omic, computational, and physiological approach was employed to examine the (previously unexplored) role of microRNAs (miRNAs) as regulators of IAS smooth muscle contractile phenotype and basal tone. MicroRNA profiling, genome wide expression, validation and network analyses were employed to assess changes in mRNA and miRNA expression in IAS smooth muscles from young vs. aging rats. Multiple miRNAs, including rno-miR-1, rno-miR-340-5p, rno-miR-185, rno-miR-199a-3p, rno-miR-200c, rno-miR-200b, rno-miR-31, rno-miR-133a and rno-miR-206 were found to be up-regulated in aging IAS. qRT-PCR confirmed the up-regulated expression of these miRNAs and down regulation of multiple, predicted targets (Eln, Col3a1, Col1a1, Zeb2, Myocd, SRF, Smad1, Smad2, RhoA/ROCK2, Fn1, Sm22-v2, Klf4, and Acta2) involved in regulation of SM contractility. Subsequent studies demonstrated an aging-associated increase in the expression of miR-133a, corresponding decreases in RhoA, ROCK2, MYOCD, SRF and SM22a protein expression, RhoA-signaling, and a decrease in basal and agonist (U-46619 (thromboxane A2 analog))-induced increase in the IAS tone. Moreover, in vitro transfection of miR-133a caused a dose-dependent increase of IAS tone in strips, which was reversed by anti-miR-133a. Lastly, in vivo perianal injection of anti-miR-133a reversed the loss of IAS tone associated with age. This work establishes the important regulatory effect of miRNA-133a on basal and agonist-stimulated IAS tone. Moreover, reversal of age-associated loss of tone via anti-miR delivery strongly implicates miR dysregulation as a causal factor in the aging-associated decrease in IAS tone, and suggests miR-133a is feasible therapeutic target in aging-associated rectoanal incontinence.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27634012" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79471" }, "primaryId" : "GEO:GSE79471", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79471" } ] }, "title" : "Gene expression profiling in male rat germ cells after chronic cyclophosphamide treatment", "dateAssigned" : "2016-03-22T00:00:00.000-05:00", "summary" : "To further understand the effects of chronic cyclophosphamide treatment on spermatogenesis, we used whole genome microarrays to identify differentially expressed genes in pachytene spermatocytes and round spermatids from treated and control male rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79566" }, "primaryId" : "GEO:GSE79566", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79566" } ] }, "title" : "Whole genome DNA methylation profile of sperm cells in mammalian species", "dateAssigned" : "2016-03-24T00:00:00.000-05:00", "summary" : "DNA methylation in sperm is among the most important factors shaping evolution of the mammalian genome. By directly altering germline mutation rates, the DNA methylation system has shaped the CpG landscape of mammalian genomes, resulting in the CpG island phenomenon. Yet little is known about how this system itself has co-evolved with its substrate during mammalian evolution. We analyzed full-genome single-CpG DNA methylation profiles in sperm from human, chimp, gorilla, rhesus, mouse, rat and dog. Our results point to an evolutionary expansion of the unmethylated portion of mammalian genomes. Within the mutually orthologous genome this trend is driven both by the birth of unmethylated regions and by widening of intervals that are unmethylated in ancestors. We find strikingly divergent global features in rodents. At the same time, we observe the evolutionary emergence of methylome features in mouse sperm bears association with similar pathways to those found in human. Together,these results revealed general principles in mammalian epigenome evolution.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29259021" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79651" }, "primaryId" : "GEO:GSE79651", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79651" } ] }, "title" : "End Sequence Analysis ToolKit (ESAT) expands the extractable information from single cell RNA-Seq data", "dateAssigned" : "2016-03-28T00:00:00.000-05:00", "summary" : "Test data used for the evaluation of ESAT performance and results files for data from 3' and 5' end-sequencing RNA-Seq protocols and droplet-based single-cell RNA-Seq.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27470110" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79715" }, "primaryId" : "GEO:GSE79715", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79715" } ] }, "title" : "Gene expression analysis in liver of rats fed with atherogenic diet (1% cholesterol) and supplemented with 5% Geneva or 5% Hayward kiwifruit lyophylisate", "dateAssigned" : "2016-03-30T00:00:00.000-05:00", "summary" : "Transcriptional profiling of liver tissue from rats fed with standard diet with 1% cholesterol (control diet) and the same diet supplemented with 5% Geneva (test sample1) or 5% Hayward (test sample2) kiwifruit lyophylisate. The goal was to determine the anti-atherogenic effect of kiwi fruit supplementation and their impact on gene expression preventing hepatic steatosis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:39683393" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79727" }, "primaryId" : "GEO:GSE79727", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79727" } ] }, "title" : "microRNA profiling in normal and hyperplastic human and murine parathyroid glands", "dateAssigned" : "2016-03-30T00:00:00.000-05:00", "summary" : "Secondary hyperparathyroidism (SHP) is a common complication of chronic kidney disease (CKD) and correlates with morbidity and mortality. In this study we profiled microRNAs (miRNA) in parathyroids from different experimental SHP models and uremic patients and studied the function of specific miRNA using antagonizing oligonucleotides (anti-miRs). miRNA profiles established by small RNA deep sequencing showed that human, rat and mouse parathyroids share the same most abundant miRNAs. Principal component analyses clearly segregated parathyroids from SHP rats from normal rats, based on their miRNA expression profiles. Similar findings were observed in hyperplastic parathyroids from CKD patients compared to normal parathyroids from patients without kidney disease. We identifed specific parathyroid miRNAs that were dysregulated in all experimental SHP models studied. let-7i was decreased and miR-141 and miR-148a were increased in the parathyroids of rats with prolonged CKD induced by an 8 w adenine high phosphorus diet. Down-regulation of let-7 by anti-miRs increased PTH secretion in normal and in CKD rats, as well as in parathyroid organ cultures. Anti-miR-148 prevented the increase in serum PTH in CKD rats and decreased secreted PTH in parathyroid organ cultures. Our findings characterized parathyroid miRNA profiles and demonstrated conservation of the abundant miRNAs in different species. The evolutionary conservation of abundant miRNAs and their regulation in SHP suggest that miRNAs are important for parathyroid function and the development of SHP. Down-regulation of let-7 and miR-148 affects PTH secretion in vivo and in vitro, suggesting a role for these miRNAs in SHP. We propose that let-7 restrains while miR-148 promotes PTH secretion. In CKD, the decrease in parathyroid let-7 and the increase in miR-148 miRNAs may contribute to the development of SHP.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28298326" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79730" }, "primaryId" : "GEO:GSE79730", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79730" } ] }, "title" : "RNA-seq of Odora cells exposed to zinc gluconate", "dateAssigned" : "2016-03-30T00:00:00.000-05:00", "summary" : "Zinc is both an essential and potentially toxic metal. It is widely believed that oral zinc supplementation can reduce the effects of the common cold; however, there is strong clinical evidence that intranasal (IN) zinc gluconate (ZG) gel treatment for this purpose causes anosmia, or the loss of the sense of smell, in humans. Using the rat olfactory neuron cell line, Odora, we investigated the molecular mechanism by which zinc exposure exerts its toxic effects on olfactory neurons. Following treatment of Odora cells with 100 and 200 µM ZG for 0-24 h, RNA-seq and in silico analyses revealed up-regulation of pathways associated with zinc metal response, oxidative stress, and ATP production. We observed that Odora cells recovered from zinc-induced oxidative stress, but ATP depletion persisted with longer exposure to ZG. ZG exposure increased levels of NLRP3 and IL-1ß protein levels in a time-dependent manner, suggesting that zinc exposure may cause an inflammasome-mediated cell death, pyroptosis, in olfactory neurons.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79749" }, "primaryId" : "GEO:GSE79749", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79749" } ] }, "title" : "Distinct Combinatorial Events Generated by ECM Degradation Dictate Cell Behavior", "dateAssigned" : "2016-03-31T00:00:00.000-05:00", "summary" : "It is well established that the expression profiles of multiple and possibly redundant matrix remodeling proteases (e.g. collagenases) strongly differ in health, disease and development. Although enzymatic redundancy might be inferred from their close similarity in structure, their in-vivo activity can lead to extremely diverse tissue-remodeling outcomes. We observed that proteolysis of collagen-rich natural extracellular matrix (ECM), generated uniquely by individual homologous proteases, leads to specific combinatorial events, which eventually affects overall ECM topography, visco-elastic properties and composition. We reveal striking differences in the movement and signaling patterns, morphology, and gene expression profiles of cells interacting with natural collagen-rich ECM degraded by different collagenases. Thus, unlike envisioned before matrix-remodeling systems are not redundant and give rise to precise ECM-cell crosstalk. As ECM proteolysis is an abundant biochemical process critical to tissue homoeostasis, these results improve our fundamental understanding of combinatorial factors dictating cell behavior.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27630193" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79860" }, "primaryId" : "GEO:GSE79860", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79860" } ] }, "title" : "A switch from neuronal network development to maintenance during postnatal development of rat prefrontal cortex", "dateAssigned" : "2016-04-03T00:00:00.000-05:00", "summary" : "To unravel the gene expression changes during postnatal prefrontal cortex development, RNA-seq was performed in the rat medial prefrontal cortex at five time points from early life to adulthood (postnatal day 8, 14, 21, 35 and 70) and differential expression of protein-coding genes, lincRNAs and alternative exons was analyzed. A switch from neuronal network development to maintenance during postnatal rat prefrontal cortex development was shown.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28108491" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79867" }, "primaryId" : "GEO:GSE79867", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79867" } ] }, "title" : "Transcriptomic responses of the liver and adipose tissues to altered carbohydrate-fat ratio in diet: An isoenergetic study in young rats", "dateAssigned" : "2016-04-04T00:00:00.000-05:00", "summary" : "3-week-old rats were fed three kind of diets: low, moderate and high fat diets (L, M and H) containing a different ratio of carbohydrate:fat (C:F) (65:15, 60:20 and 35:45 in energy percent, respectively).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28405243" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79894" }, "primaryId" : "GEO:GSE79894", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79894" } ] }, "title" : "Regular physical activity followed by detraining increases the sensitivity of global gene expression to acute exercise stress", "dateAssigned" : "2016-04-04T00:00:00.000-05:00", "summary" : "To determine the influence of a previous physcial activity period (e.g., exercise) on global gene expression, we compared differential expression in sedentary (SED) and detrained (DETR) rats relative to trained (TR) rats with regular access to physcial activity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79906" }, "primaryId" : "GEO:GSE79906", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79906" } ] }, "title" : "Gene Expression of brain cortex microvessels in two rat models of acute liver failure (ALF)", "dateAssigned" : "2016-04-04T00:00:00.000-05:00", "summary" : "Two different well stablished rat models were analyzed: Portacaval anastomosis plus hepatic artery ligation and portacaval anastomosis plus total hepatectomy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79909" }, "primaryId" : "GEO:GSE79909", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79909" } ] }, "title" : "Gene expression analysis of serotonin transporter knock-out and wildtype rats during rat postnatal prefrontal cortex development", "dateAssigned" : "2016-04-04T00:00:00.000-05:00", "summary" : "To unravel the effect of increased extracellular serotonin levels on brain development, RNA-seq was performed in the medial prefrontal cortex of serotonin transporter knockout and wildtype rats at five time points from early life to adulthood (postnatal day (PND) 8, 14, 21, 35 and 70). Differential expression of protein-coding genes was analyzed and we demonstrate that a lack of functional 5-HTT especially affects gene expression in early postnatal life (PND8).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79983" }, "primaryId" : "GEO:GSE79983", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE79983" } ] }, "title" : "miRNA profiles in livers with different mass deficits after partial hepatectomy and miR-106b~25 cluster accelerating hepatocyte proliferation in rats", "dateAssigned" : "2016-04-06T00:00:00.000-05:00", "summary" : "To query the relationship between miRNA profiles and deficits in liver mass after PH and the miRNAs linked to liver regeneration, we compared the miRNA expression profile after 2/3 PH, a standard procedure that leads to robust DNA synthesis, with that after 1/3 PH, a procedure that causes minimal replication. The patterns and dynamics of miRNA profiles after PH were featured, providing a rich resource of miRNAs underlying mechanisms of liver regeneration.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80030" }, "primaryId" : "GEO:GSE80030", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80030" } ] }, "title" : "mRNA profile between 1/3 partial hepatectomy (PH) and 2/3 PH at 24 hours", "dateAssigned" : "2016-04-07T00:00:00.000-05:00", "summary" : "Six rats underwent partial hepatectomy (PH) (3, 1/3PH; 3, 2/3PH). The total mRNA of three rats each group were pooled and compared by microarray to selected the mRNA which differs between between 2/3PH with robust DNA replication and 1/3PH with a minimal replicative response.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80123" }, "primaryId" : "GEO:GSE80123", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80123" } ] }, "title" : "microRNA expression profile in whole lung of rat pups at P10 or P21 day of life after a intrauterine growth restriction due to a low protein diet during gestation", "dateAssigned" : "2016-04-11T00:00:00.000-05:00", "summary" : "MicroRNA expression were assessed in the lungs of five animals per group at P10 and P21 after birth in a rat model of low protein diet-induced IUGR.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29287116" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80174" }, "primaryId" : "GEO:GSE80174", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80174" } ] }, "title" : "Analysis of Post-TBI Gene Expression Signature Reveals Tubulins, NFE2L2, NFkB, CD44, and S100A4 as Treatment Targets for Traumatic Brain Injury", "dateAssigned" : "2016-04-12T00:00:00.000-05:00", "summary" : "TBI was induced with lateral fluid-percussion injury in adult male rats. Genome-wide RNA-seq of the perilesional cortex, ipsilateral thalamus and dorsal hippocampus was performed at 3 months post-TBI. The data highlighted chronic transcriptional changes, particularly, in the perilesional cortex and thalamus. Genes showing a significantly altered expression both in the cortex and thalamus were submitted to the LINCS web query to identify novel pharmacotherapies to improve post-TBI outcome.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27530814" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80257" }, "primaryId" : "GEO:GSE80257", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80257" } ] }, "title" : "Fingerprinting of the hNGF P61R100E gene expression in rat Dorsal Root Ganglion detected by microarray analysis", "dateAssigned" : "2016-04-13T00:00:00.000-05:00", "summary" : "Nerve Growth Factor (NGF) is being considered as a therapeutic candidate for Alzheimer's disease (AD) treatment, not merely as a long-lasting cholinergic maintainer and neuroprotective agent but also as a direct anti-amyloidogenic factor. However, the development of a NGF-based therapy for neurodegenerative diseases is limited by the partial access of NGF to the brain and to its potent nociceptive actions in animals and humans. Indeed, NGF is involved in pain transmission and perception. The nociceptive activity of NGF is mediated through the activation of TrkA and p75NTR receptors on sensory nerve endings. Our group recently studied forms of NGF, mutated at residue R100, inspired by the human genetic disease HSAN V (Hereditary Sensory Autonomic Neuropathy Type V), which would allow increasing the dose of NGF without triggering pain. This “painless” hNGF hNGFP61S/R100E displays full neurotrophic and anti-amyloidogenic activities in neuronal cultures, and a reduced nociceptive activity in vivo, via a selective alteration of TrkA versus p75NTR binding and signaling. The molecular mechanism through which pNGF reduces nociceptive activity has never been investigated, therefore we performed gene expression microarray analysis to investigated the effect of hNGF hNGFP61S/R100E delivery in rat Dorsal Root Ganglia.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80339" }, "primaryId" : "GEO:GSE80339", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80339" } ] }, "title" : "Gene expression analysis of ambient or 0.5% oxygen exposed rat trophoblast stem (TS) cells", "dateAssigned" : "2016-04-15T00:00:00.000-05:00", "summary" : "Analysis of transcriptomic profile of TS cells grown in ambient (21% oxygen) and hypoxic (0.5% oxygen) conditions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27807143" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80340" }, "primaryId" : "GEO:GSE80340", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80340" } ] }, "title" : "Gene expression analysis of ambient or 10.5% oxygen exposed rat gestation d13.5 metrial gland tissues. The animals were exposed to low oxygen from gestation day 6.5 to 13.5.", "dateAssigned" : "2016-04-15T00:00:00.000-05:00", "summary" : "Analysis of transcriptomic profile of metrial gland tissue in ambient (21% oxygen) and hypoxic (10.5% oxygen) conditions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27807143" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80371" }, "primaryId" : "GEO:GSE80371", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80371" } ] }, "title" : "Comprehensive assessment of shockwave intensity: transcriptomic biomarker discovery for primary blast-induced mild traumatic brain injury (mTBI) using the mammalian hair follicle", "dateAssigned" : "2016-04-18T00:00:00.000-05:00", "summary" : "Primary blast-induced mild traumatic brain injury (mTBI) represents a common injury experienced during modern warfare. With virtually no apparent physical damage or symptoms presented, an effective source with minimum-invasion for mTBI biomarker discovery is required. In this study, we measure the transcriptomic sensitivity of the hair follicles in relation to the severity of primary blast-derived TBI.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80416" }, "primaryId" : "GEO:GSE80416", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80416" } ] }, "title" : "Mincle-mediated signaling leads to characteristic gene expressions in rat mast cells", "dateAssigned" : "2016-04-19T00:00:00.000-05:00", "summary" : "Mincle-mediated signaling stimulated characteristic gene expression, such as IL-3, IL-4, IL-9, IL-13, IL-31 and TNFa.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80439" }, "primaryId" : "GEO:GSE80439", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80439" } ] }, "title" : "miR-219 Cooperates with miR-338 in Myelination and Promotes Myelin Repair in the CNS", "dateAssigned" : "2016-04-19T00:00:00.000-05:00", "summary" : "microRNAs (miRNAs) have been implicated in oligodendrogenesis and demyelinating diseases; however, identification of individual miRNAs responsible has remained elusive. Through targeted mutagenesis, we find that miR-219 is required for proper oligodendrocyte differentiation and myelination in vivo. Deletion of miR-338 together with miR-219 further exacerbates hypomyelination phenotypes. Temporally specific ablation reveals a critical role for miR-219 in oligodendrocyte remyelination after demyelination, while overexpression of miR-219 promotes precocious oligodendrocyte maturation and myelin regeneration. Accordingly, administration of miR-219 mimics to lysolecithin-induced demyelinating lesions in the murine spinal cord and brain enhances myelin restoration. Through integrating analyses of transcriptome profiling and biotin-affinity miRNA pull-down, we identify a set of stage-specific targets of miR-219, including Etv5 and Lingo1, as oligodendrocyte differentiation inhibitors. Inhibiting Etv5 and Lingo1 leads to a partial rescue of differentiation defects observed in miR-219-mutant OLs in vitro. Together, our findings identify context-specific miRNA-regulated checkpoints that control CNS myelinogenesis and myelin repair.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28350989" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80453" }, "primaryId" : "GEO:GSE80453", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80453" } ] }, "title" : "Reciprocal regulation of cardiac chromatin by the chromatin structural proteins HMGB and CTCF", "dateAssigned" : "2016-04-20T00:00:00.000-05:00", "summary" : "Transcriptome remodeling in heart disease occurs through the coordinated actions of transcription factors, histone modifications and other chromatin features at pathology-associated genes. It remains unknown the extent to which genome-wide chromatin reorganization also contributes to the pathologic gene expression. We examined the roles of two chromatin structural proteins, CTCF (CCCTC-binding factor) and HMGB2 (high mobility group protein B2), in regulating pathologic transcription and chromatin remodeling. Our data demonstrate a reciprocal relationship between HMGB2 and CTCF in controlling aspects of chromatin structure and gene expression. Both proteins regulate each other’s expression as well as transcription in cardiac myocytes: however, only HMGB2 does so in a manner that involves global reprogramming of chromatin accessibility. We demonstrate that the actions of HMGB2 on local chromatin accessibility are conserved across genomic loci, whereas the effects on transcription are loci-dependent and emerge in concert with histone modification and other chromatin features. Lastly, while both proteins share gene targets, HMGB2 and CTCF neither bind these genes simultaneously nor do they physically co-localize in myocyte nuclei. Our study uncovers a previously unknown relationship between these two ubiquitous chromatin proteins and provides a mechanistic explanation for how HMGB2 regulates gene expression and cellular phenotype. Furthermore, we demonstrate direct evidence for hierarchical remodeling of chromatin on a genome-wide scale in the setting of cardiac disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27226577" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80515" }, "primaryId" : "GEO:GSE80515", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80515" } ] }, "title" : "Modulation of the diet and gastrointestinal microbiota normalizes systemic inflammation and β-cell chemokine expression associated with autoimmune diabetes susceptibility", "dateAssigned" : "2016-04-21T00:00:00.000-05:00", "summary" : "Sequencing of the bacterial 16S rRNA gene revealed that these treatments significantly altered the ileal and cecal microbiota, resulting in increases in the Firmicutes:Bacteriodetes ratio, and abundances of lactobacilli and butyrate producing genera. Both treatments partially normalized the peripheral inflammatory state, reducing plasma cytokine, chemokine and TLR-4 activity levels. The proinflammatory islet transcriptome was more extensively normalized by HCD and immune-fluorescent staining revealed reductions in β-cell chemokine expression. HCD and antibiotic treatment did not normalize BB rat PBMC hyper-responsiveness to ex vivo mitogen stimulation. Combined, these studies link islet-level T1D susceptibility in BB rats to a genetically controlled innate inflammatory state that is influenced by environmental determinants encompassing the diet and the intestinal microbiota.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29293587" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80516" }, "primaryId" : "GEO:GSE80516", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80516" } ] }, "title" : "Modulation of the gastrointestinal microbiota normalizes the systemic inflammation and islet immunocyte recruitment capacity associated with autoimmune diabetes (in Biobreeding rats) [RatIslet_Longitudinal]", "dateAssigned" : "2016-04-21T00:00:00.000-05:00", "summary" : "Sequencing of the bacterial 16S rRNA gene revealed that these treatments significantly altered the ileal and cecal microbiota, resulting in increases in the Firmicutes:Bacteriodetes ratio, and abundances of lactobacilli and butyrate producing genera. Both treatments partially normalized the peripheral inflammatory state, reducing plasma cytokine, chemokine and TLR-4 activity levels. The proinflammatory islet transcriptome was more extensively normalized by HCD and immune-fluorescent staining revealed reductions in β-cell chemokine expression. HCD and antibiotic treatment did not normalize BB rat PBMC hyper-responsiveness to ex vivo mitogen stimulation. Combined, these studies link islet-level T1D susceptibility in BB rats to a genetically controlled innate inflammatory state that is influenced by environmental determinants encompassing the diet and the intestinal microbiota.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80517" }, "primaryId" : "GEO:GSE80517", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80517" } ] }, "title" : "Modulation of the gastrointestinal microbiota normalizes the systemic inflammation and islet immunocyte recruitment capacity associated with autoimmune diabetes (in Biobreeding rats) [RatPBMC_D30HCD-ABS]", "dateAssigned" : "2016-04-21T00:00:00.000-05:00", "summary" : "Sequencing of the bacterial 16S rRNA gene revealed that these treatments significantly altered the ileal and cecal microbiota, resulting in increases in the Firmicutes:Bacteriodetes ratio, and abundances of lactobacilli and butyrate producing genera. Both treatments partially normalized the peripheral inflammatory state, reducing plasma cytokine, chemokine and TLR-4 activity levels. The proinflammatory islet transcriptome was more extensively normalized by HCD and immune-fluorescent staining revealed reductions in β-cell chemokine expression. HCD and antibiotic treatment did not normalize BB rat PBMC hyper-responsiveness to ex vivo mitogen stimulation. Combined, these studies link islet-level T1D susceptibility in BB rats to a genetically controlled innate inflammatory state that is influenced by environmental determinants encompassing the diet and the intestinal microbiota.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80638" }, "primaryId" : "GEO:GSE80638", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80638" } ] }, "title" : "Alteration of gene expression profile of cerebelllar neuron-enriched cultures from neonatal rats by nicotine, acetamiprid, or imidacloprid treatment [nicotine]", "dateAssigned" : "2016-04-25T00:00:00.000-05:00", "summary" : "Neonicotinoids are considered safe because of their low affinities to mammalian nicotinic acetylcholine receptors (nAChRs) relative to insect nAChRs. However, because of importance of nAChRs in mammalian brain development, there remains a need to establish the safety of chronic neonicotinoid exposures with regards to children’s health. Here we examined the effects of long-term (14 days) and low dose (1 µM) exposure of neuron-enriched cultures from neonatal rat cerebellum to nicotine and two neonicotinoids: acetamiprid and imidacloprid. Immunocytochemistry revealed no differences in the number or morphology of immature neurons or glial cells in any group versus untreated control cultures. However, a slight disturbance in Purkinje cell dendritic arborization was observed in the exposed cultures. Next we performed transcriptome analysis on total RNAs using microarrays, and identified significant differential expression (p < 0.05, q < 0.05, =1.5 fold) between control cultures versus nicotine-, acetamiprid-, or imidacloprid-exposed cultures in 34, 48, and 67 genes, respectively. Common to all exposed groups were nine genes essential for neurodevelopment, suggesting that chronic neonicotinoid exposure alters the transcriptome of the developing mammalian brain in a similar way to nicotine exposure. Our results highlight the need for further careful investigations into the effects of neonicotinoids in the developing mammalian brain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27782041" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80652" }, "primaryId" : "GEO:GSE80652", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80652" } ] }, "title" : "Alteration of gene expression profile of cerebelllar neuron-enriched cultures from neonatal rats by nicotine, acetamiprid, or imidacloprid treatment [acetamiprid]", "dateAssigned" : "2016-04-25T00:00:00.000-05:00", "summary" : "Neonicotinoids are considered safe because of their low affinities to mammalian nicotinic acetylcholine receptors (nAChRs) relative to insect nAChRs. However, because of importance of nAChRs in mammalian brain development, there remains a need to establish the safety of chronic neonicotinoid exposures with regards to children’s health. Here we examined the effects of long-term (14 days) and low dose (1 µM) exposure of neuron-enriched cultures from neonatal rat cerebellum to nicotine and two neonicotinoids: acetamiprid and imidacloprid. Immunocytochemistry revealed no differences in the number or morphology of immature neurons or glial cells in any group versus untreated control cultures. However, a slight disturbance in Purkinje cell dendritic arborization was observed in the exposed cultures. Next we performed transcriptome analysis on total RNAs using microarrays, and identified significant differential expression (p < 0.05, q < 0.05, =1.5 fold) between control cultures versus nicotine-, acetamiprid-, or imidacloprid-exposed cultures in 34, 48, and 67 genes, respectively. Common to all exposed groups were nine genes essential for neurodevelopment, suggesting that chronic neonicotinoid exposure alters the transcriptome of the developing mammalian brain in a similar way to nicotine exposure. Our results highlight the need for further careful investigations into the effects of neonicotinoids in the developing mammalian brain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27782041" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80653" }, "primaryId" : "GEO:GSE80653", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80653" } ] }, "title" : "Alteration of gene expression profile of cerebelllar neuron-enriched cultures from neonatal rats by nicotine, acetamiprid, or imidacloprid treatment [imidacloprid]", "dateAssigned" : "2016-04-25T00:00:00.000-05:00", "summary" : "Neonicotinoids are considered safe because of their low affinities to mammalian nicotinic acetylcholine receptors (nAChRs) relative to insect nAChRs. However, because of importance of nAChRs in mammalian brain development, there remains a need to establish the safety of chronic neonicotinoid exposures with regards to children’s health. Here we examined the effects of long-term (14 days) and low dose (1 µM) exposure of neuron-enriched cultures from neonatal rat cerebellum to nicotine and two neonicotinoids: acetamiprid and imidacloprid. Immunocytochemistry revealed no differences in the number or morphology of immature neurons or glial cells in any group versus untreated control cultures. However, a slight disturbance in Purkinje cell dendritic arborization was observed in the exposed cultures. Next we performed transcriptome analysis on total RNAs using microarrays, and identified significant differential expression (p < 0.05, q < 0.05, =1.5 fold) between control cultures versus nicotine-, acetamiprid-, or imidacloprid-exposed cultures in 34, 48, and 67 genes, respectively. Common to all exposed groups were nine genes essential for neurodevelopment, suggesting that chronic neonicotinoid exposure alters the transcriptome of the developing mammalian brain in a similar way to nicotine exposure. Our results highlight the need for further careful investigations into the effects of neonicotinoids in the developing mammalian brain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27782041" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80721" }, "primaryId" : "GEO:GSE80721", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80721" } ] }, "title" : "Effect of high fat diet on the rat germ cell transcriptome", "dateAssigned" : "2016-04-27T00:00:00.000-05:00", "summary" : "CONCLUSIONS: HFD consumption by maternal grandfathers results in a disrupted metabolic phenotype in grandsons. This effect is not mediated by alterations to the GC transcriptome.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27550193" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80953" }, "primaryId" : "GEO:GSE80953", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80953" } ] }, "title" : "Temporal comparison of transcriptomic alterations in human, mouse and rat primary B lymphocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)", "dateAssigned" : "2016-04-29T00:00:00.000-05:00", "summary" : "RNA-Seq was used to analyze and compare temporal TCDD-induced gene expression changes in primary human, mouse and rat B cells. Most of the differentially expressed genes exibited species-specific expression. Cross-species comparison identified 28 orthologs commonly deregulated in all 3 species. The study provides new insight into mechanisms of TCDD-induced suppression of B cell effector function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27913140" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80965" }, "primaryId" : "GEO:GSE80965", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80965" } ] }, "title" : "Increased gene expression in the peridontium of unopposed molars in rats", "dateAssigned" : "2016-04-29T00:00:00.000-05:00", "summary" : "We used microarrays to detail gene expression underlying post-emergent tooth eruption and identified distinct classes of up-regulated genes during this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80967" }, "primaryId" : "GEO:GSE80967", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE80967" } ] }, "title" : "Genome-wide characterization of CREB-dependent transcriptional programs in astrocytes", "dateAssigned" : "2016-04-29T00:00:00.000-05:00", "summary" : "Transcriptome profiling of astrocyte cultures treated with forskolin (FSK), noradrenaline (NE) or infected with adenovirus carrying a constitutively active form of CREB (VP16-CREB) vs. untreated or infected with null virus. Goal is to characterize the transcriptional programs elicited by CREB activation in astrocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28743894" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81061" }, "primaryId" : "GEO:GSE81061", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81061" } ] }, "title" : "Remodeling of synaptic transmission genomic fabrics in a model of infantile spasms", "dateAssigned" : "2016-05-03T00:00:00.000-05:00", "summary" : "We profiled the whole transcriptomes of male rat hypothalamic arcuate nuclei to determine the remodeling of the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission in epilepsy and recovery following different treatments. The rats were prenatally exposed (G15) to betamethasone (or just saline for control) followed by repeated adiministration of N-Methyl-D-Aspartic acid on postnatal days 12, 13 and 15 which triggered infantile spasms. Pups were treated with either ATCH, PMX53 (a potent C5ar1 antagonist) or saline to act as a control, on days 13, 14 and 15 prior to NMDA administration to determine what effects each treatment had on transcriptome recovery. Our Genomic Fabric Paradigm (GFP) is proposed as a transformative research approach to enhance the understanding of the brain transcriptomic alterations in epileptic rats and recovery following various treatments. The genomic fabric of a particular synapse is the structured transcriptome associated with the most interconnected and stably expressed gene network responsible for that type of neurotransmission. GFP refines the description of functional pathways by selecting the most prominent genes and determining their networking. Moreover, it quantifies the remodeling of functional pathways and their interplay in disease and recovery in response to a treatment. We found that priming with betamethasone had substantial consequences on the topology of the genomic fabrics of all kind of synaptic transmission and that NMDA-induced spasms strongly exacerbated the remodeling of these fabrics. However, ACTH treatment, which is effective in significantly improving seizure outcomes, recovered 49% of the normal transcriptome in the hypothalamic arcuate nucleus. Surprisingly, PMX53 treatment recovered 64% of the normal transcriptome despite having no significant effect on behavioural seizure outcomes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81114" }, "primaryId" : "GEO:GSE81114", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81114" } ] }, "title" : "RNA-Seq analysis of the cystic fibrosis rat small intestine", "dateAssigned" : "2016-05-04T00:00:00.000-05:00", "summary" : "Background: A recently developed animal model of the genetic disease is the cystic fibrosis (CF) rat, which similar to other animal models of CF exhibits a lethal intestinal phenotype. To begin characterizing the CF rat intestinal phenotype, we investigated global gene expression in the CF rat small intestine. Methods: Total RNA was extracted from full thickness of the entire small intestines of wild type (WT) and CF rats just before weaning. Results: There were 890 genes with significantly different expression levels (1.2-fold cutoff) comparing CF to wild type (WT), including 485 genes increased and 405 decreased in the CF intestine. The major pathways associated with these changes were inflammation, lipid metabolism, cytochrome P450-mediated degradative pathways, and cell growth/death. Comparison of the rat RNA-Seq dataset to earlier microarray analysis using a CFTR knockout mouse showed significant overlap with the CF rat small intestine. Conclusions: The small intestine of the new CF rat model exhibits numerous alterations in gene expression similar to other animal models of CF which indicate this will be an additional new model to study the gut effects CF.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81216" }, "primaryId" : "GEO:GSE81216", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81216" } ] }, "title" : "SpermBase - A database for sperm-borne RNA contents", "dateAssigned" : "2016-05-06T00:00:00.000-05:00", "summary" : "Conclusions: Our study demonstrates an effective, near-universal approach to the study of sperm-borne RNAs, and identifies conserved characteristics in the large and small RNA populations of mammalian sperm.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81302" }, "primaryId" : "GEO:GSE81302", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81302" } ] }, "title" : "Expression data from rat brain following ischemic stroke or undercut", "dateAssigned" : "2016-05-10T00:00:00.000-05:00", "summary" : "Despite well-known risk factors such as stroke and head trauma, it has not been clinically effective to prevent acquired epilepsy. To do so, it is crucial to understand what commonly drives neural hyperexcitability. Using comparative transcriptome analyses with different models of acquired epilepsy including stroke and head trauma (the present GEO case), as well as blood-brain barrier (BBB) disruption, albumin, and TGFβ application (GEO accession number: GSE12304), we show that TGFβ signaling activation following BBB disruption commonly occurs regardless of brain region and insult types, accompanied by the strong upregulation of genes relevant to inflammation and extracellular matrix (ECM) modulation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28794441" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81331" }, "primaryId" : "GEO:GSE81331", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81331" } ] }, "title" : "Alterations in Tissue microRNA after Heat Stress in the Conscious Rat: Potential Biomarkers of Organ-Specific Injury", "dateAssigned" : "2016-05-11T00:00:00.000-05:00", "summary" : "Heat illness, which remains an occupational and environmental hazard, can be caused by excessive strain or heat load in combination with other factors. In the 10-year period from 1999 to 2009, an average of 658 annual heat-related deaths occurred in the United States. While heat stress at the cellular level has been studied, a paucity of risk assessment and injury biomarkers as well as therapeutic interventions remains. To identify novel biomarkers and to further understand the molecular mechanisms of heat stress, we identified differentially expressed microRNAs (miRNAs) in the heart, liver, and kidney from a conscious rat model at three time points. We distinguished the effect in animals with histopathological evidence of heart injury from those without evidence of organ injury. In animals without evidence of injury, we identified a total of 45 unique modulated miRNAs, whereas in the three animals with evidence of injury, we identified 171 unique differentially expressed miRNAs. The majority of the perturbed miRNAs were both time and tissue specific. Using the data from a microarray companion study, we identified the mRNAs that are the predicted targets of the differentially expressed miRNAs and performed pathway enrichment analysis. The enrichment analysis suggested that the perturbed miRNAs are involved in biological pathways related to energy metabolism, the unfolded protein response, and organ injury. These miRNAs may serve as organ-specific heat stress biomarkers of exposure or effect, as well as identify potential targets of heat illness prevention.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81346" }, "primaryId" : "GEO:GSE81346", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81346" } ] }, "title" : "Microarray analysis of gene expression in liver, adipose tissue and skeletal muscle in response to chronic dietary administration of NDGA to high-fructose fed dyslipidemic rats", "dateAssigned" : "2016-05-11T00:00:00.000-05:00", "summary" : "A high-fructose diet (HFrD) fed rat model of hypertriglyceridemia, dyslipidemia, insulin resistance and hepatic steatosis was employed to investigate the global transcriptional changes in the lipid metabolizing pathways in three insulin sensitive tissues:, liver, skeletal muscle and adipose tissue in response to chronic dietary administration of NDGA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27708683" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81400" }, "primaryId" : "GEO:GSE81400", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81400" } ] }, "title" : "microRNAs profiles of contrast-induced acute kidney injury rats", "dateAssigned" : "2016-05-13T00:00:00.000-05:00", "summary" : "Contrast-induced acute kidney injury (CI-AKI) is typically defined by an increase in serum creatinine (SCr) after intravascular administration of contrast medium. Since creatinine is an unreliable indicator for acute changes in kidney function, an early biomarkers for CI-AKI diagnosis is important for initiating therapy.We assessed the hypothesis that circulating microRNAs (miRNAs) could be served as potential biomarkers to early detect CI-AKI.The rat model of acute kidney injury was developed as we previously described. We first detect miRNA profile of plasma and kidney tissue using Agilent microarray platform. 3 miRNA species with > 1.5-fold increase in plasma samples of CI-AKI rats, including miRNA-30a, miRNA-30e and miRNA-188, were selected as candidate miRNAs of potential biomarkers.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81418" }, "primaryId" : "GEO:GSE81418", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81418" } ] }, "title" : "Expression data from Rattus norvegicus cornea", "dateAssigned" : "2016-05-13T00:00:00.000-05:00", "summary" : "We used whole transcriptome microarray to monitor gene expression profies of several genes", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27561355" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81437" }, "primaryId" : "GEO:GSE81437", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81437" } ] }, "title" : "A microRNA-129-5p/Rbfox crosstalk coordinates homeostatic downscaling of excitatory synapses.", "dateAssigned" : "2016-05-13T00:00:00.000-05:00", "summary" : "Using quantitative proteomics we identified group of synaptic genes with decreased protein synthesis during homeostatic plasticity. To obtain further information about their mRNA levels/sequences (3’UTR) we performed polyA RNAseq. At the end, small RNAseq helped us to identify miRNAs that are increased during homeostatic plasticity and might regulate downregulated genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28487411" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81563" }, "primaryId" : "GEO:GSE81563", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81563" } ] }, "title" : "Expression data of normal and under developed testes obtained from sexually mature rats.", "dateAssigned" : "2016-05-18T00:00:00.000-05:00", "summary" : "Zucker (fa/fa) obese rats often have non-identical and different sized paired testes, leaving one testis underdeveloped. Our earlier study found that the underdeveloped testes have a selective decrease in docosapentaenoic acid (DPA, C22:5n-6), a dominant fatty acid in the testes", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81583" }, "primaryId" : "GEO:GSE81583", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81583" } ] }, "title" : "Notch induced changes in gene expression in NRK52-cells", "dateAssigned" : "2016-05-18T00:00:00.000-05:00", "summary" : "Overexpression of intracellular domain(NICD) of Notch1 affected the expression level of more than 1000 genes", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81628" }, "primaryId" : "GEO:GSE81628", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81628" } ] }, "title" : "Integrative genomics outlines a biphasic glucose response and a ChREBP-ROR¿ axis regulating proliferation in ß-cells", "dateAssigned" : "2016-05-19T00:00:00.000-05:00", "summary" : "Glucose is an important regulator of pancreatic ß-cell function. In addition to the acute stimulation of insulin secretion, glucose stimulates long-term adaptive changes in gene expression that can either promote or antagonize the proliferative potential and function of ß-cells. The glucose-sensing transcription factor carbohydrate response element binding protein (ChREBP) has been shown to promote both ß-cell proliferation and dysfunction; however, the molecular mechanisms underlying these pleiotropic effects of ChREBP and glucose are not well understood. Here, we have generated time-resolved profiles of enhancer and transcriptional activity in response to glucose in the INS-1E pancreatic ß-cell line. Our data outline a biphasic response with a first wave during which metabolic genes are activated, and a second wave where cell cycle genes are induced and ß-cell identity genes are repressed. We show that ChREBP directly activates first wave genes, whereas repression and activation of second wave genes by ChREBP is indirect. By integrating motif enrichment within late-regulated enhancers with expression profiles of the associated transcription factors, we identify multiple putative regulators of the second wave, including RAR-related orphan receptor (ROR) ¿, which we demonstrate is a novel direct ChREBP target gene. Importantly, we show that ROR¿ activity is necessary for full glucose-induced proliferation of both INS-1E and primary rat ß-cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27545881" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81636" }, "primaryId" : "GEO:GSE81636", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81636" } ] }, "title" : "MicroRNA-31 promotes adverse cardiac remodeling and dysfunction in ischemic heart disease.", "dateAssigned" : "2016-05-19T00:00:00.000-05:00", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28865712" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81657" }, "primaryId" : "GEO:GSE81657", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81657" } ] }, "title" : "Rat Primary Cultured Hepatocytes: Control vs SQ1 or Pravastatin treatment.", "dateAssigned" : "2016-05-19T00:00:00.000-05:00", "summary" : "Transcriptional profiling of rat primary cultured hepatocytes comparing control (untreated), SQ1, and Pravastatin treated hepatocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27225895" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81669" }, "primaryId" : "GEO:GSE81669", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81669" } ] }, "title" : "DNase Hypersensitivity Peaks from Rat Schwann Cells", "dateAssigned" : "2016-05-20T00:00:00.000-05:00", "summary" : "We utilized DNase-Seq to identify open chromatin regions within Schwann cells. This data was used in conjunction with sequence conservation and transcription factor binding site prediction to identify putative cis-regulatory elements critical for Schwann cells. We used three independent biological replicates, and for our studies used sample 'barcode4' as a representative sample for all three. DNase HSS peaks were identified using F-Seq and HOMER, and overlapped to prioritize candidate regions. These regions were then verified using luciferase assays.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27821050" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81703" }, "primaryId" : "GEO:GSE81703", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81703" } ] }, "title" : "Nerve-derived Schwann cell precursors, acting in a paracrine fashion, are essential for mammalian digit tip regeneration [RAT]", "dateAssigned" : "2016-05-20T00:00:00.000-05:00", "summary" : "Multi-tissue regenerative capacity is lost in adult mammals with the exception of the distal digit, which regenerates via largely-uncharacterized mechanisms. Here, we demonstrate that following adult mouse distal digit removal, nerve-associated Schwann cell precursors (N-SCPs) dedifferentiate and secrete growth factors that promote expansion of the blastema and digit regeneration. Specifically, when N-SCPs were dysregulated or ablated, mesenchymal precursor proliferation in the blastema was decreased, nail and bone regeneration were impaired, and regeneration could be rescued by transplantation of exogenous N-SCPs. We show that N-SCPs secreted factors that promoted self-renewal of mesenchymal precursors, and we used transcriptomic and proteomic analysis to define candidate factors. Two of these, oncostatin M (OSM) and PDGF-AA, were made by N-SCPs in the regenerating digit, and rescued the deficits in regeneration caused by loss of N-SCPs due to denervation. Since nerves innervate every peripheral tissue, these results have broad implications for mammalian tissue repair and regeneration.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27376984" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81709" }, "primaryId" : "GEO:GSE81709", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81709" } ] }, "title" : "RNA-Seq experiments performed on rat Schwann (S16) cells", "dateAssigned" : "2016-05-20T00:00:00.000-05:00", "summary" : "We utilized RNA-Seq on rat Schwann (S16) cells to determine global gene expression. This information was generated as part of a larger effort to characterize cis-regulatory elements and global gene expression within Schwann cells. To achieve this, we generated RPKM values across two independent biological replicates. This dataset was also used to predict cis-regulatory element function on genes following CRISPR knockout studies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29716548" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81792" }, "primaryId" : "GEO:GSE81792", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81792" } ] }, "title" : "Transcriptome response to endoplasmic reticulum stress in rat oligodendrocyte precursor cells", "dateAssigned" : "2016-05-23T00:00:00.000-05:00", "summary" : "In the US, there are approximately 12,000 new cases of traumatic spinal cord injury (SCI) each year. Currently there are no neuroprotective treatments to improve outcome of SCI. Our previous research has revealed that endoplasmic reticulum stress response (ERSR) is an important contributor to oligodendrocyte death and subsequent white matter loss and locomotor impairment after contusive spinal cord injury in mice. ERSR affects activity of multiple transcription factors regulating either pro-survival- or apoptosis-promoting genes. Therefore, we characterized transcriptomic changes in ERSR-challenged oligodendrocytes as a first step to identify new targets for therapies that may attenuate their loss after SCI.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81811" }, "primaryId" : "GEO:GSE81811", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81811" } ] }, "title" : "Temporal Transcriptomic and Proteomic Landscapes of Deteriorating Pancreatic Islets in Type 2 Diabetic Rats", "dateAssigned" : "2016-05-24T00:00:00.000-05:00", "summary" : "Progressive reductions in β-cell mass and function comprise the core of the pathogenesis mechanism leading to type 2 diabetes (T2D). To understand the molecular events in this process, we quantified the temporal transcriptome and proteome of pancreatic islets from Goto-Kakizaki (GK) rats at different stages of diabetes. Integrated omics analysis allowed us to unravel the chronological order of T2D-related molecular events during GK islet deterioration. Two major events occur early in the disease, specifically, a reduction in β-cell mass caused by defective neogenesis and senescence-related low proliferation, and metabolic shift caused by mitochondrial dysfunction. Furthermore, our data revealed the evolution of compensation failure in GK islets and two distinct stages of islet inflammation: priming and amplification. Our study offers a valuable resource for the diabetes research community and will facilitate further studies aimed at protecting β-cell mass and function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28559245" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81864" }, "primaryId" : "GEO:GSE81864", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81864" } ] }, "title" : "RNA-Seq transcriptome analysis on Pdx1 + Ngn3 co-transfected rat bmMSCs", "dateAssigned" : "2016-05-25T00:00:00.000-05:00", "summary" : "We report the application of RNA-Seq technology for transcriptome analysis on Pdx1 + Ngn3 co-transfected bmMSCs. Bioinformatics analyses indicated that clean reads of the two libraries accounted for 97.24% and 97.97% of the total reads, which indicated high quality of the raw datasets. Total 2325 differentially expressed genes (DEGs) were identified in reprogrammed bmMSCs compared to the negative control, including 1476 genes up-regulated and 849 genes down-regulated. The RNA-Seq analysis globally validated in the reprogrammed cells the expression of a large number of genes involved in pancreas development, endocrine specification and islet differentiation. To the best of our knowledge, this is the first application of RNA-Seq analysis on reprogrammed MSCs towards pancreatic cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81907" }, "primaryId" : "GEO:GSE81907", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81907" } ] }, "title" : "Gene expression profiling of rat footpad skin in radiation dermatitis", "dateAssigned" : "2016-05-25T00:00:00.000-05:00", "summary" : "Radiation dermatitis is a side effect in cancer radiotherapy, where ionizing radiation is delivered to eradicate cancer. Normal tissue such as the skin is also damaged by this treatment. We report here the gene expression change in a rat footpad model of this disease.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81914" }, "primaryId" : "GEO:GSE81914", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81914" } ] }, "title" : "microRNA data from atrophied rat gastrocnemius of 5 days post denervation versus sham control", "dateAssigned" : "2016-05-26T00:00:00.000-05:00", "summary" : "We used microarrays to examine microRNA profiles in rat gastrocnemius muscle of 5 days after denervation of sciatic nerve versus sham control.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28541289" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81972" }, "primaryId" : "GEO:GSE81972", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE81972" } ] }, "title" : "Determination of the RNA linked to the paraspeckle in the GH4C1 cell line", "dateAssigned" : "2016-05-27T00:00:00.000-05:00", "summary" : "The goal of this study was to determine the identity of the RNA linked to the paraspeckles in the rat GH4C1 cell line.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27441387" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82112" }, "primaryId" : "GEO:GSE82112", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82112" } ] }, "title" : "Characterization of aldehyde dehydrogenase 1 high ovarian cancer cells: Towards targeted stem cell therapy [FNAR-C1]", "dateAssigned" : "2016-06-01T00:00:00.000-05:00", "summary" : "Conclusions: Based on functional characterization, ALDHhigh ovarian cancer cells represent an ovarian CSC population. Differential gene expression identified drugable targets that have the potential for therapeutic efficacy against ovarian CSCs from multiple subtypes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27017984" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82145" }, "primaryId" : "GEO:GSE82145", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82145" } ] }, "title" : "A Potential Role of the Unfolded Protein Response in the Impaired Production and Release of Epinephrine in Recurrent Hypoglycemia", "dateAssigned" : "2016-06-01T00:00:00.000-05:00", "summary" : "In order to gain further insight into the molecular mechanism(s) mediating the blunted epinephrine responses following recurrent hypoglycemia we utilized global gene expression profiling approach. Our results indicate the association between defective counterregulation (impaired epinephrine release) and the activation of the unfolded protein response as well as increased neuropeptide signaling, altered ion homeostasis and downregulation of proteins involved in Ca2+-dependent exocytosis of secretory vesicles.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28234964" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82146" }, "primaryId" : "GEO:GSE82146", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82146" } ] }, "title" : "Polysomal and total RNA in controls and after 10 min global brain ischemia and 8 hours of reperfusion", "dateAssigned" : "2016-06-02T00:00:00.000-05:00", "summary" : "We used microarrays to compared total and polysome-bound mRNAs in CA1 and CA3 at 8 hr reperfusion after 10 min CGBI in Long Evans male rats to ascertain differences in total vs polysome-bound gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27381823" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82165" }, "primaryId" : "GEO:GSE82165", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82165" } ] }, "title" : "The lncRNA genomic landscape of oligodendrocytes reveals myelination control by a lncOL1/Suz12 complex in the CNS [ChIPSeq]", "dateAssigned" : "2016-06-02T00:00:00.000-05:00", "summary" : "Long noncoding RNAs (lncRNAs) are emerging as important regulators of cellular functions, but their roles in myelination in the CNS remain undefined. Through de novo transcriptome reconstruction at multiple stages, we establish dynamic expression profiles of lncRNAs during oligodendrocyte lineage progression and uncover a cohort of oligodendrocyte-enriched lncRNAs. Co-expression network analysis reveals a cohort of lncRNAs is linked to protein-coding genes associated with oligodendrocyte maturation. We identify a conserved chromatin-associated oligodendrocyte-restricted lncRNA, lncOL1. Overexpression of lncOL1 promotes oligodendrocyte differentiation in the developing brain, whereas genetic inactivation of lncOL1 causes defects in myelination and remyelination in the CNS. We further show that lncOL1 interacts with Suz12, a component of polycomb repressive complex 2, to promote oligodendrocyte differentiation in part through Suz12-mediated silencing of a differentiation inhibitory network that antagonizes OL maturation. Together, our findings demonstrate lncRNAs as a key layer of the genetic circuitry that controls CNS myelination and myelin repair.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28041882" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82195" }, "primaryId" : "GEO:GSE82195", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82195" } ] }, "title" : "Changes in mRNA in the dorsal root ganglion after CNS injury and intramuscular neurotrophin-3 treatment", "dateAssigned" : "2016-06-02T00:00:00.000-05:00", "summary" : "Brain and spinal injury often impair sensorimotor processing in the spinal cord and reduce mobility. We established that complete transection of corticospinal pathways in the pyramids leads to increased spasms, excessive mono- and polysynaptic spinal reflexes and impaired locomotion in rats. Intramuscular neurotrophin-3 treatment at a clinically-feasible time-point after injury reduced these signs of spasticity. We found Neurotrophin-3 reduced spastic movements and improved neurophysiological sensorimotor control. Furthermore, the balance of inhibitory and excitatory synapses in the cord and the level of an ion transporter in motor neuron membranes required for normal reflexes were normalized. We discovered that Neurotrophin-3 is transported in sensory afferents from muscles to the dorsal root ganglia. Using genome-wide RNA sequencing of the whole cervical level 6-8 dorsal root ganglia, we explored mRNA changes in afferent neurons that were present 10 weeks after bilateral pyramidotomy. Many of the dysregulated genes are involved in axon guidance and plasticity. Intramuscular neurotrophin-3 treatment normalized many of those gene changes and may be one of the mechanisms how reflexes, functional recovery and molecular markers in the spinal cord are restored. This identifies neurotrophin-3 as a therapy that treats the underlying causes of spasticity and not only its symptoms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30364576" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82196" }, "primaryId" : "GEO:GSE82196", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82196" } ] }, "title" : "Changes in miRNAs in the dorsal root ganglion after CNS injury and intramuscular neurotrophin-3 treatment", "dateAssigned" : "2016-06-02T00:00:00.000-05:00", "summary" : "Brain and spinal injury often impair sensorimotor processing in the spinal cord and reduce mobility. We established that complete transection of corticospinal pathways in the pyramids leads to increased spasms, excessive mono- and polysynaptic spinal reflexes and impaired locomotion in rats. Intramuscular neurotrophin-3 treatment at a clinically-feasible time-point after injury reduced these signs of spasticity. We found Neurotrophin-3 reduced spastic movements and improved neurophysiological sensorimotor control. Furthermore, the balance of inhibitory and excitatory synapses in the cord and the level of an ion transporter in motor neuron membranes required for normal reflexes were normalized. We discovered that Neurotrophin-3 is transported in sensory afferents from muscles to the dorsal root ganglia. Using genome-wide small RNA sequencing of the whole cervical level 6-8 dorsal root ganglia, we explored miRNA changes in afferent neurons that were present 10 weeks after bilateral pyramidotomy. Many of the dysregulated genes are involved in axon guidance and plasticity. Intramuscular neurotrophin-3 treatment normalized many of those gene changes and may be one of the mechanisms how reflexes, functional recovery and molecular markers in the spinal cord are restored. This identifies neurotrophin-3 as a therapy that treats the underlying causes of spasticity and not only its symptoms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30364576" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82215" }, "primaryId" : "GEO:GSE82215", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82215" } ] }, "title" : "Gene expression profiles of mesenterial adipose tissue of newborn rats from dams that were either fed a vitamin D adequate (1,000 IU vitamin D/kg diet) or a vitamin D deficient diet (0 IU vitamin D/kg diet)", "dateAssigned" : "2016-06-03T00:00:00.000-05:00", "summary" : "The aim of the study was to investigate the role of vitamin D on adipocyte development. To this end, rat dams (Sprague-Dawley rats ) were fed diets with 0 or 1,000 IU vitamin D3 per kg diet 5 weeks prior to conception until the end of lactation. By using high-density DNA microarrays, we analyzed the gene-expression profile of mesenterial adipose tissue of both groups of newborn rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82243" }, "primaryId" : "GEO:GSE82243", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82243" } ] }, "title" : "Signal-Dependent Recruitment of BRD4 to Cardiomyocyte Super-Enhancers is Suppressed by a MicroRNA [ChIP-Seq]", "dateAssigned" : "2016-06-03T00:00:00.000-05:00", "summary" : "BRD4 governs pathological cardiac gene expression by binding acetylated chromatin, resulting in enhanced RNA polymerase II (Pol II) phosphorylation and transcription elongation. Here, we describe a signal-dependent mechanism for regulation of BRD4 in cardiomyocytes. BRD4 expression is suppressed by microRNA-9 (miR-9), which targets the 3’ untranslated region of the Brd4 transcript. In response to stress stimuli, miR-9 is downregulated, leading to derepression of BRD4 and enrichment of BRD4 at long-range super-enhancers (SEs) associated with pathological cardiac genes. A miR-9 mimic represses stimulus-dependent targeting of BRD4 to SEs and blunts Pol II phosphorylation at proximal transcription start sites, without affecting BRD4 binding to SEs that control constitutively expressed cardiac genes. These findings suggest that dynamic enrichment of BRD4 at SEs genome-wide serves a crucial role in the control of stress-induced cardiac gene expression, and define a miR-dependent signaling mechanism for the regulation of chromatin state and Pol II phosphorylation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82247" }, "primaryId" : "GEO:GSE82247", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82247" } ] }, "title" : "Expression data from SHP specific siRNA or nonspecefic siRNA transfected rat astrocytes [extended study]", "dateAssigned" : "2016-06-03T00:00:00.000-05:00", "summary" : "To clarify the effect of SHP in LXRs-mediated signaling pathway, we performed global gene expression analysis of SHP siRNA transfected- or control siRNA transfected- astrocytes after IFN-¿ and LXRs agonist. Microarray analysis revealed that expression of several genes encoding inflammatory mediators were reversed in SHP siRNA transfected-astrocytes, when compared with control siRNA transfected-astrocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27485016" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82339" }, "primaryId" : "GEO:GSE82339", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE82339" } ] }, "title" : "LncRNA Chaer contributes to the transcriptome reprogramming during phenylephrine-induced hypertrophy in neonatal rat ventricular myocytes", "dateAssigned" : "2016-06-07T00:00:00.000-05:00", "summary" : "We compared the transcriptome modified by siRNA-mediated cardiac hypertrophy associated epigenentic regulator (Chaer) with negative control siRNA treated neonatal rat ventricular myocytes with or without phenylephrine treatment. The results suggest that Chaer knockdown broadly blocks the phenylephrine-induced hypertrophic programming of the transcriptome.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27618650" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83105" }, "primaryId" : "GEO:GSE83105", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83105" } ] }, "title" : "Expression data from Sertoli cells treated with 0.1µM NP, 0.1mM MBP, 0.1µM NP+0.1mM MBP and solvent control", "dateAssigned" : "2016-06-08T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes and miRNAs after treated with 0.1µM NP, 0.1mM MBP, 0.1µM NP+0.1mM MBP and solvent control.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83106" }, "primaryId" : "GEO:GSE83106", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83106" } ] }, "title" : "Expression data from 9-day-old rat Sertoli cells and MBP-treated rat Sertoli cells", "dateAssigned" : "2016-06-08T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated and down-regulated genes during this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83220" }, "primaryId" : "GEO:GSE83220", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83220" } ] }, "title" : "High-Fat High-Sugar Diet Induces Polycystic Ovary Syndrome in a Rodent Model", "dateAssigned" : "2016-06-10T00:00:00.000-05:00", "summary" : "Obesity has been linked with a host of metabolic and reproductive disorders including polycystic ovary syndrome (PCOS). While a distinct link exists between obesity and PCOS, the exact pathogenesis of the disease remains less understood and limited research has explored the impact of diet on the development of PCOS. With the primary symptoms of PCOS including hyperandrogenism, anovulation, and polycystic ovaries, most animal models utilize androgen treatment to effectively induce PCOS. However, these models fail to address the underlying causes of disease symptoms and do not effectively demonstrate the metabolic features of the disease such as hyperinsulinemia. Here, we present a novel rodent model of diet-induced obesity that recapitulates both the metabolic and reproductive phenotypes of human PCOS. In utilizing a high-fat high-sugar (HFHS) diet, we have created a model of PCOS that allows for the study of metabolic parameters and their impact on ovarian follicle development and reproductive health. Animals on the HFHS diet not only demonstrated signs of metabolic impairment, but they also developed polycystic ovaries and experienced irregular estrous cycling marked by an extended period spent in estrus. Though hyperandrogenism was not characteristic of HFHS diet animals as a group, testosterone levels were predictive of a polycystic ovarian morphology. Importantly, PCOS was induced similarly to the disease etiology in humans, allowing this model to offer the unique opportunity to study PCOS at its genesis rather than following the development of disease symptoms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28203719" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83228" }, "primaryId" : "GEO:GSE83228", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83228" } ] }, "title" : "Signal-Dependent Recruitment of BRD4 to Cardiomyocyte Super-Enhancers is Suppressed by a MicroRNA [RNA-Seq]", "dateAssigned" : "2016-06-10T00:00:00.000-05:00", "summary" : "BRD4 governs pathological cardiac gene expression by binding acetylated chromatin, resulting in enhanced RNA polymerase II (Pol II) phosphorylation and transcription elongation. Here, we describe a signal-dependent mechanism for regulation of BRD4 in cardiomyocytes. BRD4 expression is suppressed by microRNA-9 (miR-9), which targets the 3’ untranslated region of the Brd4 transcript. In response to stress stimuli, miR-9 is downregulated, leading to derepression of BRD4 and enrichment of BRD4 at long-range super-enhancers (SEs) associated with pathological cardiac genes. A miR-9 mimic represses stimulus-dependent targeting of BRD4 to SEs and blunts Pol II phosphorylation at proximal transcription start sites, without affecting BRD4 binding to SEs that control constitutively expressed cardiac genes. These findings suggest that dynamic enrichment of BRD4 at SEs genome-wide serves a crucial role in the control of stress-induced cardiac gene expression, and define a miR-dependent signaling mechanism for the regulation of chromatin state and Pol II phosphorylation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83308" }, "primaryId" : "GEO:GSE83308", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83308" } ] }, "title" : "Differential analysis of testosterone induced genes by peritubular cells", "dateAssigned" : "2016-06-13T00:00:00.000-05:00", "summary" : "Agilent's whole genome microarray platform was used to profile differentially expressed genes induced upon testosterone treatment of testicular myoid peritubular cells isolated from adult rat testes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83323" }, "primaryId" : "GEO:GSE83323", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83323" } ] }, "title" : "Loss of MeCP2 in the rat models regression, impaired sociability and transcriptional deficits of Rett syndrome", "dateAssigned" : "2016-06-14T00:00:00.000-05:00", "summary" : "The goal of this study was to characterize a novel Mecp2 allele in the laboratory rat, a distinct rodent species from the laboratory mouse with unique features. The allele was created by zinc finger-nuclease (ZFN) targeting (SAGE/Horizon) of the X-linked gene, Methyl-CpG-Binding Protein 2 (Mecp2), resulting in normal Mecp2 RNA abundance, but absent protein in male rats as expected due to the presence of only one copy of mutant Mecp2, and an approximate 50% reduction in female rats as expected from animals that harbor one wild-type copy and one mutant copy of Mecp2. Behavioral characterization of female rats with the Mecp2 ZFN allele and wild-type littermates was conducted, and Mecp2 ZFN/+ female rats showed behavioral phenotypes that were consistent with disease-like features present during the early stages of disease onset in the neurological disorder Rett syndrome. The goal of conducting RNAseq studies was to compare existing gene expression alterations in the Mecp2 rat with one of the most widely studied Mecp2 mouse model. Hypothalami were obtained from males with complete loss of MeCP2 (ZFN/y) and wild-type littermate male rats for RNA-seq studies. Common and unique gene expression alterations among the Mecp2 rodents that were then tested in human Rett and control postmortem brain revealed the benefit of combining findings from both models, suggesting the predictive validity of this approach for future studies for the identification of potential preclinical outcome measures. QPCR validation in an independent set of rats was conducted with a subset of genes from the Mecp2 ZFN rat RNA-seq data as an additional control measure. Taken together, these findings demonstrate that the Mecp2 rat model is a complementary tool with unique features for the study of RTT and highlight the potential benefit of cross-species analyses in identifying potential disease-relevant preclinical outcome measures.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27365498" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83336" }, "primaryId" : "GEO:GSE83336", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83336" } ] }, "title" : "Epigenetics and energetics in ventral hippocampus mediate rapid antidepressant action: implications for treatment-resistance", "dateAssigned" : "2016-06-14T00:00:00.000-05:00", "summary" : "Although regulation of energy metabolism has been linked with multiple disorders, its role in depression and responsiveness to antidepressants is less-known. We found that an epigenetic and energetic agent, acetyl-L-carnitine (LAC, oral administration), rapidly rescued the depressive- and central and systemic metabolic-like phenotype of LAC-deficient Flinders Sensitive Line (FSL) rats. After acute stress during LAC treatment, a subset of FSL continued to respond to LAC (rFSL), whereas the other subset did not respond (nrFSL). RNAseq for the ventral dentate-gyrus (vDG), a mood-regulatory region, identified metabolic factors as key markers predisposing to depression (insulin receptors Insr, glucose transporters Glut-4 and Glut-12, the regulator of appetite Cartpt) and to LAC responsiveness (leptin receptors Lepr, metabotropic glutamate receptors-2 mGlu2, neuropeptide-Y NPY, and mineralocorticoid receptors MR). Furthermore, we found that stress-induced treatment-resistance in nrFSL shows a new gene profile, including the metabolic regulator factors Elovl7 and Cyb5r2 and the synaptic regulator NPAS4. Finally, while improving central energy regulation and exerting rapid antidepressant-like effects, LAC corrected a systemic hyperinsulinemia and hyperglycemia.tance in rFSL and failed to do that in nrFSL. These findings establish CNS energy regulation as factor to be considered for the development of better therapeutics. Agents, like LAC, which regulate metabolic factors and reduce glutamate overflow, could rapidly ameliorate depression and could also be considered for treatment of insulin-resistance in depressed subjects. The approach here serves as a model for identifying markers and underlying mechanisms of predisposition to diseases and treatment responsiveness that may be useful in translation to human behavior and psychopathology.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27354525" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83349" }, "primaryId" : "GEO:GSE83349", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83349" } ] }, "title" : "Gene modulation in acetic acid-induced oral ulcerative mucositis", "dateAssigned" : "2016-06-14T00:00:00.000-05:00", "summary" : "To reveal the molecular mechanisms underlying oral ulcerative mucositis-induced pain, we investigated putative pain-associated mediators, pain-related behaviors and gene modulation in a rat oral mucositis model. On day 1 after acetic acid treatment, the mucosal area showed slight redness and swelling but no evidence of ulceration or pain induction. On day 2, oral ulcers were obvious, as was the induction of spontaneous and mechanical pain. In the treated mucosal area, bacterial loading and prostaglandin E2 increased beginning on day 2; no significant changes were observed on day 1. DNA microarray analysis of trigeminal ganglion tissue collected on day 2 identified 32 significantly regulated genes (>1.5-fold change in expression). The up-regulation of the top 3 genes, Hamp (hepcidin antimicrobial peptide), Reg3b (regenerating islet-derived 3ß) and Serpina3n (serine peptidase inhibitor A3N), was validated through quantitative RT-PCR. Systemic antibiotic pre-treatment did not increase the mRNA levels. Therefore, we conclude that the oral ulcerative mucositis-induced pain is caused by infectious inflammation of the ulcerative area and stimulates anti-bacterial and anti-peptidase gene expressions in sensory neurons.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83385" }, "primaryId" : "GEO:GSE83385", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83385" } ] }, "title" : "Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia", "dateAssigned" : "2016-06-15T00:00:00.000-05:00", "summary" : "Levodopa-induced dyskinesia (LID) is a persistent behavioral sensitization that develops after repeated levodopa (L-DOPA) exposure in Parkinson disease (PD) patients. we used reduced representation bisulfite sequencing to determine the methylation status of cytosines genome wide at base pair resolution following a parkinsonian-like lesion and LID development. Due to the enrichment of RRBS, we focused our analysis to cytosines in a CpG context and observed extensive locus-specific changes in DNA methylation, including a preponderance of demethylation, in the dorsal striatum following the development of dyskinetic behaviors in our animal model system. Changes in DNA methylation were concentrated in putative regulatory regions of many genes known to be aberrantly transcribed following L-DOPA exposure and enriched for genes relevant to mechanisms of synaptic plasticity. In the areas of the genome exhibiting the highest levels of effect, the magnitudes of change to methylation were strongly correlated with dyskinetic behaviors.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27307239" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83401" }, "primaryId" : "GEO:GSE83401", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83401" } ] }, "title" : "Targeting PI3K/mTOR signaling exerts potent antitumor activity in pheochromocytoma in vivo", "dateAssigned" : "2016-06-15T00:00:00.000-05:00", "summary" : "Transcriptomic analyses of tumors from rats treated with BEZ235 or placebo identified potential mediators of therapy response. Slc6a2, encoding the norepinephrine transporter (NET), was downregulated in a dose-dependent manner by BEZ235 in rat PCCs. Moreover, BEZ235 reduced Slc6a2/NET expression also in PCC cell lines (PC12, MPC, MTT). Studies of a BEZ235-resistant derivative of the MPC cell line (MPCR) confirmed that the reduction of NET expression associates with the response to the drug. Reduction of NET expression following BEZ235 treatment in vivo could be monitored by Positron Emission Tomography (PET) using a tracer targeting NET. Altogether, we demonstrate the efficacy of BEZ235 against PCC in vivo, and show that functional imaging can be employed to monitor the response of PCC to PI3K/mTOR inhibition therapy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27811202" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83610" }, "primaryId" : "GEO:GSE83610", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83610" } ] }, "title" : "Renal fibrosis mRNA classifier: validation in experimental lithium-induced interstitial fibrosis in the rat kidney", "dateAssigned" : "2016-06-22T00:00:00.000-05:00", "summary" : "In this investigation, gene expression was examined in a rat model to investigate whether the previously described MARGS based fibrosis classifier had diagnostic value in an experimental rat model of lithium-induced renal fibrosis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28002484" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83718" }, "primaryId" : "GEO:GSE83718", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83718" } ] }, "title" : "Role of PARP1 in cocaine-related memory retrieval", "dateAssigned" : "2016-06-25T00:00:00.000-05:00", "summary" : "Reward-related memory is an important factor in cocaine seeking. One necessary signaling mechanism for long-term memory formation is the activation of poly(ADP-ribose) polymerase-1 (PARP-1), via poly(ADP-ribosyl)ation. We demonstrate herein that auto-poly(ADP-ribosyl)ation of activated PARP-1 was significantly pronounced during retrieval of cocaine-associated contextual memory, in the central amygdala (CeA) of rats expressing cocaine-conditioned place preference (CPP). Intra-CeA pharmacological and shRNA depletion of PARP-1 activity during cocaine-associated memory retrieval abolished CPP. In contrast, PARP-1 inhibition after memory retrieval did not affect CPP reconsolidation process and subsequent retrievals. Chromatin Immuoprecipitation (ChIP) sequencing revealed that PARP-1 binding in the CeA is highly enriched in genes involved in neuronal signaling. We identified amongst PARP targets in CeA a single gene, yet uncharacterized and encoding a putative transposase inhibitor, at which PARP-1 enrichment dramatically increases during cocaine-associated memory retrieval and positively correlates with CPP. Our findings have important implications for understanding drug-related behaviors, and suggest possible future therapeutic targets for drug abuse.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27595592" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83776" }, "primaryId" : "GEO:GSE83776", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83776" } ] }, "title" : "DNA Methylation profile for male SD Rats with and without traumatic brain injury (TBI) by RNA-Seq, batch2", "dateAssigned" : "2016-06-27T00:00:00.000-05:00", "summary" : "To investigate the effects of TBI on affecting DNA methylations in the WBC of male SD rats by RRBS.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28174132" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83953" }, "primaryId" : "GEO:GSE83953", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE83953" } ] }, "title" : "Transcriptional signature in rat colonocytes in response to a high protein diet", "dateAssigned" : "2016-07-01T00:00:00.000-05:00", "summary" : "High protein diet alter gut microbiota composition and activity. The objective of this study is to determine the consequences of a high protein diet for the colonic epithelium in rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84011" }, "primaryId" : "GEO:GSE84011", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84011" } ] }, "title" : "ChIP-seq analysis of oligodendrocytes treated with demyelinating compound lysolecithin", "dateAssigned" : "2016-07-05T00:00:00.000-05:00", "summary" : "We performed a series of ChIP-Seq analysis, and demonstrated that Olig2 and its downstream target Gpr17 were the key factors functioning in demyelination process. During demyelination, Olig2 was significantly up-regulated, and Gpr17 was the top ranking Olig2 transcriptional target.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27733608" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84021" }, "primaryId" : "GEO:GSE84021", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84021" } ] }, "title" : "Male Rat DNA methylation in the Prefrontal Cortex at postnatal day 62 following prenatal restraint stress", "dateAssigned" : "2016-07-05T00:00:00.000-05:00", "summary" : "DNA methylation profiling of Prefrontal Cortex of male rats at postnatal day 62 whose mothers were exposed to restraint stress from gestation day 14 until delivery", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84178" }, "primaryId" : "GEO:GSE84178", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84178" } ] }, "title" : "SIMVASTATIN ATTENUATES LIVER INJURY IN RODENTS WITH BILIARY CIRRHOSIS SUBMITTED TO HEMORRHAGE/RESUSCITATION", "dateAssigned" : "2016-07-08T00:00:00.000-05:00", "summary" : "In variceal bleeding liver function deterioration is a major cause of death. The effects of bleeding on intrahepatic microvascular dysfunction, which contributes to liver injury in cirrhosis, are largely unknown. The aims of this study were to evaluate the impact of hemorrhage/resuscitation (H/R) on cirrhotic microcirculation, and whether simvastatin, a drug that improves liver microcirculation, has hepatoprotective effects. The study was performed in three groups of rats: controls, rats with biliary cirrhosis (CBDL) and CBDL rats pre-treated with 3 doses (5 mg*Kg-1*day-1) of simvastatin. Rats were submitted to H/R or sham procedure. Subsequently, livers were isolated and perfused for functional assessment of liver microcirculation. Liver transcriptome was assessed with microarrays. H/R significantly impaired endothelial-dependent vasorelaxation in cirrhotic (p=0.035) but not control livers. H/R induced a similar increase in ALT in control and cirrhotic rats, whereas the increase in AST was 10 times higher in cirrhotic than in control rats (p=0.007). Simvastatin prevented the impairment in endothelial-dependent vasorelaxation induced by H/R, and reduced by half the increase in ALT and AST (p<0.05). Transcriptomics showed a marked upregulation of genes related to inflammatory response after H/R in cirrhotic livers, but not in controls, and this was blunted by simvastatin. In conclusion, H/R aggravates liver microvascular dysfunction in cirrhosis, and upregulates liver inflammatory pathways. This does not occur in control livers. Simvastatin prevented H/R-induced liver endothelial dysfunction, and attenuated liver injury and liver inflammatory response, suggesting that it might have potential for protecting the cirrhotic liver during bleeding complications.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27559696" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84179" }, "primaryId" : "GEO:GSE84179", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84179" } ] }, "title" : "Effects of digested onion extracts on intestinal gene expression using rat intestine slices", "dateAssigned" : "2016-07-08T00:00:00.000-05:00", "summary" : "Rat small intestine precision cut slices were exposed for 6 hours to in vitro digested yellow (YOd) and white onion extracts (WOd) that was followed by transcriptomics analysis. The digestion was performed to mimic the digestion that in vivo takes place in the stomach and small intestine. The transcriptomics response of the rat small intestine precision cut slices was compared to that of human Caco-2 cells and the pig in-situ small intestinal segment perfusion. The microarray data for the human Caco-2 cells (GSE83893) and the pig in-situ small intestinal segment perfusion (GSE83908) have been submitted separately from the current data on rat intestine. The goal was to obtain more insight into to which extent mode of actions depend on the experimental model. A main outcome was that each of the three models pointed to the same mode of action: induction of oxidative stress and particularly the Keap1-Nrf2 pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27631494" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84202" }, "primaryId" : "GEO:GSE84202", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84202" } ] }, "title" : "Two Populations of Glucocorticoid Receptor-Binding Sites in the Male Rat Hippocampal Genome", "dateAssigned" : "2016-07-08T00:00:00.000-05:00", "summary" : "In the present study, genomic binding sites of glucocorticoid receptors (GR) were identified in vivo in the rat hippocampus applying chromatin immunoprecipitation followed by next-generation sequencing. We identified 2470 significant GR-binding sites (GBS) and were able to confirm GR binding to a random selection of these GBS covering a wide range of P values. Analysis of the genomic distribution of the significant GBS revealed a high prevalence of intragenic GBS. Gene ontology clusters involved in neuronal plasticity and other essential neuronal processes were overrepresented among the genes harboring a GBS or located in the vicinity of a GBS. Male adrenalectomized rats were challenged with increasing doses of the GR agonist corticosterone (CORT) ranging from 3 to 3000 µg/kg, resulting in clear differences in the GR-binding profile to individual GBS. Two groups of GBS could be distinguished: a low-CORT group that displayed GR binding across the full range of CORT concentrations, and a second high-CORT group that displayed significant GR binding only after administering the highest concentration of CORT. All validated GBS, in both the low-CORT and high-CORT groups, displayed mineralocorticoid receptor binding, which remained relatively constant from 30 µg/kg CORT upward. Motif analysis revealed that almost all GBS contained a glucocorticoid response element resembling the consensus motif in literature. In addition, motifs corresponding with new potential GR-interacting proteins were identified, such as zinc finger and BTB domain containing 3 (Zbtb3) and CUP (CG11181 gene product from transcript CG11181-RB), which may be involved in GR-dependent transactivation and transrepression, respectively. In conclusion, our results highlight the existence of 2 populations of GBS in the rat hippocampal genome. - See more at: http://press.endocrine.org/doi/10.1210/en.2012-2187?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed#sthash.LqK088DP.dpuf", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27457949" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84242" }, "primaryId" : "GEO:GSE84242", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84242" } ] }, "title" : "Recognition memory-induced gene expression in the perirhinal cortex: a transcriptomics analysis.", "dateAssigned" : "2016-07-11T00:00:00.000-05:00", "summary" : "It is possible to identify the key genes and pathways involved in specific physiological processes using transcriptome analyses. However, these powerful new deep sequencing-based methods have rarely been applied to studies of memory function. We used the bow-tie maze to train rats by exposing them to highly familiar objects or to novel objects. Total RNA sequencing was then used to compare the transcriptome of the perirhinal cortices of naïve control rats and rats exposed to novel and familiar stimuli. Differentially expressed genes were identified between group Novel and group Familiar rats and these included genes coding for transcription factors and extracellular matrix-related proteins. Moreover, differences in alternative splicing were also detected between the two groups. To conclude, this study shows that RNA sequencing can be used as a tool to identify differences in gene expression in behaving animals undergoing the same task but encountering different exposures.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28389337" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84249" }, "primaryId" : "GEO:GSE84249", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84249" } ] }, "title" : "Adrenalectomy plus corticosterone treatment, rat hippocampal RNA-seq", "dateAssigned" : "2016-07-11T00:00:00.000-05:00", "summary" : "Male Sprague-Dawley rats 8 weeks old, were adrenalectomized, treated with 300ug/kg corticosterone or vehicle 3 days after surgery then sacrificed 1 hour later. Hippocampi were removed and RNA extracted and processed for sequencing at the Massachusetts General Hospital Nex-Generation Sequening Core.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27457949" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84261" }, "primaryId" : "GEO:GSE84261", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84261" } ] }, "title" : "Adult Female Rat Hippocampal Tissue: Naïve vs. Contextual Fear Conditioned (Trained)[Experiment 1]", "dateAssigned" : "2016-07-11T00:00:00.000-05:00", "summary" : "naïve and trained rats 24 hours after exposure to the contextual fear conditioning paradigm. Biological replicates: 3 independent pools of 3 animals each, 6 naïve and 6 trained animals, independently conditioned and tissues were independently isolated. One replicate per array.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28001126" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84262" }, "primaryId" : "GEO:GSE84262", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84262" } ] }, "title" : "Adult Female Rat Hippocampal Tissue: Naïve vs. Contextual Fear Conditioned (Trained)[Experiment 2]", "dateAssigned" : "2016-07-11T00:00:00.000-05:00", "summary" : "naïve and trained rats 24 hours after exposure to the contextual fear conditioning paradigm. Biological replicates: 4 naïve and 4 trained animals, independently conditioned and tissues were independently isolated. One replicate per array.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28001126" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84265" }, "primaryId" : "GEO:GSE84265", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84265" } ] }, "title" : "H3K27me3 ChIP-seq in rat peripheral nerve", "dateAssigned" : "2016-07-11T00:00:00.000-05:00", "summary" : "ChIP-seq of H3K27me3 in rat peripheral nerve was used to identify sites of polycomb repression associated with genes in Schwann cells, which constitute the majority of cells in peripheral nerve. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27581455" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84272" }, "primaryId" : "GEO:GSE84272", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84272" } ] }, "title" : "Histone H3K4 trimethylation in rat peripheral nerve", "dateAssigned" : "2016-07-11T00:00:00.000-05:00", "summary" : "ChIP-seq of H3K4me3 in rat peripheral nerve was used to identify transcription start sites associated with Schwann cell-expressed genes. The analysis was performed in injured and control nerve to identify injury-responsive changes in Schwann cells. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27581455" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84289" }, "primaryId" : "GEO:GSE84289", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84289" } ] }, "title" : "Temporal analysis of hippocampal gene co-expression networks in the hyperthermia model of febrile seizures", "dateAssigned" : "2016-07-12T00:00:00.000-05:00", "summary" : "This study sought to investigate temporal changes in hippocampal gene co-expression networks during the development of rats submitted to hyperthermic seizures", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84294" }, "primaryId" : "GEO:GSE84294", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84294" } ] }, "title" : "Decreases in 15-lipoxigenase metabolites in Olmsted syndrome model rats", "dateAssigned" : "2016-07-12T00:00:00.000-05:00", "summary" : "Infiltration of mast cells, eosinophils, and neutrophils and an increase in fibrotic region were detected in unaffected skin area of Ht rats. Among ~600 lipid species examined, levels of 15-lipoxygenase (LOX) metabolites, the precursors of anti-inflammatory and pro-resolving lipid mediators, and dihydroceramides were decreased by =16-fold in Ht rats compared to wild type rats. Consistent with the decreases in the 15-LOX metabolites, expression levels of the 15-LOXs, Alox15 and Alox15b, were largely reduced. On the other hand, expression levels of the cytokines/chemokines Il36b, Ccl20, Cxcl1, and Cxcl2 and those of the Ca2+-binding proteins S100a8 and S100a9, which are implicated in epidermal proliferation, were increased. The pro-inflammatory state of Ht rats caused by decreases in 15-LOX metabolites and increases in cytokines/chemokines may contribute to the pathogenesis of OS.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28024685" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84304" }, "primaryId" : "GEO:GSE84304", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84304" } ] }, "title" : "Gene expression profiling reveals cytoplasmic U1 snRNA accumulation may cause cancers", "dateAssigned" : "2016-07-12T00:00:00.000-05:00", "summary" : "In this study, we built a model of cytoplasmic aggregation of U1 snRNA in a rat cell line. By comparing the gene expression profiling of U1 snRNA accumulated cells with their controls, 916 (about 4% of 20,000) genes were identified significantly differentially expressed. These 595 over-expressed genes and 321 repressed genes were further analyzed by GO and KEGG pathway enrichment. As a result, three of 12 enriched pathways are well-known cancer pathways, while nine of them were associated to cancers in previous studies. These findings suggest that cytoplasmic U1 snRNA accumulation may cause cancers.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84381" }, "primaryId" : "GEO:GSE84381", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84381" } ] }, "title" : "Patterns of host gene expression associated with harboring a foregut microbial community", "dateAssigned" : "2016-07-13T00:00:00.000-05:00", "summary" : "We compared gene expression in the foregut tissues of two rodent species: Stephen's woodrat (Neotoma stephensi), which harbors a dense foregut microbial community, and the lab rat (Rattus norvegicus), which lacks such a community. We found that woodrats have higher abundances of transcripts associated with smooth muscle processes, specifically a higher expression of the smoothelin-like 1 gene, which may assist in contractile properties of this tissue to retain food material in the foregut chamber. The expression of genes associated with keratinization and cornification exhibited a complex pattern of differences between the two species, suggesting distinct molecular mechanisms for this process in each of the two species. Lab rats exhibited higher abundances of transcripts associated with immune function, likely to inhibit microbial growth in the foregut of this species. Some of our results were consistent with previous findings in ruminants (high expression of facilitative glucose transporters, lower expression of B4galnt2), suggestive of possible convergent evolution, while other results were unclear, and perhaps represent novel host-microbe interactions in rodents. Overall, our results suggest that harboring a foregut microbiota is associated with changes to the functions and host-microbe interactions of the foregut tissues.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84496" }, "primaryId" : "GEO:GSE84496", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84496" } ] }, "title" : "Expressional profile of liver of CGMCC No.8730 Eurotium cristatum fermented dark tea fed high-fat diet rats", "dateAssigned" : "2016-07-18T00:00:00.000-05:00", "summary" : "Microbial fermentation is involved in the processing of a dark tea popular for centuries in Northwest China which has shown many health benefits. This study will examine anti-obesity, hyperlipidemic and hyperglycemic effects of CGMCC No.8730 Eurotium cristatum (EC) fermented dark tea (8730DT).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84524" }, "primaryId" : "GEO:GSE84524", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84524" } ] }, "title" : "Effect of a salt restriction diet on cardiac damage in a rat model of metabolic syndrome", "dateAssigned" : "2016-07-18T00:00:00.000-05:00", "summary" : "We thus performed an Agilent microarray experiment in order to identify expression variations in left ventricles of rats having a normal sodium diet (0,64%) or a low sodium diet (less than 0,01%)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28254494" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84563" }, "primaryId" : "GEO:GSE84563", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84563" } ] }, "title" : "Kidney Hypothermic Perfusion with Mesenchymal Stromal Cells or Microvesicles Protects Rat Kidney from Ischemia By Upregulation of Cell Energy Metabolism and Ion Membrane Transport Key Genes", "dateAssigned" : "2016-07-19T00:00:00.000-05:00", "summary" : "We evaluated in a rat model of Donor after Circulatory Death (DCD) the effects of pretransplant kidney conditioning with Mesenchymal Stromal Cells (MSC) or MSC derived microvescicles (MV) on ischemic injury. Fisher rats (F) were used as kidney donors, Transgenic Sprague-Dawley rats expressing Enhanced Green Fluorescence Protein (EGFP) as MSC donors. After 20 min of warm ischemia nephrectomy was performed and kidneys were perfused withBelzer solution (BS), BS supplemented with MSC (MSC) or withMV (MV) for 4 h, at 4°C. Renal damage was evaluated by histology, renal gene expression by microarray analysis and RT-PCR. Malondialdehyde, lactate, LDH, glucose and pyruvate were measured in effluent fluid. MSC/MV kidneys showed a significant minor global ischemic damage and up-regulation of three genes encoding proteins that improve cell energy metabolism (Isocitrate dehydrogenase 2, NADH dehydrogenase Fe-S protein 8, Pyruvate dehydrogenase beta) and three genes encoding proteins involved in ion membrane transport (Calbindin 1, Monocarboxylate transporter 1, Vacuolar H+-ATPase d2 subunit). Lactate, LDH and malondialdehyde in effluent fluid were significantly lower in MSC/MV kidneys than BS. Glucose was lower while pyruvate higher in MSC/MV effluent than BS, suggesting a larger use of energy substrates by MSC/MV kidneys. MSC/MV perfusion of kidneys in addition to BS through HMP protects from ischemia injury by preserving the enzymatic machinery essential for cell viability and prepares kidney to reperfusion damage.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84585" }, "primaryId" : "GEO:GSE84585", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84585" } ] }, "title" : "Remodeling of synaptic transmission genomic fabrics in the hypothalamic arcuate nucleus of a rat female model of infantile spasms", "dateAssigned" : "2016-07-19T00:00:00.000-05:00", "summary" : "We profiled the whole transcriptomes of female rat hypothalamic arcuate nuclei to determine the remodeling of the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission in epilepsy and recovery following different treatments. The rats were prenatally exposed (G15) to betamethasone (or just saline for control) followed by repeated adiministration of N-Methyl-D-Aspartic acid (NMDA) on postnatal days 12, 13 and 15 which triggered infantile spasms. Pups were treated with either ATCH, PMX53 (a potent C5ar1 antagonist) or saline to act as a control, on days 13, 14 and 15 prior to NMDA administration to determine what effects each treatment had on transcriptome recovery. Our Genomic Fabric Paradigm (GFP) is proposed as a transformative research approach to enhance the understanding of the brain transcriptomic alterations in epileptic rats and recovery following various treatments. The genomic fabric of a particular synapse is the structured transcriptome associated with the most interconnected and stably expressed gene network responsible for that type of neurotransmission. GFP refines the description of functional pathways by selecting the most prominent genes and determining their networking. Moreover, it quantifies the remodeling of functional pathways and their interplay in disease and recovery in response to a treatment. We found that priming with betamethasone had substantial consequences on the topology of the genomic fabrics of all kind of synaptic transmission and that NMDA-induced spasms strongly exacerbated the remodeling of these fabrics. Contrary to our findings in male rats, neither ACTH or PMX53 treatment recovered the normal synaptic transcriptomes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84596" }, "primaryId" : "GEO:GSE84596", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84596" } ] }, "title" : "Effect of chronic MDPV on striatal gene expression", "dateAssigned" : "2016-07-19T00:00:00.000-05:00", "summary" : "The bath salt constituent 3,4-methylenedioxypyrovalerone (MDPV) is often detected in blood of patient’s presenting at emergency rooms with a psychosis-like syndrome involving agitation, panic, confusion/cognitive impairment, violent behavior, depression, and other adverse behavioral symptoms. The mechanisms underlying MDPV’s behavioral disturbances and its effect on brain gene expression patterns, particularly effects of chronic use on genetic changes in striatum and cortex are unknown. Such changes in gene expression are expected to reflect altered changes in brain function and structure as a consequence of MDPV abuse. A major objective of these experiments is to determine the relationship between repeated MDPV exposure and genes encoding dopaminergic, vascular, central inflammatory markers (e.g., IL6, IL10, IL1β, IFNγ, TNFα), particularly in prefrontal cortex, striatum, hypothalamus, and amygdala.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84687" }, "primaryId" : "GEO:GSE84687", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84687" } ] }, "title" : "Effect of erythropoietin (EPO) and leukemia-inhibitory factor (LIF) on gene expression profiling in differentiating rat CG4-EPOR oligodendrocytes", "dateAssigned" : "2016-07-21T00:00:00.000-05:00", "summary" : "Analysis of the gene expression profile in differentiating rat CG4-EPOR oligodendrocytes treated with EPO, LIF or their combination for 1h or 20h", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84704" }, "primaryId" : "GEO:GSE84704", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84704" } ] }, "title" : "Role of mast cells in pulmonary hypertension with left heart disease", "dateAssigned" : "2016-07-21T00:00:00.000-05:00", "summary" : "Whole rat genome microarray analyses were performed in lung homogenates of three rats with established PH following supracoronary aortic banding and in three sham-operated controls. Out of a total of 28,000 analysed genes, differential expression defined as 2-fold change with p<0.05 was evident for 120 genes. Of these, 76 were upregulated and 44 downregulated in aortic banding compared with control lungs gene. Enrichment analysis revealed regulation of mast cell specific genes - 13 out of 20 genes were significantly upregulated in aortic banding compared with control lungs. To test for a putative functional role of mast cells in lung vascular remodelling and PH in LHD, we applied a pharmacological approach by treatment of aortic banding rats with the mast cell stabiliser ketotifen. Microarray analysis then compared rats that were treated with untreated.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84719" }, "primaryId" : "GEO:GSE84719", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84719" } ] }, "title" : "Bayesian bisulphite sequencing analysis reveals changes in macrophage DNA methylation in glomerulonephritis", "dateAssigned" : "2016-07-22T00:00:00.000-05:00", "summary" : "DNA methylation is one of the key epigenetic modifications involved in gene regulation. While whole-genome bisulfite sequencing (WGBS) allows the genome-wide quantification of DNA methylation at the single-base pair resolution, the contribution of DNA methylation in disease susceptibility remains to be fully understood. Here, we present a novel Bayesian smoothing approach (called ABBA) to accurately detect differentially methylated regions (DMRs) from WGBS data, and employ ABBA to map DNA methylation changes in disease. ABBA enables the genome-wide modeling of single-base resolution DNA methylation data, automatically adapting to different correlation structures in CpG methylation across the genome without requiring user-defined parameters and accounts for covariates and non-genetic confounding factors. First, we demonstrate the approach by an extensive simulation study and benchmarked ABBA against recently proposed alternative methods. We show the better performance of ABBA across a range of relevant parameters, including sequencing depth, number of replicates and noise level originating from incomplete bisulfite conversion. Second, we generated WGBS data from primary macrophages derived from an experimental rat model of glomerulonephritis and control rats, and employed ABBA to identify DMRs (>1,000 at 5% FDR) genome-wide that were associated with disease susceptibility. Investigation of the DMRs revealed differential DNA methylation localized to the promoter of the Ifitm3 gene and comparisons with existing DMR detection methods shows the enhanced interpretability of the results provided by ABBA. Additional ChIP-seq and RNA-seq analyses in the same experimental system showed differential transcription factor binding at the Ifitm3 promoter by JunD (an established determinant of glomerulonephritis) and consistent differential expression of Ifitm3. Taken together, these data suggest a role for DNA methylation alteration of the Ifitm3 gene in the pathogenesis of glomerulonephritis, and provide a proof of concept of using ABBA for differential methylation analysis of WGBS data.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28213474" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84831" }, "primaryId" : "GEO:GSE84831", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84831" } ] }, "title" : "Fetal metabolic programing increases the susceptibility of cardiovascular diseases in the offspring due to maternal high-fat-diet during diabetic pregnancy", "dateAssigned" : "2016-07-26T00:00:00.000-05:00", "summary" : "Increasing trends of obesity in childbearing women with a concurrent gestational diabetes are often associated with adverse fetal metabolic cues. Not only the carbohydrates but also fats are considered to contribute additional dietary fuels to the fetal hearts. To examine the hitherto unknown epigenetic mechanisms on the offspring’s cardiometabolic health due to maternal high-fat (HF) diet (40% kcal) or streptozotocin (STZ)-induced diabetic pregnancy, or both, we carried out an epigenetic characterization of neonatal heart tissue using chromatin immunoprecipitation (ChIP) sequening and a previously validated rat model. Chromatin landscape of offspring’s heart tissue revealed differential peaks distribution on various promoter regions mapped to the rat genome due to histone (H3) modifications by acetylation (H3Ac) or trimethylations of lysine 4 and 27 (H3K4me3 and H3K27me3, respectively). Ongoing evaluations include gene ontology and disease ontology analyses. Together, it is expected that the findings will show that maternal HF-diet with or without gestational diabetes changes the cardiac histone signature in rat offspring, potentially leading to development of novel disease prevention strategies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28425976" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84850" }, "primaryId" : "GEO:GSE84850", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84850" } ] }, "title" : "Cyclin Y-mediated changes in RNA-sequencing based transcriptome profiling in hippocampal neurons", "dateAssigned" : "2016-07-26T00:00:00.000-05:00", "summary" : "We report the transcriptome changes mediatedby Cyclin Y in rat hippocampal neurons.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28241067" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84886" }, "primaryId" : "GEO:GSE84886", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84886" } ] }, "title" : "Longitudinal transcriptomic and metabolomic data demonstrate altered lipid metabolism following the onset of hyperglycemia in spontaneously diabetic rats", "dateAssigned" : "2016-07-27T00:00:00.000-05:00", "summary" : "We hypothesized that a lack of insulin reaching the liver contributes to the metabolic shift towards lipid oxidation observed in humans with type 1 diabetes and rodent models of the disease. To test our hypothesis, we measured changes in the hepatic gene expression and serum metabolome of a BioBreeding rat model of type 1 diabetes before and after the onset of hyperglycemia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28192442" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84925" }, "primaryId" : "GEO:GSE84925", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84925" } ] }, "title" : "RT quantitative PCR analysis of Rosveratrol plus N-acetylcysteine of oxidative stress and inflammation genes in rat choclea.", "dateAssigned" : "2016-07-27T00:00:00.000-05:00", "summary" : "Two month-old male Wistar rats received either resveratrol (10 mg/kg) plus N-acetylcysteine (400 mg/kg) or vehicle during 5 consecutive days. The second day of treatment, a concentrated solution of kanamycin and furosemide was placed on the round window of the right ears of rats receiving treatment or vehicle. Hearing was assessed by recording auditory brainstem responses before and 5, 16 and 23 days after starting the treatment with resveratrol and N-acetylcysteine. Cochlear samples were taken at the end of the treatment (5 days) and once the treatment had been suspended (23 days) to study cochlear cytoarchitecture and the evolution of the expression of oxidative stress, antioxidant defense and inflammation genes by using PCR arrays and RT-qPCR.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84932" }, "primaryId" : "GEO:GSE84932", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE84932" } ] }, "title" : "RNA-Seq of tissues from Rat eye and retina samples", "dateAssigned" : "2016-07-27T00:00:00.000-05:00", "summary" : "We report RNA-Seq experiments of eye and retinal tissues from Rattus Norvegicus", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27875314" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85051" }, "primaryId" : "GEO:GSE85051", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85051" } ] }, "title" : "Acute hemarthrosis in the hemophilia A rat generates a local and systemic pro-inflammatory response", "dateAssigned" : "2016-08-01T00:00:00.000-05:00", "summary" : "Replacement therapy with coagulation factor VIII (FVIII) products concurrent with bleeds (on-demand) in hemophilia A (HA) patients, seems to increase the risk for developing anti-drug antibodies (i.e. inhibitors). A danger signal environment characterized by tissue damage and inflammation at the site of a bleed is thought to contribute to the anti-FVIII response. The nature of this inflammatory reaction is however not fully known. The purpose of this study was to characterize the inflammatory response, locally and systemically, during the first 24h following a knee joint bleed in the HA rat. HA rats received either a needle induced knee joint bleed (n=83) or a sham procedure (n=41). Blood samples were collected at selected time-points from 0-24h post injury/sham. Synovial fluid as well as intra-articular knee tissue and popliteal lymph nodes were collected at 24h. Cytokine and chemokine concentrations and mRNA gene expression on tissue samples were measured. Gene expression analysis revealed a rapid inflammatory response in the injured knees, accompanied by significantly increased levels of specific gene products in the synovial fluid; IL-1β, TNFα, KC/GRO, IL-6, Eotaxin, MCP-1, MCP-3, MIP-1α, MIP-2, RANTES, A2M and AGP. Plasma analysis demonstrated significantly increased systemic levels of KC/GRO, IL-6 and AGP in the blood of injured rats, already few hours following the injury. In conclusion, a rapid pro-inflammatory response, both locally and systemically, characteristic of innate immunity, was demonstrated following an induced knee joint bleed in the HA rat. Results reveal a more comprehensive inflammatory picture than previously shown, with resemblance to human hemophilic arthropathy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85139" }, "primaryId" : "GEO:GSE85139", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85139" } ] }, "title" : "A transcriptomic analysis of the bioactive properties of a polypropylene surgical mesh modified with silver-containing microparticles.", "dateAssigned" : "2016-08-03T00:00:00.000-05:00", "summary" : "Permanent synthetic meshes are a prized option to promote soft-tissue support and repair in several surgical procedures. Contrariwise, the risk to develop biomaterial-associated infection (BAI) has not been solved. Intrinsically antibacterial materials, such as those that include metals with antimicrobial activity as part of their composition, are an advanced approach to be further explored for BAI prevention. In this study, a panel of in vitro, ex vivo and in vivo assays was used to compare a novel polypropylene-based surgical mesh modified with silver-containing microparticles with a commercially available similar device normally used for hernia repair. To comprehensively identify specific mechanisms of how the new silver-containing meshes influence the full host-tissue response in the presence and absence of infection, prostheses were screened for cytotoxicity, biological integration and transcriptomic responses, and additional antibiofilm production behaviour. Silver-modified polypropylene meshes exhibited good properties in terms of mechanical and cytotoxic values, as well as a modest prevention of biofilm formation. Moreover, they promoted connective tissue deposition and angiogenesis and, outstandingly, induced “immunomodulating” effects that may be potentially useful in the clinical context. Overall, the results substantiate the potential use of polypropylene surgical meshes modified with silver-containing microparticles as a means to prevent BAI in soft tissue repair.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85167" }, "primaryId" : "GEO:GSE85167", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85167" } ] }, "title" : "Expression data from rat peripheral blood mononuclear cells (PBMCs)", "dateAssigned" : "2016-08-03T00:00:00.000-05:00", "summary" : "the Wistar Kyoto(WKY) and Lewis (LEW) rat PBMCs were isolated following a CAF or standard diet and subjected to whole genome expression analysis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27483348" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85337" }, "primaryId" : "GEO:GSE85337", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85337" } ] }, "title" : "Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells", "dateAssigned" : "2016-08-08T00:00:00.000-05:00", "summary" : "Transcriptional regulatory changes have been shown to contribute to phenotypic differences between species, but many questions remain about how gene expression evolves. Here we report the first comparative study of nascent transcription in primates. We used PRO-seq to map actively transcribing RNA polymerases in resting and activated CD4+ T-cells in multiple human, chimpanzee, and rhesus macaque individuals, with rodents as outgroups. This approach allowed us to directly measure active transcription separately from post-transcriptional processes. We observed general conservation in coding and non-coding transcription, punctuated by numerous differences between species, particularly at distal enhancers and non-coding RNAs. Transcription factor binding sites are a primary determinant of transcriptional differences between species. We found evidence for stabilizing selection on gene expression levels and adaptive substitutions associated with lineage-specific transcription. Finally, rates of evolutionary change are strongly correlated with long-range chromatin interactions. These observations clarify the role of primary transcription in regulatory evolution.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85420" }, "primaryId" : "GEO:GSE85420", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85420" } ] }, "title" : "Perinatal Exposure to 2,2’,4’4’ –Tetrabromodiphenyl Ether Impairs Male Reproductive Health in Adult Rats", "dateAssigned" : "2016-08-10T00:00:00.000-05:00", "summary" : "Toxicity of PBDE for male reproductive system was shown in several human and animal studies, however long lasting effects of perinatal exposures on male reproduction are yet poorly understood. In this study pregnant Wistar rats were exposed to 0.2 mg/kg 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47) from gestation day 8 till postnatal day 21 and testis transcriptome was analyzed on postnatal day 120 in offspring. Exposed animals had significant change in testes transcriptome including suppression of genes essential for spermatogenesis and activation of immune response genes. In particular exposed animals had on average 4 fold decreased expression of protamine and transition protein genes in testes suggesting that histone-protamine exchange may be dysregulated in the course of spermatogenesis resulting in exposure legacy transfer to the next generation via aberrant sperm epigenome.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85451" }, "primaryId" : "GEO:GSE85451", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85451" } ] }, "title" : "DLX3 binding sites in rat enamel organ", "dateAssigned" : "2016-08-10T00:00:00.000-05:00", "summary" : "DLX3 is a homeodomain transcription factor involved in amelogenesis. Mutations in DLX3 in human lead to Tricho-Dento-Osseous syndrome featuring enamel hypoplasia and hypomineralization. Here we investigated the distribution of DLX3 DNA binding sites in rat enamel organ using ChIP-seq.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27760456" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85454" }, "primaryId" : "GEO:GSE85454", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85454" } ] }, "title" : "Molecular Changes in the Nasal Cavity after 5 days of N, N-dimethyl-p-toluidine Exposure", "dateAssigned" : "2016-08-10T00:00:00.000-05:00", "summary" : "A total of 2,561 gene transcripts were differentially expressed due to DMPT treatment (false discovery rate (FDR) < 0.05).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27099258" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85500" }, "primaryId" : "GEO:GSE85500", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85500" } ] }, "title" : "Expression data from nucleus accumbens of rats infused with lentivirus LV-GFP and LV-miR-495 overexpression constructs", "dateAssigned" : "2016-08-11T00:00:00.000-05:00", "summary" : "We used Rat Gene 2.0 ST Affymetrix expression arrays ( to identify genes whose expression levels were downregulated by overexpression of miR-495.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28044061" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85577" }, "primaryId" : "GEO:GSE85577", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85577" } ] }, "title" : "Expression of rat hepatocytic progenitor cells with and without hepatic Thy1-positive cells in retrorsine/partial hepatectomy treated rats models.", "dateAssigned" : "2016-08-13T00:00:00.000-05:00", "summary" : "We used microarrays to detail the gene expression of receptors of growth factors of SHPCs clusters with and without Thy1+ cells transplantation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27925343" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85618" }, "primaryId" : "GEO:GSE85618", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85618" } ] }, "title" : "Estrogen receptor-dependent attenuation of hypoxia-induced changes in the lung genome of pulmonary hypertension rats", "dateAssigned" : "2016-08-15T00:00:00.000-05:00", "summary" : "17β-estradiol (E2) exerts complex and context-dependent effects in pulmonary hypertension. In hypoxia-induced pulmonary hypertension (HPH), E2 attenuates lung vascular remodeling through estrogen receptor (ER)-dependent effects; however, ER target genes in the hypoxic lung remain unknown. In order to identify the genome regulated by the E2-ER axis in the hypoxic lung, we performed a microarray analysis in lungs from HPH rats treated with E2 (75 mcg/kg/d) ± ER-antagonist ICI182,780 (3 mg/kg/d). Untreated HPH rats and normoxic rats served as controls. Using a false discovery rate of 10%, we identified a significantly differentially regulated genome in E2-treated vs. untreated hypoxia rats. Genes most up-regulated by E2 encoded matrix metalloproteinase 8, S100 calcium binding protein A8, and IgA Fc receptor; genes most down-regulated by E2 encoded olfactory receptor 63, secreted frizzled-related protein 2, and thrombospondin 2. Several genes affected by E2 changed in the opposite direction after ICI182,780 co-treatment, indicating an ER-regulated genome in HPH lungs. The bone morphogenetic protein antagonist Grem1 (gremlin 1) was up-regulated by hypoxia, but found to be among the most down-regulated genes after E2 treatment. Gremlin 1 protein was reduced in E2-treated vs. untreated hypoxic animals, and ER-blockade abolished the inhibitory effect of E2 on Grem1 mRNA and protein. In conclusion, E2 ER-dependently regulates several genes involved in proliferative and inflammatory processes during hypoxia. Gremlin 1 is a novel target of the E2-ER axis in HPH. Understanding the mechanisms of E2 gene regulation in HPH may allow for selectively harnessing beneficial transcriptional activities of E2 for therapeutic purposes. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28680582" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85752" }, "primaryId" : "GEO:GSE85752", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85752" } ] }, "title" : "Real-time quantitative PCR analysis of retrogradely labeled stellate neurons in LII of the rat medial entorhinal cortex", "dateAssigned" : "2016-08-17T00:00:00.000-05:00", "summary" : "We compared miRNA expression in FACS-sorted, retrogradely labeled stellate neurons with other medial entorhinal cells, and found 7 miRNAs to be upregulated in stellate cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28260163" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85753" }, "primaryId" : "GEO:GSE85753", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85753" } ] }, "title" : "miRNA expression in rat medial entorhinal cortex layers during postnatal development", "dateAssigned" : "2016-08-17T00:00:00.000-05:00", "summary" : "To examine how miRNAs differ between medial entorhinal cortex layers during postnatal development, we analyzed the miRNA expression in layer II and the deep layers (III-VI) at postnatal ages P2, P9, P23 and P45 in wildtype Long Evans rats. The expression of the two most significantly differentially expressed miRNAs were validated by in situ hybridization.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28260163" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85785" }, "primaryId" : "GEO:GSE85785", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85785" } ] }, "title" : "Leptin-Mediated Gene Expression Profiling Exhibits New Candidate Genes Associated with Osteoarthritis in Rat", "dateAssigned" : "2016-08-18T00:00:00.000-05:00", "summary" : "Osteoarthritis (OA) is the most prevalent chronic joint disease and the precise genetic mechanisms are yet to be fully elucidated. The aim of this study is to evaluate, for the first time, the differences in gene expression profiles of healthy and leptin-induced cartilage in rat. To investigate the underlying pathogenic factors in OA, alterations in gene expression between leptin-induced articular cartilage rat models and healthy control rat models were investigated using the Whole Rat Genome Oligo Microarray. In the present study, 1857 differentially expressed genes (DEGs; 1197 up-regulated and 660 down-regulated) were identified. Expression of some OA-related known genes is known to be associated with leptin induction, including matrix metalloproteinase (MMP), inflammatory factors, growth factors and genes involved in cell death, apoptosis and osteoclast differentiation. However, some new candidate genes that had never been reported to be related with OA, such as BCL2L11, were consistently observed to be up-regulated, suggesting they might be involved in OA progression. Our findings indicate that leptin plays an important role in the progression of OA by mediating expression change in multiple genes, although the molecular mechanisms need to be further clarified. Further study of these leptin-induced genes may provide new insights into understanding the molecular mechanisms underlying OA.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85788" }, "primaryId" : "GEO:GSE85788", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85788" } ] }, "title" : "Very deep small RNA sequencing of whole rat medial entorhinal cortex", "dateAssigned" : "2016-08-18T00:00:00.000-05:00", "summary" : "We performed very deep small RNA sequencing on one sample of medial entorhinal cortex of a Long Evans rat aged P23 to see which small RNAs could be detected in this brain area.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28260163" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85789" }, "primaryId" : "GEO:GSE85789", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85789" } ] }, "title" : "Molecular substrates for differences between layers and regions of the entorhinal cortex during postnatal development in rats", "dateAssigned" : "2016-08-18T00:00:00.000-05:00", "summary" : "We report the first full transcriptome analysis of layer II and deep layers of the medial and lateral entorhinal cortex during postnatal development. Our analysis showed that postnatal timepoint was the most important element in entorhinal cortex transcriptional dynamics, followed by laminar differences. There were fewer differentially expressed genes between the medial and lateral parts of the entorhinal cortex, and most of these were found in layer II.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85811" }, "primaryId" : "GEO:GSE85811", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85811" } ] }, "title" : "Effects of glucose and insulin resistance on gene expression profiling in the isolated working rat heart", "dateAssigned" : "2016-08-18T00:00:00.000-05:00", "summary" : "The changes were highly similar to gene alterations occurring in the right atrium and left ventricle of open heart surgery patients, and included the up-regulation of the three master regulators of metabolic reprogramming MYC, NR4A1 and NR4A2. Targeted pathway analysis revealed an up-regulation of metabolic processes associated with the proliferation and activation of tissue-resident macrophages and fibroblasts. Although the remodeling occurred independently from glucose, glucose further increased the expression of a subset of genes associated with polarization of tissue reparative M2 macrophages. However, glucose failed to enhance the expression of M2-related markers in the isolated heart from rats rendered insulin resistant by high-sucrose feeding. These results expose the cellular components of the heart as a significant source of proinflammatory mediators released in response to stress associated with cardiac surgery with CPB, and suggest a major role for glucose as a signal in the determination of resident cardiac macrophage polarization.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27940566" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85825" }, "primaryId" : "GEO:GSE85825", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85825" } ] }, "title" : "MicroRNA miR-92a-2 targets TFPI2 to ameliorate oxidative stress of the hypoxia neuron [mRNA]", "dateAssigned" : "2016-08-19T00:00:00.000-05:00", "summary" : "Comparison of the differential expression mRNA profiles from the brain cortex of hypoxia and normaixa rats by silica microarray chip", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85872" }, "primaryId" : "GEO:GSE85872", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85872" } ] }, "title" : "Identification of long non coding RNAs associated with self-renewal capacity of rat neural stem cells exposed to sevoflurane", "dateAssigned" : "2016-08-20T00:00:00.000-05:00", "summary" : "To identify the differential porfile of long non coding RNAs in neural stem cells exposed to sevoflurane compared with control gas(21% oxygen,5%CO2,),We employed the rat long non-coding RNA array as a discovery platform to identify genes with potential to regulate self-renewal capacity of rat neural stem cells exposed to sevoflurane.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85952" }, "primaryId" : "GEO:GSE85952", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85952" } ] }, "title" : "Design, characterization, and use of a novel amyloid ß-protein control for assembly, neurotoxicity, and gene expression studies", "dateAssigned" : "2016-08-23T00:00:00.000-05:00", "summary" : "A key pathogenic agent in Alzheimer’s disease (AD) is the amyloid ß-protein (Aß), which self-assembles into a variety of neurotoxic structures. Establishing structure-activity relationships for these assemblies is critical for proper therapeutic target identification and design. We examined the effects of Aß monomers, dimers, higher-order oligomers, and fibrils on gene expression in primary rat hippocampal neurons. As opposed to “reverse” Aß or non-Aß peptides typically used as controls in such studies, we designed novel scrambled Aß peptides predicted to behave distinctly from native Aß. Significant changes in gene expression were observed for all peptide assemblies, but fibrils induced the largest changes. Significant changes in gene expression were observed for all peptide assemblies, but fibrils induced the largest changes. Weighted gene co-expression network analysis (WGCNA) revealed two predominant gene modules related to Aß treatment. Many genes within these modules were associated with inflammatory signaling pathways", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27505174" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85957" }, "primaryId" : "GEO:GSE85957", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE85957" } ] }, "title" : "Expression data from kidneys of rats with and without cisplatin treatment", "dateAssigned" : "2016-08-23T00:00:00.000-05:00", "summary" : "We investigated an acute kidney injury (AKI) model in rats induced by cisplatin (Cp) administration. The cisplatin is widely used since its biochemical and histopathological characteristics are representative of drug-induced AKI in humans. Male Wistar rats were dosed once ip with 0, 1 and 3 mg/kg cisplatin. Tubular necorsis was observed histopathologically in all treated rats and war recovery on day 26. Gene expression profiling of the kidney cortex with microarrays 3, 5, 8, and 26 days after single administration of 3mg/kg Cp revealed a major profile pattern characterized by maximally increased and decreased mRNA levels on day 8, with clear changes already found 3 days after treatment for about half of the mRNAs. The mRNA expression pattern after administration of 1mg/kg Cp was overall similar, yet with a dose-dependent smaller fold-change. In summary we found 274 mRNAs showing significantly altered levels in the kidney of which 162 were increased and 112 decreased, respectively. Functional interpretation of the proteins encoded by these mRNAs revealed induction of a DNA damage response likely caused by the known molecular activity of Cp as DNA alkylating agent. Increased mRNAs associated with apoptosis (encoded by the corresponding genes like B-cell lymphoma 3-encoded protein, Bcl3; mouse double minute 2 homolog, Mdm2; p21/WAF1 also known as cyclin-dependent kinase inhibitor 1), cell cycle regulation (encoded by the corresponding genes like Cyclin-G1, Ccng1; B-cell translocation gene 2, Btg2) and stress response may have partly been induced by the DNA damage, but also by the kidney damage associated with Cp administration. Increased levels of mRNAs indicating regeneration (encoded by the corresponding genes like SPARC- related modular calcium-binding protein 2, Smoc2; Tenascin C, Tnc) and decreased levels of mRNAs coding for proteins related to kidney function, indicating dedifferentiation, are likely related to the observed kidney injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24880025" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86033" }, "primaryId" : "GEO:GSE86033", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86033" } ] }, "title" : "MicroRNA miR-92a-2 targets TFPI2 to ameliorate oxidative stress of the hypoxia neuron [miRNA]", "dateAssigned" : "2016-08-25T00:00:00.000-05:00", "summary" : "Comparison of the differential expression mRNA profiles from the brain cortex of hypoxia and normaixa rats by silica microarray chip.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86252" }, "primaryId" : "GEO:GSE86252", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86252" } ] }, "title" : "mRNA state in normal and irradiated skin of rattus", "dateAssigned" : "2016-08-30T00:00:00.000-05:00", "summary" : "We report the difference of mRNA and Long-non-coding RNA state between normal and irradiated skin of rattus", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86270" }, "primaryId" : "GEO:GSE86270", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86270" } ] }, "title" : "Dietary zinc deficiency and supplementation in early life and mammary tumors development in adulthood female rats", "dateAssigned" : "2016-08-31T00:00:00.000-05:00", "summary" : "Zinc deficiency during pregnancy and postnatal life can adversely affect the health and predispose to an increased risk of developing human diseases at adulthood. The present study was designed to evaluate whether dietary zinc deficiency or supplementation during the pregnancy, lactation and juvenile stages interferes with the development of mammary tumors induced by 7,12-dimethylbenzanthracene (DMBA) in female Sprague-Dawley (SD) rats. Pregnant females SD were allocated into three groups: dams received diets containing adequate (35 mg/Kg chow), deficient (3 mg/Kg chow) or supplemented (180 mg/Kg chow) zinc levels during gestational day 10 (GD 10) until the litters weaning. Female offspring were allocated into three groups and received the same diets as their dams until postnatal day (PND) 51. At PND 51, females SD (n=16 each group) received a single dose of DMBA (50 mg/kg, ig) for initiation of mammary carcinogenesis, adequate zinc diets and were euthanized at PND 180. Tumors samples were collected and processed for histological evaluation and microarray analysis. Dietary zinc deficiency induced a significant reduction in female offspring body weight evolution at parturition, weaning and pubertal phases. At late in life, the early in life dietary zinc deficiency or supplementation did not alter the latency, incidence, multiplicity and volume or histological types of mammary tumors in relation to the adequate zinc group, and changed the expression of a small amount of genes. The present findings indicate that early-in life dietary zinc deficiency or supplementation did not significantly modify the susceptibility to development of mammary tumors induced by DMBA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28427009" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86329" }, "primaryId" : "GEO:GSE86329", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86329" } ] }, "title" : "Increased expression of proenkephalin and prodynorphin mRNAs in the nucleus accumbens of compulsive methamphetamine taking rats", "dateAssigned" : "2016-09-01T00:00:00.000-05:00", "summary" : "Addiction to psychostimulants is associated with neuroadaptive changes in various brain regions. In this experiment we use a model of methamphetamine self-administration during which we use footshocks as adverse consequences to divide rats into animals that continue to press an active lever to get the drug (shock-resistant) whereas other rats stop or significantly reduce pressing the lever (shock-sensitive) in the presence of these adverse consequences. To investigate potential molecular bases for the divergent phenotype, we performed a whole rat transcriptome study using Affymetrix rat arrays that cover more than 24,000 coding transcripts. The array experiments revealed that there were 24 differentially expressed genes between the resistant and sensitive rats, with 15 up- and 9 downregulated transcripts. Ingenuity pathway analysis revealed that these transcripts belong in a network of genes involved in nervous system development and function, cell signaling, behavior, and disorders of the basal ganglia. These genes included proenkephalin (PENK) and prodynorphin (PDYN), among others. Because PDYN and PENK are expressed in dopamine D1- and D2-containing NAc neurons, respectively, these findings suggest that mechanisms that impact both cell types may play a role in the regulation of compulsive methamphetamine taking by rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86346" }, "primaryId" : "GEO:GSE86346", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86346" } ] }, "title" : "Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development [microRNA]", "dateAssigned" : "2016-09-01T00:00:00.000-05:00", "summary" : "Some neuropsychiatric disease, including schizophrenia, may originate during prenatal development, following periods of gestational hypoxia and placental oxidative stress. Here we investigated if gestational hypoxia promotes damaging secretions from the placenta that affect fetal development and whether a mitochondria-targeted antioxidant MitoQ might prevent this. Gestational hypoxia caused low birth-weight and changes in young adult offspring brain, mimicking those in human neuropsychiatric disease. Exposure of cultured neurons to fetal plasma or to secretions from the placenta or from model trophoblast barriers that had been exposed to altered oxygenation caused similar morphological changes. The secretions and plasma contained altered microRNAs whose targets were linked with changes in gene expression in the fetal brain and with human schizophrenia loci. Molecular and morphological changes in vivo and in vitro were prevented by a single dose of MitoQ bound to nanoparticles, which were shown to localise and prevent oxidative stress in the placenta but not in the fetus. We suggest the possibility of developing preventative treatments that target the placenta and not the fetus to reduce risk of psychiatric disease in later life.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28831049" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86350" }, "primaryId" : "GEO:GSE86350", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86350" } ] }, "title" : "Expression data from brain stem of rats with and without rotenone treatment", "dateAssigned" : "2016-09-01T00:00:00.000-05:00", "summary" : "We investigated an subacute study in male Wistar rats, treated daily with 400 ppm rotenone for 1, 3, or 14 consecutive days, followed by necropsy 24h after the last application. Rotenone is a strong mitochondrial respiratory chain complex I inhibitor. Inhibitors of complex I are suggested to exert anti-tumor activity of those tumors relying on oxidative metabolism and are therefore of interest in oncology research. Nevertheless, the safety profile of these inhibitors needs to be rigorously assessed. Rotenone has shown anti-carcinogenic activity in several studies. In this context we used rotenone in our study as tool compound with the aim to identify suitable biomarker candidates and enhance mechanistic insights into the biologic and cellular effects of complex I inhibitors at the organ level after in vivo treatment. Various parameters, including hematology, clinical chemistry and histopathology, major blood cell population phenotyping using FACS and enzymatic activity assays were measured and/or evaluated. Moreover gene expression profiles were determined to investigate pathways and functions affected by rotenone at the molecular level. As organs, liver, heart and brain stem were chosen due to the high metabolic activity, the high energy demand and due to the known neurotoxic effect of rotenone, respectively. The strongest rotenone-induced effects on gene expression were observed in the liver (1444 deregulated genes) compared to heart (650 deregulated genes) and brain stem (52 deregulated genes). These findings, together with the histopathological results, show that liver is a target organ of rotenone.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28374803" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86351" }, "primaryId" : "GEO:GSE86351", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86351" } ] }, "title" : "Expression data from hearts (lest ventricle apex) of rats with and without rotenone treatment", "dateAssigned" : "2016-09-01T00:00:00.000-05:00", "summary" : "We investigated an subacute study in male Wistar rats, treated daily with 400 ppm rotenone for 1, 3, or 14 consecutive days, followed by necropsy 24h after the last application. Rotenone is a strong mitochondrial respiratory chain complex I inhibitor. Inhibitors of complex I are suggested to exert anti-tumor activity of those tumors relying on oxidative metabolism and are therefore of interest in oncology research. Nevertheless, the safety profile of these inhibitors needs to be rigorously assessed. Rotenone has shown anti-carcinogenic activity in several studies. In this context we used rotenone in our study as tool compound with the aim to identify suitable biomarker candidates and enhance mechanistic insights into the biologic and cellular effects of complex I inhibitors at the organ level after in vivo treatment. Various parameters, including hematology, clinical chemistry and histopathology, major blood cell population phenotyping using FACS and enzymatic activity assays were measured and/or evaluated. Moreover gene expression profiles were determined to investigate pathways and functions affected by rotenone at the molecular level. As organs, liver, heart and brain stem were chosen due to the high metabolic activity, the high energy demand and due to the known neurotoxic effect of rotenone, respectively. The strongest rotenone-induced effects on gene expression were observed in the liver (1444 deregulated genes) compared to heart (650 deregulated genes) and brain stem (52 deregulated genes). These findings, together with the histopathological results, show that liver is a target organ of rotenone.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28374803" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86352" }, "primaryId" : "GEO:GSE86352", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86352" } ] }, "title" : "Expression data from livers of rats with and without rotenone treatment", "dateAssigned" : "2016-09-01T00:00:00.000-05:00", "summary" : "We investigated an subacute study in male Wistar rats, treated daily with 400 ppm rotenone for 1, 3, or 14 consecutive days, followed by necropsy 24h after the last application. Rotenone is a strong mitochondrial respiratory chain complex I inhibitor. Inhibitors of complex I are suggested to exert anti-tumor activity of those tumors relying on oxidative metabolism and are therefore of interest in oncology research. Nevertheless, the safety profile of these inhibitors needs to be rigorously assessed. Rotenone has shown anti-carcinogenic activity in several studies. In this context we used rotenone in our study as tool compound with the aim to identify suitable biomarker candidates and enhance mechanistic insights into the biologic and cellular effects of complex I inhibitors at the organ level after in vivo treatment. Various parameters, including hematology, clinical chemistry and histopathology, major blood cell population phenotyping using FACS and enzymatic activity assays were measured and/or evaluated. Moreover gene expression profiles were determined to investigate pathways and functions affected by rotenone at the molecular level. As organs, liver, heart and brain stem were chosen due to the high metabolic activity, the high energy demand and due to the known neurotoxic effect of rotenone, respectively. The strongest rotenone-induced effects on gene expression were observed in the liver (1444 deregulated genes) compared to heart (650 deregulated genes) and brain stem (52 deregulated genes). These findings, together with the histopathological results, show that liver is a target organ of rotenone.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28374803" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86390" }, "primaryId" : "GEO:GSE86390", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86390" } ] }, "title" : "Short-term inhalation exposure to copper oxide nanoparticles induces gene expression changes associated with inflammation and cell proliferation in rat bronchoalveolar epithelium", "dateAssigned" : "2016-09-02T00:00:00.000-05:00", "summary" : "Copper oxide nanoparticles (CuO NPs) are considered for various technological and consumer applications, leading to growing concerns for potential human hazards resulting from inhalation. Recent studies have revealed a dose-dependent toxicity of CuO NPs in rats following short-term inhalation exposure. Here, we utilized transcriptomics approaches to further investigate the responses in rats exposed via inhalation for five consecutive days to two doses of CuO NPs, 3.3 (low dose, LD) and 13.2 (high dose, HD) mg/m3, with collection of lung tissues on days 6 (1 day post-exposure) and 28 (i.e., after a 22-day post-exposure recovery period). Histopathology confirmed an acute inflammatory response that was resolved during the post-exposure phase. Global gene expression analyses yielded about 1,000 differentially expressed genes in HD rats and 200 in LD on day 6, and less than 20 after the recovery period. Pathway analysis indicated cell proliferation/survival and inflammation as the main processes triggered by exposure and identified epithelial cell transforming protein 2 (Ect2) as a potential gene of interest implicated in cell proliferation. Indeed, ECT2 was upregulated in exposed lungs and was localized in the cytoplasm of alveolar epithelial cells in HD rats, in hyperplasic foci identified based on the Ki67 antigen, a marker of cell proliferation. Monocyte chemoattractant protein 1 (MCP-1, also known as CCL2), with an important role in the regulation of inflammatory processes and cell proliferation, was also upregulated and this was confirmed immunohistochemically. Finally, we could not find any evidence for aberrant DNA methylation of inflammation-associated genes in response to CuO NP exposure. In summary, the current findings suggest that airborne CuO NPs cause an acute response that translates into inflammation and cellular proliferation in bronchoalveolar epithelium, with upregulation of neoplasia-related factors even after a short-term exposure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86392" }, "primaryId" : "GEO:GSE86392", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86392" } ] }, "title" : "Genome-wide Transcriptome Analysis of Hippocampus, Frontal cortex and Pituitary gland in Rats Elucidated the Pathogenisis of Depressive Disorder Induced by Chronic Restraint", "dateAssigned" : "2016-09-02T00:00:00.000-05:00", "summary" : "Conclusions: Our study represents the first detailed analysis of the hippocampal, frontal cortex and pituitary gland genome-wide transcriptomes in depression rats under CRS by RNA-seq technology. The results of this study revealed multiple DEGs and possible mechanisms specifying the function of hippocampal, frontal cortex and pituitary gland in depression rats induced by CRS. These results provide a basis for further investigation of the signaling mechanisms that affect central nervous system output related to stress-sensitive depressive disorder development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29098013" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86408" }, "primaryId" : "GEO:GSE86408", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86408" } ] }, "title" : "Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development [RNAseq]", "dateAssigned" : "2016-09-02T00:00:00.000-05:00", "summary" : "Some neuropsychiatric disease, including schizophrenia, may originate during prenatal development, following periods of gestational hypoxia and placental oxidative stress. Here we investigated if gestational hypoxia promotes damaging secretions from the placenta that affect fetal development and whether a mitochondria-targeted antioxidant MitoQ might prevent this. Gestational hypoxia caused low birth-weight and changes in young adult offspring brain, mimicking those in human neuropsychiatric disease. Exposure of cultured neurons to fetal plasma or to secretions from the placenta or from model trophoblast barriers that had been exposed to altered oxygenation caused similar morphological changes. The secretions and plasma contained altered microRNAs whose targets were linked with changes in gene expression in the fetal brain and with human schizophrenia loci. Molecular and morphological changes in vivo and in vitro were prevented by a single dose of MitoQ bound to nanoparticles, which were shown to localise and prevent oxidative stress in the placenta but not in the fetus. We suggest the possibility of developing preventative treatments that target the placenta and not the fetus to reduce risk of psychiatric disease in later life.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28831049" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86523" }, "primaryId" : "GEO:GSE86523", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86523" } ] }, "title" : "Hepatocytic parental progenitor cells of rat small hepatocytes", "dateAssigned" : "2016-09-07T00:00:00.000-05:00", "summary" : "The hepatocytic parental progenitor cells possess self-renewal capability. These cells maintain the ability to differentiate into mature hepatocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28397810" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86552" }, "primaryId" : "GEO:GSE86552", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86552" } ] }, "title" : "TonEBP/NFAT5 regulates inflammatory gene expression in nucleus pulposus cells", "dateAssigned" : "2016-09-07T00:00:00.000-05:00", "summary" : "RNA sequencing of nucleus pulposus cells transduced with control or TonEBP shRNA and cultured under hypertonic conditions", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27875309" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86567" }, "primaryId" : "GEO:GSE86567", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86567" } ] }, "title" : "Changes in miRNA in the lung and blood after whole thorax irradiation in rats: biomarkers for radiation-induced injuries", "dateAssigned" : "2016-09-08T00:00:00.000-05:00", "summary" : "We used a rat model of whole thorax x-ray irradiation to profile the microRNA (miRNA) in lung and blood up to 4 weeks after radiation. Small RNA from normal and irradiated Wistar rat lungs and blood were analyzed by next-generation sequencing and the changes by radiation were identified by deRNA-seq at 1, 2, 3 and 4 weeks after irradiation. The average total reads/library was 2,703,137 with a mean of 88% mapping to the rat genome. Detailed profiles of 100 of the most abundant miRNA in rat blood and lung are described.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28303893" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86579" }, "primaryId" : "GEO:GSE86579", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86579" } ] }, "title" : "The dentate gyrus after traumatic brain injury [mRNA]", "dateAssigned" : "2016-09-08T00:00:00.000-05:00", "summary" : "Analysis of the dentate gyrus of traumatic brain injury model. Results provide insight into the molecular mechanism underlying TBI.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86595" }, "primaryId" : "GEO:GSE86595", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86595" } ] }, "title" : "Identification of gene expression changes in RGC neurons treated with synaptogenic proteins", "dateAssigned" : "2016-09-08T00:00:00.000-05:00", "summary" : "Astrocyte-secreted proteins induce synapse formation between isolated retinal ganglion cell (RGC) neurons in culture. We asked whether 2 of these proteins, glypican 4 (Gpc4) or thrombospondin 1 (TSP1) induce synapse formation by regulating gene expression in RGCs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29024665" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86614" }, "primaryId" : "GEO:GSE86614", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86614" } ] }, "title" : "The dentate gyrus after traumatic brain injury [miRNA]", "dateAssigned" : "2016-09-09T00:00:00.000-05:00", "summary" : "Analysis of the dentate gyrus of traumatic brain injury model. Results provide insight into the molecular mechanism underlying TBI.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86862" }, "primaryId" : "GEO:GSE86862", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86862" } ] }, "title" : "Transcriptome outcome of oligodendrocyte precursor cells following VCAM1 knockdown", "dateAssigned" : "2016-09-13T00:00:00.000-05:00", "summary" : "Transcriptome outcome of rat oligodendrocyte precursor cells, which were knocked down with short-hairpin RNA (shRNA) for vascular cell adhesion molecule 1 (VCAM1)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27876794" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86893" }, "primaryId" : "GEO:GSE86893", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86893" } ] }, "title" : "mRNA profiles from dorsal raphe and amygdala of high-responder and low-responder rats", "dateAssigned" : "2016-09-13T00:00:00.000-05:00", "summary" : "We identified 271 transcripts as differentially regulated in the dorsal raphe and/or the amygdala of high-responder and low-responder rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27865919" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86934" }, "primaryId" : "GEO:GSE86934", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86934" } ] }, "title" : "microRNA profiles from dorsal raphe and amygdala of high-responder and low-responder rats", "dateAssigned" : "2016-09-14T00:00:00.000-05:00", "summary" : "We report 33 microRNAs are differentially expressed in the dorsal raphe and/or amygdala of rats selectively bred for high and low locomotor response to novelty (high responder and low responder rats)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27865919" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86941" }, "primaryId" : "GEO:GSE86941", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE86941" } ] }, "title" : "Infiltrating monocyte-derived macrophages polarizes in to anti-inflammatory and neuro-protective phenotype in a rat model of cerebral ischemia", "dateAssigned" : "2016-09-14T00:00:00.000-05:00", "summary" : "To summarize our results, we found microglia and MDMs are functionally heterogeneous population contributing differently to the disease phenotype. Our data, suggest that during post-ischemic inflammation microglia exhibit pro-inflammatory phenotype, while infiltrating MDMs display anti-inflammatory and neuro-protective phenotype. Apart from up-regulation of some of the classical M2 marker in MDMs, our gene expression profiling using RNA-sequencing revealed a unique signature of MDMs with the up-regulation of genes associated with wound healing, MHCII antigen-presentation and tissue repair. Our results strongly suggest that MDMs infiltrating the CNS parenchyma during the sub-acute of post-ischemic inflammation might contribute to the endogenous mechanism of neuroprotection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30485549" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87045" }, "primaryId" : "GEO:GSE87045", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87045" } ] }, "title" : "Sex hormone responsive genes in rat choroid plexus", "dateAssigned" : "2016-09-17T00:00:00.000-05:00", "summary" : "In order to gain additional insight into the functional role of sex steroid hormones in the choroid plexus, the present study compared gene expression patterns between sham and gonadectomized female/male rats choroid plexus.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23585832" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87082" }, "primaryId" : "GEO:GSE87082", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87082" } ] }, "title" : "Gene expression within the prefrontal cortex and amygdala in a developing model of high and low anixety and depression-like behavior in rats", "dateAssigned" : "2016-09-19T00:00:00.000-05:00", "summary" : "All samples were generated from Sprague-Dawley male rats selectively bred for high novelty response (HRs) or low novelty response (LRs).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26979051" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87099" }, "primaryId" : "GEO:GSE87099", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87099" } ] }, "title" : "CD8aa+MHC-II+ Cell with Capacity to Terminate Autoimmune Inflammation Is A Novel Antigen-Presenting NK-like cell in Rats", "dateAssigned" : "2016-09-19T00:00:00.000-05:00", "summary" : "Discovery of immune tolerance mechanisms, which inhibit pre-existing autoimmune inflammation, may provide us with new strategies for treating autoimmune diseases. We have identified a CD8aa+MHC-II+ cell with professional APC capacity during our investigation on spontaneous recovery from autoimmune glomerulonephritis in a rat model. This cell actively invades inflamed target tissue to terminate an on-going autoimmune inflammation by selective killing of effector autoreactive T cells. Now, we showed that this cell used a cytotoxic machinery of Ly49s+ NK cells in killing of target T cells. Thus, this CD8aa+MHC-II+ cell, which previously was thought a professional APC, is an antigen presenting-NK (AP-NK) cell. Following its coupling with target T cells through antigen presentation, killing stimulatory receptor Ly49s6 and co-receptor CD8aa on this cell used non-classic MHC-I RT1CE16 on the target T cells as a ligand to initiate killing. Thus, activated effector T cells with elevated expression of RT1CE16 were highly susceptible to the killing by the CD8aa+ AP-NK cell. Granule cytolytic perforin/granzyme C from this cell subsequently mediated cytotoxicity, and thus, inhibition of granzyme C effectively attenuated the killing. As it can recognize and eliminate effector autoreactive T cells in the inflamed target tissue, CD8aa+ AP-NK cell not only represents a new type of immune cell involved in immune tolerance, but also is a potential candidate for developing a cell-based therapy for pre-existing autoimmune diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27799310" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87107" }, "primaryId" : "GEO:GSE87107", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87107" } ] }, "title" : "Conserved and species specific molecular denominators in mammalian aging [rat]", "dateAssigned" : "2016-09-19T00:00:00.000-05:00", "summary" : "Aging is a complex phenomenon involving functional decline in multiple physiological systems. We focused on skeletal muscle to identify pathways that modulate function and healthspan by global expression profiles and specific mechanisms fundamental to aging processes. Our experimental design integrated comparative analysis of mice, rats, rhesus monkeys and humans and targeted three key time points during their lifespans. Pathways related to oxidative stress, inflammation and nutrient signaling, which function collectively to affect the quality and status of mitochondria, emerged across all species with age. Notably, mitochondrial transcript levels were better preserved in aging human muscle, suggesting an evolution-driven fitness more robust than in other species. The identification of these conserved pathways uncovers common molecular mechanisms intrinsic to health and lifespan, while unveiling of species-specific pathways emphasizes the importance of human studies for devising optimal therapeutic modalities to slow the aging process.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28649426" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87122" }, "primaryId" : "GEO:GSE87122", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87122" } ] }, "title" : "microRNAs regulated by aldosterone/salt in rat left ventricles in vivo", "dateAssigned" : "2016-09-20T00:00:00.000-05:00", "summary" : "Primary aldosteronism is characterized by excess aldosterone (ALDO) secretion independent of the renin-angiotensin system and accounts for ~10% of hypertensive patients. Excess ALDO, inappropriate for the salt intake status, causes cardiac hypertrophy, inflammation, fibrosis and hypertension. The molecular mechanisms that trigger the onset and progression of ALDO-mediated cardiac injury are poorly understood. MicroRNAs (miRNAs) are endogenous, small, non-coding RNAs that have been implicated in diverse cardiac pathologies, yet very little is known about their regulation and role in ALDO-mediated cardiac injury. To elucidate the regulation of miRNAs in ALDO-mediated cardiac injury, we performed a time-series analysis of left ventricle (LV) miRNA expression. Uninephrectomized male Sprague Dawley rats were treated with ALDO (0.75 µg/h) infusion and SALT (1.0% NaCl/0.3% KCl) in the drinking water for up to 8 weeks. ALDO/SALT time-dependently modulated the expression of multiple miRNAs in the LV. miR-21 was the most upregulated miRNA after 2 weeks of treatment and remained elevated until the end of the study. To elucidate the role of miR-21 in ALDO/SALT-mediated cardiac injury, miR-21 was downregulated using antagomirs in ALDO/SALT-treated rats. miR-21 downregulation exacerbated ALDO/SALT-mediated cardiac hypertrophy, fibrosis and inflammation markers gene expression, interstitial and perivascular fibrosis, OH-proline content and cardiac dysfunction. These results suggest that ALDO/SALT-mediated cardiac miR-21 upregulation may be a compensatory mechanism that mitigates ALDO/SALT-mediated cardiac deleterious effects. We speculate that miR-21 supplementation would have beneficial effects in reverting or mitigating cardiac injury and dysfunction in patients with primary aldosteronism.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28368454" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87129" }, "primaryId" : "GEO:GSE87129", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87129" } ] }, "title" : "01 Chemical-induced gene expression changes in rat liver", "dateAssigned" : "2016-09-20T00:00:00.000-05:00", "summary" : "Bromodichloromethane-induced gene expression changes in rat liver", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87135" }, "primaryId" : "GEO:GSE87135", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87135" } ] }, "title" : "02 Chemical-induced gene expression changes in rat liver", "dateAssigned" : "2016-09-20T00:00:00.000-05:00", "summary" : "N-Nitrosodimethylamine-induced gene expression changes in rat liver", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87137" }, "primaryId" : "GEO:GSE87137", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87137" } ] }, "title" : "03 Chemical-induced gene expression changes in rat liver", "dateAssigned" : "2016-09-20T00:00:00.000-05:00", "summary" : "1-Amino-2,4-Dibromoanthraquinone-induced gene expression changes in rat liver", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87138" }, "primaryId" : "GEO:GSE87138", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87138" } ] }, "title" : "04 Chemical-induced gene expression changes in rat liver", "dateAssigned" : "2016-09-20T00:00:00.000-05:00", "summary" : "N-Nitrosodimethylamine-induced gene expression changes in rat liver", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87140" }, "primaryId" : "GEO:GSE87140", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87140" } ] }, "title" : "05 Chemical-induced gene expression changes in rat liver", "dateAssigned" : "2016-09-20T00:00:00.000-05:00", "summary" : "Phenolphthalein-induced gene expression changes in rat liver", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87141" }, "primaryId" : "GEO:GSE87141", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87141" } ] }, "title" : "06 Chemical-induced gene expression changes in rat liver", "dateAssigned" : "2016-09-20T00:00:00.000-05:00", "summary" : "tert-Butyl alcohol-induced gene expression changes in rat liver", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87142" }, "primaryId" : "GEO:GSE87142", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87142" } ] }, "title" : "07 Chemical-induced gene expression changes in rat liver", "dateAssigned" : "2016-09-20T00:00:00.000-05:00", "summary" : "o-Anthranilic acid-induced gene expression changes in rat liver", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87143" }, "primaryId" : "GEO:GSE87143", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87143" } ] }, "title" : "08 Chemical-induced gene expression changes in rat liver", "dateAssigned" : "2016-09-20T00:00:00.000-05:00", "summary" : "Tris(2-Chloroethyl) Phosphate hydrochloride-induced gene expression changes in rat liver", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87145" }, "primaryId" : "GEO:GSE87145", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87145" } ] }, "title" : "09 Chemical-induced gene expression changes in rat liver", "dateAssigned" : "2016-09-20T00:00:00.000-05:00", "summary" : "2,2-Bis(Bromomethyl)-1,3-Propanediol-induced gene expression changes in rat liver", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87146" }, "primaryId" : "GEO:GSE87146", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87146" } ] }, "title" : "10 Chemical-induced gene expression changes in rat liver", "dateAssigned" : "2016-09-20T00:00:00.000-05:00", "summary" : "Nitrilotriacetic acid trisodium monohydrate-induced gene expression changes in rat liver", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87188" }, "primaryId" : "GEO:GSE87188", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87188" } ] }, "title" : "Gene Expression Profiling in the Hippocampus of Orchidectomized Rats", "dateAssigned" : "2016-09-21T00:00:00.000-05:00", "summary" : "The present study was conducted to identify relevant genes that could be involved in the action of androgens in rat hippocampus. We compared hippocampal gene expression between controls and orchidectomized male rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24760298" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87229" }, "primaryId" : "GEO:GSE87229", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87229" } ] }, "title" : "Gene expression changes of 1,2,3-trichloropropane-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 1,2,3-trichloropropane, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87230" }, "primaryId" : "GEO:GSE87230", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87230" } ] }, "title" : "Gene expression changes of 1,2-dibromoethane-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 1,2-dibromoethane, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87232" }, "primaryId" : "GEO:GSE87232", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87232" } ] }, "title" : "Gene expression changes of 1-amino-2,4-dibromoanthraquinone-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 1-amino-2,4-dibromoanthraquinone, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87234" }, "primaryId" : "GEO:GSE87234", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87234" } ] }, "title" : "Gene expression changes of 2,2-bis(bromomethyl)-1,3-propanediol-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 2,2-bis(bromomethyl)-1,3-propanediol, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87236" }, "primaryId" : "GEO:GSE87236", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87236" } ] }, "title" : "Gene expression changes of 2-Amino-4-nitrophenol-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 2-Amino-4-nitrophenol, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87243" }, "primaryId" : "GEO:GSE87243", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87243" } ] }, "title" : "Gene expression changes of 4-hydroxy-m-phenylenediammonium dichloride-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 4-hydroxy-m-phenylenediammonium dichloride, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87244" }, "primaryId" : "GEO:GSE87244", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87244" } ] }, "title" : "Gene expression changes of anthraquinone-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with anthraquinone, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87245" }, "primaryId" : "GEO:GSE87245", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87245" } ] }, "title" : "Gene expression changes of benzyl acetate-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with benzyl acetate, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87246" }, "primaryId" : "GEO:GSE87246", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87246" } ] }, "title" : "Gene expression changes of bromodichloromethane-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with bromodichloromethane, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87249" }, "primaryId" : "GEO:GSE87249", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87249" } ] }, "title" : "Gene expression changes of carbon tetrachloride-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with carbon tetrachloride, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87251" }, "primaryId" : "GEO:GSE87251", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87251" } ] }, "title" : "Gene expression changes of chlorothalonil-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with chlorothalonil, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87252" }, "primaryId" : "GEO:GSE87252", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87252" } ] }, "title" : "Gene expression changes of dipropylene glycol-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with dipropylene glycol, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87253" }, "primaryId" : "GEO:GSE87253", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87253" } ] }, "title" : "Gene expression changes of ethylenediamine dihydrochloride-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with ethylenediamine dihydrochloride, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87255" }, "primaryId" : "GEO:GSE87255", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87255" } ] }, "title" : "Gene expression changes of monuron-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with monuron, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87256" }, "primaryId" : "GEO:GSE87256", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87256" } ] }, "title" : "Gene expression changes of N,N'-dinitrosopentamethylenetetramine-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with N,N'-dinitrosopentamethylenetetramine, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87258" }, "primaryId" : "GEO:GSE87258", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87258" } ] }, "title" : "Gene expression changes of n-nitrosodimethylamine-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with n-nitrosodimethylamine, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87260" }, "primaryId" : "GEO:GSE87260", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87260" } ] }, "title" : "Gene expression changes of nitrilotriacetic acid trisodium monohydrate-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with nitrilotriacetic acid trisodium monohydrate, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87261" }, "primaryId" : "GEO:GSE87261", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87261" } ] }, "title" : "Transcriptomic data to assess hexavalent chromium mode of action in mice and rats [rat]", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "In order to evaluate the mechanisms underlying hexavalent chromium (Cr(VI)) responses, mice and rats were treated with varying concentrations of Cr(VI) in drinking water, as sodium dichromate dihydrate (SDD). Potential transcriptomic responses were evaluated through microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27859739" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87263" }, "primaryId" : "GEO:GSE87263", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87263" } ] }, "title" : "Gene expression changes of ochratoxin A-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with ochratoxin A, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87264" }, "primaryId" : "GEO:GSE87264", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87264" } ] }, "title" : "Gene expression changes of phenolphthalein-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with phenolphthalein, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87265" }, "primaryId" : "GEO:GSE87265", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87265" } ] }, "title" : "Gene expression changes of phenylbutazone-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with phenylbutazone, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87267" }, "primaryId" : "GEO:GSE87267", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87267" } ] }, "title" : "Gene expression changes of potassium bromate-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with potassium bromate, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87268" }, "primaryId" : "GEO:GSE87268", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87268" } ] }, "title" : "Gene expression changes of sulfone bis(p-chlorophenyl)-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with sulfone bis(p-chlorophenyl), and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87269" }, "primaryId" : "GEO:GSE87269", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87269" } ] }, "title" : "Gene expression changes of tricresyl phosphate-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with tricresyl phosphate, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87270" }, "primaryId" : "GEO:GSE87270", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87270" } ] }, "title" : "Gene expression changes of tris(2-chloroethyl)phosphate-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with tris(2-chloroethyl)phosphate, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87271" }, "primaryId" : "GEO:GSE87271", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87271" } ] }, "title" : "Gene expression changes of 4,4'-thiobis(6-tert-butyl-m-cresol)-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 4,4'-thiobis(6-tert-butyl-m-cresol), and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87272" }, "primaryId" : "GEO:GSE87272", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87272" } ] }, "title" : "Gene expression changes of cisplatin-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with cisplatin, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87274" }, "primaryId" : "GEO:GSE87274", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87274" } ] }, "title" : "Gene expression changes of o-anisidine hydrochloride-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with o-anisidine hydrochloride, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87275" }, "primaryId" : "GEO:GSE87275", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87275" } ] }, "title" : "Gene expression changes of o-anthranilic acid-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with o-anthranilic acid, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87276" }, "primaryId" : "GEO:GSE87276", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87276" } ] }, "title" : "Gene expression changes of o-nitroanisole-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with o-nitroanisole, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87277" }, "primaryId" : "GEO:GSE87277", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87277" } ] }, "title" : "Gene expression changes of p-nitroanisole-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with p-nitroanisole, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87278" }, "primaryId" : "GEO:GSE87278", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87278" } ] }, "title" : "Gene expression changes of tert-butyl alchol-induced in renal cortex of rats", "dateAssigned" : "2016-09-22T00:00:00.000-05:00", "summary" : "This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with tert-butyl alchol, and the gene expression profiles of renal cortex were analyzed using custom microarrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87330" }, "primaryId" : "GEO:GSE87330", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87330" } ] }, "title" : "Influence of Anti-VEGFA and dexamathasone treatments on the early phase of cornea angiogenesis", "dateAssigned" : "2016-09-25T00:00:00.000-05:00", "summary" : "We used GeneChip Rat Genome 230 2.0 Array to monitor gene expression profies of several genes in the different treatment groups", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87394" }, "primaryId" : "GEO:GSE87394", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87394" } ] }, "title" : "Time course analysis of outer medulla-specific gene expression profiles in the kidneys of Sprague-Dawley rats in a repeated dose study of 2-amino-4-nitrophenol.", "dateAssigned" : "2016-09-27T00:00:00.000-05:00", "summary" : "In the present study, we performed a general toxicity test and a genome-wide gene expression analysis of rat kidney to identify the mechanisms of 2-amino-4-nitrophenol (ANP) -induced chronic renal failure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87432" }, "primaryId" : "GEO:GSE87432", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87432" } ] }, "title" : "Therapeutic Mechanisms of Chinese Herbal Medicine Qushi Huayu Decoction (QHD) in the Treatment of NAFLD", "dateAssigned" : "2016-09-28T00:00:00.000-05:00", "summary" : "We used microarrays to examine the effects of QHD and GC treatment on the liver transcriptomes of NAFLD rats induced by high fat diet and identified multiple therapeutic targets of QHD.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87439" }, "primaryId" : "GEO:GSE87439", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87439" } ] }, "title" : "The effect of Schisandra chinensis fruit extract (SCE) and Schisandrin B (SchB) on gene expression profile in TGF-β1-treated A7r5 rat aortic smooth muscle cell", "dateAssigned" : "2016-09-28T00:00:00.000-05:00", "summary" : "Schisandra chinensis fruit extract (SCE) and its active ingredient Schisandrin B (SchB), which are effective in the treatment of vascular diseases, have been known to suppress transforming growth factor β1 (TGF-β1)-mediated Smad activation and myosin light chain (MLC) phosphorylation in vascular smooth muscle cells (VSMCs). However, it is still largely unknown about the pharmacologic effects and mechanisms of SCE and SchB on TGF-β1-induced intracellular signaling pathways in vascular smooth muscle cells (VSMCs). ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29423034" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87446" }, "primaryId" : "GEO:GSE87446", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87446" } ] }, "title" : "Mechanistic roles of microRNAs in hepatocarcinogenesis: A study of thioacetamide with multiple doses and time-points of rats", "dateAssigned" : "2016-09-28T00:00:00.000-05:00", "summary" : "These findings reveal the critical role of miRNAs in the mechanisms underlying hepatocarcinogenesis and potential application for human risk assessment. Most importantly, rno-miR-34a-5p is the most suitable early and sensitive biomarker for TAA-induced hepatocarcinogenesis due to its consistent elevation during the entire treatment course.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28596526" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87521" }, "primaryId" : "GEO:GSE87521", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87521" } ] }, "title" : "Cardiotrophin 1 stimulates beneficial myogenic and vascular remodeling in the heart", "dateAssigned" : "2016-09-30T00:00:00.000-05:00", "summary" : "Primary neonatal cardiomyocytes treated with human cardiotrophin 1 (hCT1) or control (Ctrl) for 24 hours", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28785017" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87525" }, "primaryId" : "GEO:GSE87525", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87525" } ] }, "title" : "Assessment of Histone Tail Modifications and Transcriptional Profiling During Colon Cancer and Role of fish oil/pectin Diet Against Colon Carcinogen", "dateAssigned" : "2016-09-30T00:00:00.000-05:00", "summary" : "In an effort to gain insight into the extensive dimension of post-translational modifications in histones (including H3K4me3 and H3K9ac) and elucidate the chemoprotective impact of dietary bioactive compounds on transcriptional control in a colon cancer preclinical model, we generated high-resolution genome-wide RNA (RNA-Seq) and “chromatin-state” (H3K4me3-seq and H3K9ac-seq) maps for intestinal (epithelial colonocytes) crypts in rats treated with a colon carcinogen and fed bioactive (i) fish oil (ii) butyrate (in the form of a fermentable fiber a rich source of SCFA), (iii) a combination of fish oil plus butyrate or (iv) control diets. Poor correlation was observed between differentially transcribed (DE) and enriched genes (DERs) at multiple epigenetic levels in fat x fiber dietary combinations and in the presence/absence of carcinogen. We also demonstrated that the combinatorial diet (fish oil + pectin) was synergistically chemoprotective, and uniquely affected epigenetic profiles in the intestinal epithelium, e.g., upregulating lipid catabolism and beta-oxidation associated genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28315775" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87555" }, "primaryId" : "GEO:GSE87555", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87555" } ] }, "title" : "Gene expression in ATII cells transduced with adenovirus expressing constitutively active mutant HIF1a", "dateAssigned" : "2016-10-03T00:00:00.000-05:00", "summary" : "To determine HIF1a target genes in ATII cells, we transduced freshly isolated rat ATII cells with an adenoviral vector expressing either GFP or a constitutively active mutant HIF1a construct. After 24 hours, RNA was extracted and subjected to microarray.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87611" }, "primaryId" : "GEO:GSE87611", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87611" } ] }, "title" : "Conversion of terminally committed hepatocytes to culturable bipotent progenitor cells with regenerative capacity", "dateAssigned" : "2016-10-04T00:00:00.000-05:00", "summary" : "Transcriptomic analyses for freshly isolated MHs and cells cultured for the designated periods with or without YAC stimulation (Matrix 1). Transcriptomic analysis for CLiPs which underwent hepatic induction (Matrix 2). Transcriptomic comparison of hepatic inducibility between CLiPs at early passage and those at late passages (Matrix 3). Transcriptomic comparison between chimera-derived rat cells (designated as “2nd”) and primary rat MH-derived cells (designated as “1st”) (Matrix 4).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27840021" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87613" }, "primaryId" : "GEO:GSE87613", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87613" } ] }, "title" : "Transcriptome of normal mammary glands of Sprague-Dawley rats at six stages of development: pre-pubertal, peri-pubertal, pubertal, lactation, adult parous and age-matched nulliparous", "dateAssigned" : "2016-10-04T00:00:00.000-05:00", "summary" : "There is a lack of systematic investigations of large-scale transcriptome patterns associated with normal breast development. Herein, we profiled whole-transcriptome (by microarrays) of normal mammary glands in female Sprague-Dawley rats, an animal model widely used in breast cancer research, across six distinctive developmental stages – pre-pubertal, peri-pubertal, pubertal, lactation, and adult parous and age-matched nulliparous.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29956080" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87696" }, "primaryId" : "GEO:GSE87696", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87696" } ] }, "title" : "Toxicogenomic module associations with pathogenesis: A network based approach to understanding drug toxicity", "dateAssigned" : "2016-10-06T00:00:00.000-05:00", "summary" : "Despite investment in toxicogenomics, nonclinical safety studies are still used to predict clinical liabilities for new drug candidates. Network-based approaches for genomic analysis help overcome challenges with whole-genome transcriptional profiling using limited numbers of treatments for phenotypes of interest. Herein, we apply co-expression network analysis to safety assessment using rat liver gene expression data to define 415 modules, exhibiting unique transcriptional control, organized in a visual representation of the transcriptome (the ‘TXG-MAP’). Accounting for the overall transcriptional activity resulting from treatment, we explain mechanisms of toxicity and predict distinct toxicity phenotypes using module associations. We demonstrate that early network responses compliment traditional histology-based assessment in predicting outcomes for longer studies and identify a novel mechanism of hepatotoxicity involving endoplasmic reticulum stress and Nrf2 activation. Module-based molecular subtypes of cholestatic injury derived using rat translate to human. Moreover, compared to gene-level analysis alone, combining module and gene-level analysis performed in sequence identifies significantly more phenotype-gene associations, including established and novel biomarkers of liver injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28440344" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87709" }, "primaryId" : "GEO:GSE87709", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87709" } ] }, "title" : "NRSF/REST ChIP-seq binding profile in the rat paraventricular nucleus (PVN) of the hypothalamus", "dateAssigned" : "2016-10-06T00:00:00.000-05:00", "summary" : "We report genome-wide changes in NRSF binding following early life events that may be associated with resilience", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28070121" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87730" }, "primaryId" : "GEO:GSE87730", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87730" } ] }, "title" : "Toxicogenomic module associations with pathogenesis: A network based approach to understanding drug toxicity (ChIP-Seq)", "dateAssigned" : "2016-10-06T00:00:00.000-05:00", "summary" : "Despite investment in toxicogenomics, nonclinical safety studies are still used to predict clinical liabilities for new drug candidates. Network-based approaches for genomic analysis help overcome challenges with whole-genome transcriptional profiling using limited numbers of treatments for phenotypes of interest. Herein, we apply co-expression network analysis to safety assessment using rat liver gene expression data to define 415 modules, exhibiting unique transcriptional control, organized in a visual representation of the transcriptome (the ‘TXG-MAP’). Accounting for the overall transcriptional activity resulting from treatment, we explain mechanisms of toxicity and predict distinct toxicity phenotypes using module associations. We demonstrate that early network responses compliment traditional histology-based assessment in predicting outcomes for longer studies and identify a novel mechanism of hepatotoxicity involving endoplasmic reticulum stress and Nrf2 activation. Module-based molecular subtypes of cholestatic injury derived using rat translate to human. Moreover, compared to gene-level analysis alone, combining module and gene-level analysis performed in sequence identifies significantly more phenotype-gene associations, including established and novel biomarkers of liver injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28440344" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87744" }, "primaryId" : "GEO:GSE87744", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87744" } ] }, "title" : "RNA-Seq Gene Expression Analysis in Rat Metanephric Mesenchyme overexpressing Transcription Factor Tfcp2l1", "dateAssigned" : "2016-10-07T00:00:00.000-05:00", "summary" : "We identified genes regulated by Tfcp2l1 overexpression in Rat Metanephric Mesenchyme", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28577314" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87746" }, "primaryId" : "GEO:GSE87746", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87746" } ] }, "title" : "Gender differences in the cytokines and chemokines gene expression profiles within the medulla oblongata of SHRs", "dateAssigned" : "2016-10-07T00:00:00.000-05:00", "summary" : "To unveil the gender differences in the central regulation of blood pressure, we investigated the gene expression profile of cytokines and chemokines in the medulla oblongata of female SHRs compared to that of their male counterparts.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87762" }, "primaryId" : "GEO:GSE87762", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87762" } ] }, "title" : "Gene expression analysis of hyper active mutant SPORTS rat [brain]", "dateAssigned" : "2016-10-07T00:00:00.000-05:00", "summary" : "To get insight into the genetic characteristics of hyper active mutant line of rat, SPORTS, we compared gene expression profiles of the sedentary SPORTS rat and the sedentary wild type rat. Using RNA extracted from the brain of these rats, we performed microarray analysis. Subsequent GO analyses revealed that genes belonging to norepinephrine synthetic pathway and coagulation were upreguated. These results were consistent with phenotypes, such as hyper activity and thrombotic tendency, which were reported for SPORTS rat.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87855" }, "primaryId" : "GEO:GSE87855", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE87855" } ] }, "title" : "Neuronal cytoskeletal gene dysregulation drives mechanical hypersensitivity in Rett Syndrome", "dateAssigned" : "2016-10-11T00:00:00.000-05:00", "summary" : "This study investigated mechanisms of peripheral sensory abnormalities in Rett Syndrome using a MeCP2 knockout rat. Dramatic changes in peripheral innervation by DRG sensory neurons were observed in the knockout rats that strongly correlated with modality-specific sensory dysfunction. The cell-autonomous effect of MeCP2 mutation in DRG neurons disrupt axon growth mechanisms leading to the altered cutaneous innervation density. We performed RNA-Seq to compare the transcriptome of MeCP2 KO DRGs with that derived from wildtype littermates. This revealed profound impact of MeCP2 loss on axon growth regulatory pathways in sensory neurons. The findings will have significant impact on our understanding of sensory dysfunctions in Rett syndrome and Autism Spectrum Disorders at large.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28760966" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88708" }, "primaryId" : "GEO:GSE88708", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88708" } ] }, "title" : "Dysregulation of hepatic microRNA expression profiles with Clonorchis sinensis infection", "dateAssigned" : "2016-10-13T00:00:00.000-05:00", "summary" : "MiRNA microarray technology and bioinformatic analysis were used to investigate the regulatory mechanisms of host miRNA and to compare miRNA expression profiles in the liver tissues of Clonorchis sinensis-infected rats and controls.A total of eight miRNAs were downregulated and two were upregulated, which showed differentially altered expression profiles in the liver tissue of C. sinensis-infected rats. Further analysis of the differentially expressed miRNAs revealed that many important signal pathways were triggered after infection with C. sinensis, which were related to clonorchiasis pathogenesis, such as cell apoptosis and inflammation, as well as genes involved in signal transduction mechanisms, such as pathways in cancer and the Wnt and Mitogen-activated protein kinases (MAPK) signaling pathways.This dysregulation in miRNA expression may contribute to the etiology and pathophysiology of clonorchiasis. These results also provide new insights into the regulatory mechanisms of miRNAs in clonorchiasis, which may present potential targets for future C. sinensis control strategies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27899092" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88726" }, "primaryId" : "GEO:GSE88726", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88726" } ] }, "title" : "Aberrant striatal but not nigral gene expression profiles are specifically associated with dyskinesia behavior following levodopa treatment in the 6-hydroxydopamine lesioned rat", "dateAssigned" : "2016-10-13T00:00:00.000-05:00", "summary" : "Levodopa-induced dyskinesia (LID) is a common consequence of prolonged pharmacotherapy for Parkinson's disease (PD). While LID becomes more common with long term exposure to levodopa, its development can be quite variable. We leveraged the variable expression of LID in a rat model to interrogate differential gene expression in the substantia nigra and striatum of animals that develop LID and those that do not. Differential expression of genes associated with LID was found only in striatum, not substantia nigra.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88736" }, "primaryId" : "GEO:GSE88736", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88736" } ] }, "title" : "Transcriptomics of environmental enrichment and cocaine using quantitative next generation sequencing", "dateAssigned" : "2016-10-14T00:00:00.000-05:00", "summary" : "Environmental enrichment produces a protective addiction phenotype in animal models. Gene transcription is thought to mediate this protective phenotype and has a profound influence on neuronal plasticity and psychiatric disorders. Understanding the molecular and genetic mechanisms underlying environmental enrichment may lead to novel targets for pharmacotherapeutics to treat cocaine addiction. We investigated the differential regulation of transcript levels using RNA sequencing of the rat nucleus accumbens after environmental enrichment/isolation and cocaine/saline self-administration. New functional pathways were also identified for cocaine modulation and environmental enrichment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27899881" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88853" }, "primaryId" : "GEO:GSE88853", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88853" } ] }, "title" : "Gene expression analysis of hyper active mutant SPORTS rat [muscle]", "dateAssigned" : "2016-10-18T00:00:00.000-05:00", "summary" : "To get insight into the genetic characteristics of hyper active mutant line of rat, SPORTS, and the effect of exercise on gene expression, we compared gene expression profiles of exercised SPORTS rat, sedentary SPORTS rat, and sedentary wild type rat. Using RNA extracted from the muscle of these rats, we performed microarray analysis. Subsequent GO analyses revealed that genes belonging to muscle development and glycolysis were upregulated in exercised SPORTS rat compared to sedentary SPORTS rat, and genes related to coagulation were upreguated in sedentary SPORTS rat compared to wild type rat. These results were consistent with phenotypes, such as hyper activity and thrombotic tendency, which were reported for SPORTS rat.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88855" }, "primaryId" : "GEO:GSE88855", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88855" } ] }, "title" : "Expression data from the spinal cord of dmy rat with Mrs2 mutation", "dateAssigned" : "2016-10-18T00:00:00.000-05:00", "summary" : "To clarify the pathogenesis of myelin destruction in dmy rats, we performed a microarray analysis using spinal cord samples.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27977799" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88874" }, "primaryId" : "GEO:GSE88874", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88874" } ] }, "title" : "Maternal Style Selectively Shapes Amygdalar Development and Social Behavior in Rats Genetically Prone to High Anxiety", "dateAssigned" : "2016-10-18T00:00:00.000-05:00", "summary" : "All samples were generated from Sprague-Dawley male rats selectively bred for high novelty response (HRs), low novelty response (LRs) or LRs that were crossfostered to either a LR dame or HR dame.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27965039" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88910" }, "primaryId" : "GEO:GSE88910", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88910" } ] }, "title" : "Transcriptomes of rat hearts after kidney transplantation in chronic kidney disease model", "dateAssigned" : "2016-10-18T00:00:00.000-05:00", "summary" : "Transcriptomes from hearts of control and CKD rats after transplantation of healthy kidney and kidney from CKD animal.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88925" }, "primaryId" : "GEO:GSE88925", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE88925" } ] }, "title" : "Impaired post-ischemic angiogenesis in rats with chronic kidney disease", "dateAssigned" : "2016-10-19T00:00:00.000-05:00", "summary" : "We investigated potential molecular mechanisms underlying impaired angiogenesis by a systematic comparison of early gene expression in response to ischemia in rats with or without CKD", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89024" }, "primaryId" : "GEO:GSE89024", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89024" } ] }, "title" : "Quant Seq analysis of primary stretched rat alveolar type I-like epithelial (AEC-I) cells", "dateAssigned" : "2016-10-21T00:00:00.000-05:00", "summary" : "Rat AEC-I cell monolayers were generated from primary isolated type-II pneumoncytes by plating them on fibronectin-coated silastic membranes. After 4 days of culturing, type-II pneumocytes trasform into AEC-I cells and form monolayers", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89028" }, "primaryId" : "GEO:GSE89028", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89028" } ] }, "title" : "Genome wide analysis of rat renal gene expression at two different time points during hyperoxaluria development", "dateAssigned" : "2016-10-21T00:00:00.000-05:00", "summary" : "We are testing the ability of spironolactone as a NADPH oxidase inhibitor during an induced dietary oxalate overload by Ethylene Glycol in Sprague Dawley rats at two different time points. We looked into the development of hyperoxaluria and crystal deposition at two different time points and into differences between hyperoxaluria and crystal induced alterations in the kidneys. Eventually, we are expecting to see the role of spironolactone as an inhibitor of NADPH oxidase which is involved in the production of reactive oxygen species (ROS) which leads to oxidative stress in the living organisms leading to a plethora of vascular diseases, hypertension, and kidney diseases.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89054" }, "primaryId" : "GEO:GSE89054", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89054" } ] }, "title" : "Expression data from newborn rat skeletal muscle subjected to low protein diet or low protein+taurine during gestation", "dateAssigned" : "2016-10-21T00:00:00.000-05:00", "summary" : "We used microarrays to detail changes in global programme of gene expression in newborn offspring skeletal muscle brains from rats subjected to either a control diet, a low protein diet or a low protein diet + taurine supplementation", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89107" }, "primaryId" : "GEO:GSE89107", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89107" } ] }, "title" : "DNA Methylation Targets Influenced by Bisphenol A and/or Genistein Are Associated with Survival Outcomes in Breast Cancer Patients", "dateAssigned" : "2016-10-24T00:00:00.000-05:00", "summary" : "Early postnatal exposures to Bisphenol A (BPA) and genistein (GEN) have been reported to predispose for and against mammary cancer, respectively, in adult rats. Since the changes in cancer susceptibility occurs in the absence of the original chemical exposure, we have investigated the potential of epigenetics to account for these changes. DNA methylation studies reveal that prepubertal BPA exposure alters signaling pathways that contribute to carcinogenesis. Prepubertal exposure to GEN and to BPA + GEN suggests pathways involved in maintenance of cellular function, indicating that the presence of GEN either reduces or counters some of the alterations caused by the carcinogenic properties of BPA. We subsequently evaluated the potential of epigenetic changes in the rat mammary tissues to predict survival in breast cancer patients via The Cancer Genomic Atlas (TCGA). We identified 12 genes that showed strong predictive values for long-term survival in estrogen receptor positive patients. Importantly, two genes associated with improved long term survival, HPSE and RPS9, were identified to be hypomethylated in mammary glands of rats exposed prepuberally to GEN or to GEN + BPA respectively, reinforcing the suggested cancer suppressive properties of GEN.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28505145" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89130" }, "primaryId" : "GEO:GSE89130", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89130" } ] }, "title" : "Transcriptomic profiling of cardiac remodeling in high phosphate exposed cardiomyoblasts", "dateAssigned" : "2016-10-24T00:00:00.000-05:00", "summary" : "Cardiovascular disease (CVD) in chronic kidney disease (CKD) is characterized by vascular calcification and cardiac remodeling. CKD induced cardiac hypertrophy precedes cardiac fibrosis and is associated with left ventricular dysfunction. Elevated phosphate concentration due to renal failure is known to be involved in cardiac remodeling.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89138" }, "primaryId" : "GEO:GSE89138", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89138" } ] }, "title" : "Paternal high-fat diet elicits early-onset se-specific islet inflammation in rat progeny", "dateAssigned" : "2016-10-25T00:00:00.000-05:00", "summary" : "Progressive β–cell failure and apoptosis, resultant of innate immune system activation1,2 is gaining traction as a converging point for type 1 (T1D) and type 2 (T2D). Islet inflammation (insulitis), a hallmark of T1D, occurs typically during the initiation phase of the disease, subsequently orchestrating an autoimmune assault against β–cells. Whether this is a primary event or a consequence of glucotoxicity or lipotoxicity is undetermined3 but metabolic stress is demonstrated to prompt islet inflammation1,2. Here we show that paternal consumption of high fat diet (HFD) invoked distinct immuno-inflammatory transcriptional response in the pancreatic islets of their weanling daughters, in contrast to compensatory changes in the sons. Importantly, these changes occurred in conjunction with transition in islet repertoire resembling the spectrum of T2D, along with progressive development of β–cell dysfunction4. Note, these females were lean, normolipidaemic and insulin sensitive4. These findings provide experimental support for the notion that islet inflammation could be an antecedent event in T2D, leading to β–cell secretory defect, repair/regeneration and apoptosis. Importantly, these effects were transmitted via paternal nutrient stress to offspring.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89173" }, "primaryId" : "GEO:GSE89173", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89173" } ] }, "title" : "Genome-wide transcriptomic and epigenomic study of DHA in rat hypothalamus and hippocampus [RNA-seq]", "dateAssigned" : "2016-10-25T00:00:00.000-05:00", "summary" : "To investigate the effects of DHA (an omega-3 fatty acid) on brain dysfunction and metabolic disorders by sequencing the transcriptome (RNA-Seq) and epigenome (RRBS) in the hypothalamus and hippocampus of male SD rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89175" }, "primaryId" : "GEO:GSE89175", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89175" } ] }, "title" : "Genome-wide transcriptomic and epigenomic study of DHA in rat hypothalamus and hippocampus [RRBS]", "dateAssigned" : "2016-10-25T00:00:00.000-05:00", "summary" : "To investigate the effects of DHA (an omega-3 fatty acid) on brain dysfunction and metabolic disorders by sequencing the transcriptome (RNA-Seq) and epigenome (RRBS) in the hypothalamus and hippocampus of male SD rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89202" }, "primaryId" : "GEO:GSE89202", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89202" } ] }, "title" : "MiR-218 regulates heroin seeking behavior by targeting Mecp2", "dateAssigned" : "2016-10-26T00:00:00.000-05:00", "summary" : "Noncoding RNAs, especially microRNAs (miRNAs) have been implicated in the regulation of neuronal functions, such as learning, cognition and memory formation. However, the particular miRNAs involved in drug-induced behavioral plasticity are largely unknown. Here we report a novel regulator, miR-218, that inhibits heroin-induced behavioral plasticity. Network propagation-based method revealed several miRNAs that play key roles in drug-addiction, among which, miR-218 was decreased in nucleus accumbens (NAc) after chronic exposure to heroin. Lentiviral overexpression of miR-218 in NAc could inhibit heroin-induced reinforcement in both conditioning place preference (CPP) test and heroin self-administration (SA) experiment. Luciferase activity assay indicated miR-218 could regulate neuroplasticity related genes and directly target Mecp2 3’UTR. Consistently, Mecp2-/y mice exhibited reduced heroin seeking behavior in CPP test. These data reveal a functional role of miR-218 and its target, Mecp2, in the regulation of heroin-induced behavioral plasticity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28074855" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89250" }, "primaryId" : "GEO:GSE89250", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89250" } ] }, "title" : "HNF4a transduction and 5'azacytidine treatment of rat liver progenitor cells (rLEC) to promote the hepatic phenotype", "dateAssigned" : "2016-10-27T00:00:00.000-05:00", "summary" : "Therefore, we aim at studying the phenotype of rLEC by transducing the cells with HNF4a. In addition, to make the genes more sensitive to transcription and differentiation, the effect of the DNA methyl transferase inhibitor 5' azacytidine (AZA) (20 µM) was also investigated. The global expression profiles of both microRNA and mRNA were studied by means of microarray technology.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89321" }, "primaryId" : "GEO:GSE89321", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89321" } ] }, "title" : "The estrogenic activity of triclosan", "dateAssigned" : "2016-10-31T00:00:00.000-05:00", "summary" : "Triclosan is a commonly used antibacterial and antifungal agent. However, safety of TCS has been disputed. We performed gene expression profiling of TCS and estrogen-administrered rat uterus to compare genes and cellular processes to find the effects of TCS and estrogen.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28183164" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89347" }, "primaryId" : "GEO:GSE89347", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89347" } ] }, "title" : "Effect of Wakame Containing Diets on Hepatic Gene Expressions in Rat", "dateAssigned" : "2016-10-31T00:00:00.000-05:00", "summary" : "Wakame is an edible seaweed that is a common constituent in the Japanese diet. Previous studies showed that wakame consumption is associated with prevention of metabolic syndrome; however, the molecular mechanisms of this protective effect are poorly understood. To determine if the expression of hepatic genes is affected by the ingestion of brown seaweed, Undaria pinnatifida (wakame), rats were fed diets containing 0, 0.1, or 1.0 g/100 g dried wakame powder for 28 days. Administration of 1% wakame significantly decreased total serum total cholesterol levels. Hepatic gene expression was investigated using DNA microarray analysis. Microarray analysis showed that wakame suppresses the lipogenic pathway by downregulating SREBF-1. Moreover, bile acid biosynthesis and gluconeogenesis are promoted by upregulation of the PPAR signaling pathway, which leads to a reduction in the accumulation of cholesterol and promotion of β-oxidation. These results provide useful genetic information about various biochemical processes by which wakame regulates energy metabolism.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29663642" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89406" }, "primaryId" : "GEO:GSE89406", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89406" } ] }, "title" : "Limited Fluid Resuscitation Significantly Alters the Hepatic Gene Profiles in Rats with Uncontrolled Hemorrhagic Shock", "dateAssigned" : "2016-11-01T00:00:00.000-05:00", "summary" : "The study aimed to investigate the effect of limited fluid resuscitation on gene profiles of rat hepatic tissue. Limited fluid resuscitation can reduce mortality resulting from traumatic hemorrhagic shock. However, the protective mechanism of limited fluid resuscitation is not very clear. The rats were subjected to uncontrolled hemorrhagic shock and resuscitated with limited fluid resuscitation or aggressive fluid resuscitation. Following 5 h of resuscitation, hepatic RNA was isolated, and gene expression profiles were measured using a NimbleGen microarray. Gene ontology (GO) and pathway analyses were performed. Real-time reverse transcription polymerase chain reaction was used to verify the microarray findings. A total of 449 differentially expressed genes between aggressive fluid resuscitation and limited fluid resuscitation groups were found. The GO analysis of differential gene expression predicted a significant downregulation of response to stress, alcohol biosynthetic process, response to wounding, gluconeogenesis, hexose biosynthetic process, acute inflammatory response, inflammatory response, response to oxygen levels, glucose metabolic process, acute-phase response, and so forth, and upregulation of steroid biosynthetic process, sterol metabolic process, steroid metabolic process, alcohol metabolic process, lipid metabolic process, cholesterol metabolic process, glycogen catabolic process, glucan catabolic process, cellular polysaccharide catabolic process, monocarboxylic acid metabolic process, and so on. This study showed that limited fluid resuscitation can downregulate the expression of injury-associated differentially expressed genes and upregulate the expression of metabolism-associated differentially expressed genes, which may account for the attenuation of the deleterious effects and overall prosurvival effects of limited fluid resuscitation on uncontrolled hemorrhagic shock.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89407" }, "primaryId" : "GEO:GSE89407", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89407" } ] }, "title" : "Distal axotomy enhances retrograde presynaptic excitability onto injured pyramidal neurons via trans-synaptic signaling", "dateAssigned" : "2016-11-01T00:00:00.000-05:00", "summary" : "Injury of descending motor tracts remodels cortical circuitry and leads to enhanced neuronal excitability, thus influencing recovery following injury. The neuron-specific contributions remain unclear due to the complex cellular composition and connectivity of the CNS. We developed a microfluidics-based in vitro model system to examine intrinsic synaptic remodeling following axon damage. We found that distal axotomy of cultured rat pyramidal neurons caused dendritic spine loss at synapses onto the injured neurons followed by a persistent retrograde enhancement in presynaptic excitability over days. These in vitro results mirrored hyper-activity of directly injured corticospinal neurons in hindlimb motor cortex layer Vb following spinal cord contusion. In vitro axotomy-induced hyper-excitability coincided with elimination of inhibitory presynaptic terminals, including those formed onto dendritic spines. We identified netrin-1 as downregulated following axotomy and exogenous netrin-1 applied 2 days after injury normalized spine density, presynaptic excitability, and the fraction of inhibitory inputs onto injured neurons. These findings demonstrate a novel model system for studying the response of pyramidal circuitry to axotomy and provide new insights of neuron-specific mechanisms that contribute to synaptic remodeling.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89873" }, "primaryId" : "GEO:GSE89873", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89873" } ] }, "title" : "Gene expression profiling of early-activated targets of antidepressants in glia cells", "dateAssigned" : "2016-11-15T00:00:00.000-06:00", "summary" : "The identification of cell-type-specific and early-activated pharmacological targets of antidepressants might help to implement the search for alternative targets to develop drugs with safer side-effect profiles and faster onset of actions. Glia cells are active partners of neurons and blood vessels in supporting a variety of functions such as synaptic communication and blood-brain barrier permeability. Impaired glia cells (astrocytes and microglia cells) characterize postmortem brains of major depressive disorder patients, suggesting that they might be specifically modulated by pharmacological treatments to reverse disease phenotypes. Here, we have treated rat C6 glioma cells, used as a model of astrocytes, with two different classes of antidepressants (desipramine and fluoxetine) and two drugs without antidepressant properties (haloperidol and diazepam) to compare transcriptomes of glia cells after treatment with antidepressants versus drugs without antidepressant properties. To this aim, we used microarrays to detail the global early-activated cell-type-specific gene expression program and identified multiple classes of genes selectively modulated by antidepressants in astrocytes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89919" }, "primaryId" : "GEO:GSE89919", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE89919" } ] }, "title" : "Whole Genome Bisulfite sequencing for liver DNA methylation analysis of rat exposed to 0.05% Pb", "dateAssigned" : "2016-11-16T00:00:00.000-06:00", "summary" : "We generated 4 Gb of high-quality sequencing data (~1 Gb per sample). The NCD+0.05%Pb group had hypermethylation at the whole genome level, compared to NCD. Difference analysis in gene methylation aimed at TSS region indicated that a total of 2733 genes experienced DNA methylation changes, with 2320 hypermethylated genes and 413 hypomethylated genes of the NCD+0.05%Pb group compared with the NCD group.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90098" }, "primaryId" : "GEO:GSE90098", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90098" } ] }, "title" : "Comparison of miRNA expression profile between arterial plasma and venous plasma", "dateAssigned" : "2016-11-21T00:00:00.000-06:00", "summary" : "Circulating microRNAs (miRNAs) presented in venous plasma have recently been demonstrated as powerful biomarkers for the diagnosis and prognostic prediction of complex diseases like cancer. Nevertheless, those presented in arterial plasma have been ignored based on the assumption that the miRNA profiles in arterial and venous plasma would be identical. Here, we disputed this intuitive assumption by comparing arterial and venous plasma miRNA expression profiles from male rats using microarray technique. Though the microRNA profiles were largely similar, a considerable number of miRNAs showed significant differential expression, including 10 arterial highly expressed miRNAs and 14 venous highly expressed miRNAs. The differentially expressed miRNAs were validated by qRT-PCR. We performed computational analysis of the function enrichment and disease association of these miRNAs and their targets. Our analysis also suggested significant correlations between plasma miRNA expression and tissue miRNA expression. Four arterial highly expressed miRNAs showed enriched expression in specific tissues and thus could serve as novel biomarker candidates.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28212530" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90123" }, "primaryId" : "GEO:GSE90123", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90123" } ] }, "title" : "Exosome-mediated transfer of cardio-protective miRNAs between cardiomyocytes prevents apoptosis induced by hypoxia", "dateAssigned" : "2016-11-21T00:00:00.000-06:00", "summary" : "Conclusions:In brief, this study illustrated a potential mechanism that, under hypoxic stress, hypoxia pre-perceived cardiomyocytes can spontaneously secrete the hypoxamiRs enriched exosomes, loaded a large amount of cardio-protective miRNA, which mediate crosstalk among cardiomyocytes and prevent apoptosis to heighten the hypoxia adaptability of cardiomyocytes. In more detail, we first discovered that miR-152-3p and let-7i-5p, enriched in hypoxia-exosomes derived by cardiomyocytes, played an anti-apoptosis role via mitochondrial pathway(intrinsic pathway) and death receptor pathway (extrinsic pathway), respectively.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28350318" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90464" }, "primaryId" : "GEO:GSE90464", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90464" } ] }, "title" : "Rat esophagus: Control vs. NMBA vs. Tocopherols", "dateAssigned" : "2016-11-23T00:00:00.000-06:00", "summary" : "Transcriptional profiling of rat esophageal epithelium comparing control animals, NMBA treated animals, with tocopherols intervention animals. Goal was to determine the effects of tocopherols on gene expression underlying the chemoprevention of NMBA-induced esophageal carcinogenesis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90720" }, "primaryId" : "GEO:GSE90720", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90720" } ] }, "title" : "Fox Family Protein Jumu Reads 6mA-DNA Codes and Contributes to Zygotic Gene Activation", "dateAssigned" : "2016-11-30T00:00:00.000-06:00", "summary" : "N6-methyladenine (6mA) DNA modification in eukaryotic genomes has emerged as a potential epigenetic mark. However, little is known about how 6mA epigenetic codes are read and interpreted in higher eukaryotes. Here we investigate 6mA genome-wide distributions in multiple higher eukaryotes. UsingDrosophilaas a pioneer system, we show that 6mA exhibits defined patterns and preferentially marks zygotic genes in early embryos. Moreover, we identify that the Fox-family protein, Jumu, is a \"6mA-DNA reader\" and functions in concert with DMAD to contribute to zygotic gene activation. Further methylome analysis reveals that 6mA modification has common features in genomic DNA from mouse, rat and monkey, and that \"forkhead-domain-binding motifs\" are enriched in 6mA-marked DNA of these genomes, in a way similar to Drosophila. Collectively, our findings identify the 6mA DNA reader protein and suggest a conserved 6mA-based mechanism in higher eukaryotes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90744" }, "primaryId" : "GEO:GSE90744", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90744" } ] }, "title" : "Immune Escape via A Transient Gene Expression Program Enables Productive Replication of A Latent Pathogen", "dateAssigned" : "2016-12-01T00:00:00.000-06:00", "summary" : "How type I / II interferons (IFNs) prevent periodic re-emergence of latent pathogens in tissues of diverse cell-types remains unknown. Using homogenous neuron cultures latently-infected with herpes simplex virus (HSV), we show that extrinsic type I or II IFN act directly on neurons to induce unique gene expression signatures and inhibit the reactivation-specific burst of viral genome-wide transcription called Phase I. Surprisingly, IFNs suppressed reactivation only during a limited period early in Phase I preceding productive virus growth. Sensitivity to type II IFN was selectively lost if viral ICP0, which normally accumulates later in Phase I, was expressed prior to reactivation. Thus, IFNs suppress reactivation by preventing initial expression of latent genomes but are ineffective once Phase I viral proteins accumulate and limit IFN action. This demonstrates that inducible reactivation from latency is only transiently sensitive to IFNs. Moreover, it illustrates how latent pathogens escape host immune control to periodically replicate by rapidly deploying an interferon-resistant state.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28147283" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90745" }, "primaryId" : "GEO:GSE90745", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90745" } ] }, "title" : "LncRNAs and mRNAs changes in border zone of myocardial infarction in rats", "dateAssigned" : "2016-12-01T00:00:00.000-06:00", "summary" : "Border zone (BZ) of the myocardial infarction is critical to patients. Current treatments of myocardial infarction are primarily aimed to save the dying myocardial cell in the border zone. During myocardial infarction, certain changes in BZ, e.g, apoptosis, fibrosis, inflammation, etc, played an important role in deciding the survival. Impairment and recovery of BZ has been linked to gene expression changes. The aim of our study was to obtain a global expression profile of lncRNAs and mRNAs of the border zone in Wistar rats myocardial infarction, and identify the changes during myocardial infarction.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90779" }, "primaryId" : "GEO:GSE90779", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90779" } ] }, "title" : "Islet Inflammation and Ductal Proliferation, a Link to Pancreattisin Type-2 Diabetes?", "dateAssigned" : "2016-12-01T00:00:00.000-06:00", "summary" : "Pancreatitis is more frequent in type 2 diabetes (T2DM) although the underlying cause is unknown. We tested the hypothesis that ongoing beta-cell stress and apoptosis in T2DM induces ductal tree proliferation, particularly the pancreatic duct gland (PDG) compartment, and thus potentially obstructs exocrine outflow. PDG replication was increased two-fold in human pancreas from individuals with T2DM (P<0.01), and was associated with increased pancreatic intraepithelial neoplasia (PanINs) (P<0.05), lesions associated with pancreatic inflammation and with the potential to obstruct pancreatic outflow. Increased PDG replication (p<0.05) in the prediabetic HIP rat model of T2DM was concordant with increased beta-cell stress but preceding metabolic derangement. Moreover, the most abundantly expressed chemokines released by the islets in response to beta-cell stress in T2DM, CXCL1, 4 and 10, induced proliferation in human pancreatic ductal epithelium (p<0.05). Also, the diabetes medications that are reported as potential modifiers for the risk of pancreatitis in T2DM modulated PDG proliferation accordingly. We conclude that chronic stimulation and proliferation of the PDG compartment of the pancreas in response to islet inflammation in T2DM is a novel mechanism that serves as a link to the increased risk for pancreatitis in T2DM and may potentially be modified by currently available diabetes therapy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90833" }, "primaryId" : "GEO:GSE90833", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90833" } ] }, "title" : "Plant-derived compounds strigolactone GR24 and pinosylvin modulate gene expression in rat L6 skeletal muscle cells", "dateAssigned" : "2016-12-02T00:00:00.000-06:00", "summary" : "We investigated the effects of novel SIRT1 activating plant-derived compounds strigolactone GR24 and pinosylvin on gene expression in rat L6 skeletal muscle myotubes. Resveratrol was included in analyses as a reference compound.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29242624" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90837" }, "primaryId" : "GEO:GSE90837", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90837" } ] }, "title" : "Impact of melatonin on gene expression in colonic epithelium of pinealectomized rats", "dateAssigned" : "2016-12-03T00:00:00.000-06:00", "summary" : "To examine the effect of melatonin on global gene expression in the colonic epithelium, we used RNA-seq analysis to identify differentially expressed genes (DEGs) in samples from three melatonin-treated (MEL4-6) versus three vehicle-treated pinealectomized rats (VEH1-3) injected i.p. at the beginning of subjective night and sacrificed 4 h later. More than 12050 expressed genes were identified in each sample out of 18 258 genes in the database. A surprisingly small number of significant DEGs (49) was identified. The GO pathways analysis revealed that the largest group of the DEGs was associated with immune system response. Most DEGs (47) identified by RNA-seq were independently analyzed by RT-qPCR and the correlation between both methods indicates reliability of the data.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90923" }, "primaryId" : "GEO:GSE90923", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90923" } ] }, "title" : "Effect of odor inhalation of rats with restraint stress on their hypothalamic gene expression profiles", "dateAssigned" : "2016-12-06T00:00:00.000-06:00", "summary" : "Inhaled (R,S)-linalool returned the expression of 560 stress-induced probe sets to a normal status. These genes were associated with synaptic transmission via neurotransmitters including anxiolytic neuropeptides such as oxytocin and neuropeptide Y, and also included a number of major histocompatibility complex (MHC) class I necessary for neural development and plasticity. These results reveal some of the molecular mechanisms for odor inhalation under stress condition at the hypothalamus.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90956" }, "primaryId" : "GEO:GSE90956", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90956" } ] }, "title" : "Microarray analysis of aging-associated immune system alterations in the Rostral Ventral Lateral Medulla of F344 rats", "dateAssigned" : "2016-12-06T00:00:00.000-06:00", "summary" : "Progressive aging is associated with changes in sympathetic nervous system (SNS) regulation, suggesting an effect of advancing age on the functionality of central sympathetic premotor neurons. The rostral ventral lateral medulla (RVLM) contains sympathetic premotor neurons and plays a key role in SNS regulation, and it is plausible to speculate that age-related changes in the molecular mechanisms in the RVLM may contribute to alterations in SNS regulation. The present study tested the hypothesis that aging is associated with altered gene expression in the RVLM with emphasis on immune system associated gene transcripts. RVLM tissue punches from young, middle-aged, and aged F344 rats were analyzed using Agilent’s whole rat genome microarray. The RVLM gene expression profile varied with age and an association between chronological age and specific RVLM gene expression patterns was observed (p<0.05, FDR<0.3). Functional analysis of RVLM microarray data via gene ontology profiling and pathway analysis has identified up-regulation of genes associated with immune- and stress- related responses, and down-regulation of genes associated with lipid biosynthesis and neurotransmission in aged compared with middle-aged and young rats. Differentially expressed genes associated with complement system and microglial cells were further validated by quantitative PCR with separate RVLM samples (p<0.05, FDR<0.1). The present results are the first to demonstrate age-related changes in the RVLM molecular mechanisms, modifications that may provide the molecular backdrop for understanding immune-associated changes in SNS regulation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28626023" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90973" }, "primaryId" : "GEO:GSE90973", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90973" } ] }, "title" : "Effect of erythropoietin (EPO) and leukemia-inhibitory factor (LIF) on miRNA expression profiling in differentiating rat CG4-EPOR oligodendrocytes", "dateAssigned" : "2016-12-07T00:00:00.000-06:00", "summary" : "Analysis of the miRNA expression profile in differentiating rat CG4-EPOR oligodendrocytes treated with EPO, LIF or their combination for 1h or 20h", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90981" }, "primaryId" : "GEO:GSE90981", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE90981" } ] }, "title" : "Role of differentially expressed microRNA-139-5p in the regulation of phenotypic internal anal sphincter smooth muscle tone", "dateAssigned" : "2016-12-07T00:00:00.000-06:00", "summary" : "The present study focused on establishing the role of microRNA-139-5p (miRNA-139-5p) in the phenotypic expression of basal tone in rat internal anal sphincter (IAS) vs. lack of tone in truly phasic smooth muscle of anococcygeus (ASM), via RhoA-associated kinase (RhoA/ROCK2).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28469189" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE91017" }, "primaryId" : "GEO:GSE91017", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE91017" } ] }, "title" : "Cell subpopulations in cultures of rat's olfactory mucosa", "dateAssigned" : "2016-12-08T00:00:00.000-06:00", "summary" : "In order to improve our knowledge of olfactory ensheathing cells of the olfactory mucosa, we performed a wide microarray experiment to characterize the cell subpopulations found in primary olfactory mucosa cell cultures (CD90, P75 and TRKA cells). The consequences of the conditionning of TRKA cells by FBS deprivation and TGF-a supplementation was also studied.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92247" }, "primaryId" : "GEO:GSE92247", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92247" } ] }, "title" : "Neonatal Transplantation Confers Maturation of PSC-Derived Cardiomyocytes Conducive to Modeling Cardiomyopathy", "dateAssigned" : "2016-12-12T00:00:00.000-06:00", "summary" : "Pluripotent stem cell-derived cardiomyocytes (PSC-CMs) were transplanted into rats for one month to determine the change in morphology, structure, and function. Single cell RNA seq analysis was performed to compared the transcriptome of in vivo matured PSC-CMs to adult rat cardiomyocytes and in vitro cultured PSC-CMs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28076798" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92313" }, "primaryId" : "GEO:GSE92313", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92313" } ] }, "title" : "miRNAs in adipose tissue derived exosomes (Exo-AT) and adipose stem cells derived exosomes (Exo-ADSCs)", "dateAssigned" : "2016-12-13T00:00:00.000-06:00", "summary" : "The emerging evidences support that exosome cargo miRNAs function as important regulators in cell differentiation. Therefore, in order to figure out the mechanism that Exo-AT mediated adipogenesis, we profiled miRNAs in Exo-AT using high-throughput sequencing (miRNA-seq). After trimming low-quality reads, contaminants, adaptors, and reads smaller than 15 nt, the remaining reads were mapped to merged pre-miRNA data bases. To identify the conserved miRNAs in Exo exosomes, miRNAs were aligned to miRBase v21. 148 and 154 types of known miRNAs in Exo-ADSCs and Exo-AT, respectively, were identified in the two replicates. Among these miRNAs, 103 miRNAs were simultaneously detected in both Exo-ADSCs and Exo-AT. Compared to Exo-ADSCs, 45 conserved miRNAs were enriched (expressed ≥ 2 folds, FDR<0.05) in Exo-AT. KEGG Pathway analysis was performed for the targets of the most 20 enriched miRNAs in Exo-AT (compared with Exo-ADSCs) to determine their potential function. Data showed that pathways that regulate adipogenesis such as Wnt signaling pathway, Insulin signaling pathway, MAPK signaling pathway, TGF-ß signaling pathway were enriched significantly for targets of Exo-AT miRNAs. Furthermore, 14 of 45 enriched miRNAs in Exo-AT (31.11%, such as miR-30a-5p, miR-148a-3p) were reported to participate in regulation of adipogenesis while 8 miRNAs (17.78%, such as miR-93-5p, miR-150-3p) that negatively control osteoblastic differentiation of MSC have been described.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92363" }, "primaryId" : "GEO:GSE92363", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92363" } ] }, "title" : "AAV-mediated RNAi of traumatic brain injury-induced genes in the rat hippocampus", "dateAssigned" : "2016-12-13T00:00:00.000-06:00", "summary" : "To address the hypothesis that silencing deleterious or protective injury-induced genes in the rat hippocampus will reduce or increase the numbers of injured hippocampal neurons, alter cellular pathways essential for neuronal function and improve or worsen functional outcome after traumatic brain injury (TBI), we evaluated the effects of silencing neuronal nitric oxide synthase (nNOS) and glutathione peroxidase-1 (GPx-1) expression in the injured rat hippocampus.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29016640" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92500" }, "primaryId" : "GEO:GSE92500", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92500" } ] }, "title" : "Cellular and genetic factors involved in the difference among rat strains to develop procainamide - induced Autoimmunity", "dateAssigned" : "2016-12-16T00:00:00.000-06:00", "summary" : "To examine the influence cellular and genetics on the procainamide-induced autoimmune response in spleens we compared rats that are genetically Th2-predisposed (Brown Norway), Th1-predisposed (Lewis) or not genetically predisposed (Sprague Dawley). Rats were treated with procainamide three times per week. From the second week, blood samples were taken once a week for antinuclear antibody (ANA) detection. At 56d after treatment, rats were sacrificed and spleens samples were collected for microarray test and histopathology examination. Frequencies of T cell subsets and B cells in rat spleen were measured to assess the effects on splenocyte. Also, 12 serum cytokines/chemokines were determined to explored the Th1/Th2 cytokine pattern after treatment. We found that ANA were makedly elevated in BN and SD rats, while the elevated appeared earlier in BN rats, and the magnitude of its increase were much higher than that of SD rats. There was no marked change in serum ANA in Lewis rats. Histopathological analysis indicated that spleen weight increased significantly both in BN and SD rats after stimulated with procainamide. No significant changes in spleen weight and lesions were observed in Lewis rats. We also found the percentage of CD86 positive cells in spleen of BN rats was significantly increased, while the percentage of CD4+CD25+ cells was decreased in BN rats. In addition, percentage of CD11b/c positive cells were decreased, and the levels of Th-2 (IL-10), Th-1 type cytokine (IFN-γ) and chemokine (IL-1β) in serum were markedly elevated both in BN and SD rats after treatment. Th-2 type cytokine (IL-4, IL-6) in serum were markedly increased only in BN rats. Furthermore, similar immune mechanisms were found in BN and SD rat, and the altered genes were mainly associated in immune response, and inflammatory response. However, the number of differentially expressed genes (DEGs) in BN rats was higher than that in SD rats. Overall, we revealed significant differences in response to autoimmunity induced by procainamide among three strains rats, the BN rats was the most sensitive one, SD rats exhibited less sensitive while Lewis resistance to procainamide. Much more pronouncedof Th2-type responses and more complex DEGs involved in immune regulation and response in BN rats might contribute to its susceptible to drug-induced lupus erythematosus. Moreover, similar immune mechanisms were found between BN and SD rat, which suggesting that these changes would served as the potential bridge biomarkers to predict drug-induced autoimmune reactions among species. The results may also provide a scientic basis for the high sensitivity of BN rats in prediction immunotoxicity in preclinical studies.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92507" }, "primaryId" : "GEO:GSE92507", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92507" } ] }, "title" : "Overexpression of KLF genes in retinal ganglion cells", "dateAssigned" : "2016-12-16T00:00:00.000-06:00", "summary" : "Adult mammalian CNS neurons undergo a developmental switch in intrinsic axon growth ability associated with their failure to regenerate axons after injury. Krüppel-like transcription factors (KLF) regulate intrinsic axon growth ability, but signaling regulation upstream and downstream is poorly understood. Here we find that suppressing expression of KLF9, an axon growth suppressor normally upregulated 250-fold in retinal ganglion cell (RGC) development, promotes long-distance optic nerve regeneration in vivo. We identify a novel binding partner, MAPK10/JNK3, critical for KLF9’s axon growth suppressive activity. Additionally, by screening genes regulated by KLFs in RGCs, we identify dual-specificity phosphatase 14 (Dusp14) as key to limiting axon growth and regenerative ability downstream of KLF9, associated with its dephosphorylation of MAPKs critical to neurotrophic signaling of RGC axon elongation. These results now link intrinsic and extrinsic regulation of axon growth and suggest new therapeutic strategies to promote axon regeneration in the adult CNS.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29860460" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92669" }, "primaryId" : "GEO:GSE92669", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92669" } ] }, "title" : "Circular RNAs in Rat Models of Cardiovascular and Renal diseases", "dateAssigned" : "2016-12-21T00:00:00.000-06:00", "summary" : "The objective of this study was to profile circular RNAs (circRNAs) in rat genetic models of cardiovascular and renal disease. Renal profiles were obtained from the Dahl Salt-Sensitive rat (S), the Dahl Salt-Resistant rat (R), the Spontaneously Hypertensive Rat (SHR) and the Wistar Kyoto rat (WKY).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92680" }, "primaryId" : "GEO:GSE92680", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92680" } ] }, "title" : "Expression data from CD4+ T cells isolated from inguinal lymph nodes 7 days post MOG immunization", "dateAssigned" : "2016-12-21T00:00:00.000-06:00", "summary" : "DA rats treated with vitamin D supplemented, vitamin D deprived or regular diet", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28196884" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92691" }, "primaryId" : "GEO:GSE92691", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92691" } ] }, "title" : "Comparative analysis of 1-methyl-4-phenylpyridinium (MPP+) and manganese induced neurotoxic effects on DNA methylation in dopaminergic neurons", "dateAssigned" : "2016-12-21T00:00:00.000-06:00", "summary" : "Idiopathic Parkinson’s disease (iPD) and manganese-induced atypical Parkinsonism are characterized by movement disorder and nigrostriatal pathology. Although clinical features, brain region involved and responsiveness to L-DOPA differentiate both, the differences at the neuronal level are largely unknown. We investigated the morphological, physiological and molecular differences in dopaminergic neurons exposed to the PD toxin 1-methyl-4-phenylpyridinium ion (MPP+) and manganese (Mn). While Mn was neurotoxic at lower dose, MPP+ toxicity entailed oxidative damage, mitochondria dysfunction and glycolytic shift. Morphological analysis highlighted mitochondrial damage, while morphometric analysis indicated loss of neuronal processes in the MPP+ model and not in the Mn model. Elecrophysiological analysis demonstrated lower number of spikes and firing frequency in MPP+ treated cells, while it was unchanged in the Mn model. High throughput transcriptomic analysis revealed upregulation of 694 and 603 genes and down-regulation of 428 and 255 genes in the MPP+ and Mn models respectively. Many differentially expressed genes were unique to either models and contributed to neuroinflammation, metabolic and mitochondrial function, apoptosis and nuclear function, synaptic plasticity, neurotransmission and cytoskeletal architecture. Analysis of the JAK-STAT pathway with implications for neuritogenesis, neuronal proliferation and nuclear function revealed contrasting profile between Mn and MPP+ models. Genome-wide DNA methylation profile revealed significant differences between both models and substantiated the epigenetic basis of the difference in the JAK-STAT pathway. We conclude that iPD and atypical Parkinsonism represent a divergent neurotoxicological manifestation at the dopaminergic neuronal level with implications for pathobiology and to evolve novel therapeutics", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28801915" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92856" }, "primaryId" : "GEO:GSE92856", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92856" } ] }, "title" : "Gene expression profiling of cultured embryonic rat cortical neurons", "dateAssigned" : "2016-12-22T00:00:00.000-06:00", "summary" : "Embryonic CNS neurons can differentiate in culture and provide a model for maturation-related changes. A transcriptome profile over the course of maturation was perform to investigate the underlying molecular mechanism that drives maturation and its related changes such as developmental loss of intrinsic regenerative capacity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92858" }, "primaryId" : "GEO:GSE92858", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92858" } ] }, "title" : "Thyroid Dysfunction, Neurological Disorder and Immunosuppression as the Consequences of Long-term Combined Stress", "dateAssigned" : "2016-12-22T00:00:00.000-06:00", "summary" : "Stress is a powerful modulator of neuroendocrine, behavioral, and immunological functions. So far, the molecular mechanisms of response to stressors still remain elusive. In the current study, after 10 days of repeated chronic stress (hot-dry environment and electric foot-shock), a murine model of combinedstress (CS) was created in the SPF Wistar rats. Meanwhile, we established an ulcerative-colitis (UC) rat model induced by 2,4,6-trinitrobenzene sulfonic acid (TNBS)/ethanol enema according to previous studies. The blood, hypothalamus, and colon tissues of these rats from CS, normal control (NC), UC and sham (SH) groups, were collected for further investigations. Comparing to the NC group, the serum levels of T3, T4, fT3 and fT4 were obviously decreased in the CS group after chronic stress, indicating that thyroid dysfunction was induced by long-term combined stress. Moreover, the application of RNAseq and subsequent analyses revealed that neurological disorder and immunosuppression were also caused in the hypothalamus and colon tissues, respectively. Comparing with SH group, besides the induced colon infammation, thyroid dysfuntion and neurological disorder were also produced in the UC group, suggesting that hypothalamic-pituitary-thyroid (HPT) axis and gastrointestinal system might not function in isolation, but rather, have intricate crosstalks.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29540811" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92861" }, "primaryId" : "GEO:GSE92861", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92861" } ] }, "title" : "Expression data from individual MEF2A isoform knockdown in neonatal rat ventricular myocytes (NRVMs)", "dateAssigned" : "2016-12-23T00:00:00.000-06:00", "summary" : "We knocked down expression of MEF2 isoforms in a primary cell culture model of cardiomyocytes and assessed global expression pattern changes between MEF2 knockdowns, and with a negative control.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28473466" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92897" }, "primaryId" : "GEO:GSE92897", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92897" } ] }, "title" : "Exogenous miRNA expression profiling in serum of pig and rat fed with different diets", "dateAssigned" : "2016-12-23T00:00:00.000-06:00", "summary" : "We performed carefully designed and controlled animal feeding studies. We devided 9 adult rats in three group and each group fed with one type of diets in 28 days: rice, potatoes and chow. We fed piglets in triplicate either with cow milk or let them feed from sows milk for 4 weeks followed by 7 weeks of maize diet. Based on the small RNA sequencing data from 9 rat and 6 pig serum samples, we detected no transfer of plant miRNAs into rat blood, or bovine milk sequences into piglet blood.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28062594" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92956" }, "primaryId" : "GEO:GSE92956", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92956" } ] }, "title" : "Comparative analysis of time-dependent effects of dynamic stretch on gene expression in neonatal rat cardiomyocytes", "dateAssigned" : "2016-12-28T00:00:00.000-06:00", "summary" : "The present study focuses on the identification of the gene expression profile of neonatal rat cardiomyocytes (NRVCMs) after dynamic mechanical stretch through microarrays of RNA isolated from cells stretched for 2, 6 or 24 h.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92963" }, "primaryId" : "GEO:GSE92963", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE92963" } ] }, "title" : "Gene expression profile of neurotoxin exposure in rat midbrain dopaminergic neurons", "dateAssigned" : "2016-12-28T00:00:00.000-06:00", "summary" : "N27 cells are dopaminergic neurons derived from rat midbrain and are extensively employed as a model for neurodegeneration. N27 cells were challenged with 2 neurotoxins associated with Manganism (Manganese Chloride;Mn) and Parkinson's Disease (1-methyl-4-phenylpyridinium ion;MPP+). Mn and MPP+ result in movement dysfunction and are mitochondrial toxins particularly affecting complexes I.This study aimed to understand and differentiate the molecular mechanisms underlying Mn and MPP+ mediated dopaminergic insult by evaluating the differential gene expression pattern in the two models", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28801915" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93003" }, "primaryId" : "GEO:GSE93003", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93003" } ] }, "title" : "Whole-transcriptome profiling of laser-capture microdissected striatal neurons at single-cell resolution using retrograde tracing", "dateAssigned" : "2016-12-29T00:00:00.000-06:00", "summary" : "Pathway-specific striatal transcripts were identified in a neuroanatomically defined manner using retrograde tracing, laser capture micodissection and whole-transcriptome sequencing.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93111" }, "primaryId" : "GEO:GSE93111", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93111" } ] }, "title" : "Identification of miRNAs that regulate vestibular compensation", "dateAssigned" : "2017-01-04T00:00:00.000-06:00", "summary" : "To investigate which miRNAs regulate the vestibular compensation after unilateral vestibular deafferentiation (UVD), we have performed microarray for miRNAs as a discovery platform. UVD induces breakdown of the activity of ipsilesional vestibular nuclei and an unbalance of activity between bilateral vestibular nuclei. Vestibular compensation is a course of rebalancing of activities of bilateral vestibular nuclei. It takes place mainly in medial vestibular nucleus. This study was performed using seven week-old-male Sprague–Dawley rats. Based on our previous experiment about vestibular compensation course, we set two time points for harvesting medial vestibular nuclei: 4hr and 4 days after unilateral vestibular deafferentiation. Twenty four animals were divided into two experimental groups: UVD group undergoing UVD at left side (n = 12); and SO group undergoing sham operation (SO) at left side (n=12). Six animals of each group were anesthetized deeply and euthanized at 4 hr or 4 days after surgery, respectively. Medial vestibular nucleus at left side was harvested. Medial vestibular nucleus from three animals became one sample for microarray. Sequentially two samples were obtained for each time point in one group. Microarray for miRNAs was performed using the Agilent Rat miRNA Microarray 8x15K platforms. Considering the fold change of normalized signal intensities between two time points in UVD group and between UVD and SO groups at the same time, miR-31a-5p, 133a-3p, 133b-3p, 204-5p, 206-3p, 218a-5p, 219a-5p, 221-3p and 497-5p were selected as the candidate miRNAs. This result was validated by quantitative reverse transcription-PCR.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28821887" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93116" }, "primaryId" : "GEO:GSE93116", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93116" } ] }, "title" : "Genome-wide DNA Methylation Analysis in Lung Fibroblasts Co-cultured with Silica-exposed Alveolar Macrophages", "dateAssigned" : "2017-01-04T00:00:00.000-06:00", "summary" : "In the present study, we used MeDIP coupled with next-generation sequencing to profile the whole genome DNA methylation patterns of fibroblast from the co-culture model in vitro. We analyzed the data to identify possible biological pathways for fibroblast differentiating into myofibroblast as well as the interactions of related genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93150" }, "primaryId" : "GEO:GSE93150", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93150" } ] }, "title" : "Leptin treatment of offspring during lactation after caloric restriction of dams during pregnancy reverts CR-induced dysfunction", "dateAssigned" : "2017-01-04T00:00:00.000-06:00", "summary" : "16 rats were mated and the dams continued pregnancy (controls) or were subsequently caloric restricted (CR) for 20% during days 1-12. Control female/male offspring continued normal lactation, while offspring of CR-treated dams received either normal lactation (CR group) or received during lactation until PN21 leptin supplementation. Leptin treatment of offspring during lactation after caloric restriction of dams during pregnancy reverts CR-induced dysfunction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32474969" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93160" }, "primaryId" : "GEO:GSE93160", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93160" } ] }, "title" : "A Histone Deacetylase 3-Dependent Pathway Delimits Peripheral Myelin Growth and Functional Regeneration [ChIP-Seq]", "dateAssigned" : "2017-01-04T00:00:00.000-06:00", "summary" : "Schwann cell remyelination defects impair functional restoration after nerve damage, contributing to peripheral neuropathies. The mechanisms that mediate remyelination block remain elusive. Upon small-molecule epigenetic screening, we identified HDAC3, a histone-modifying enzyme, as a potent inhibitor of peripheral myelinogenesis. Inhibition of HDAC3 markedly enhances myelin growth and regeneration, and improves functional recovery after peripheral nerve injury. HDAC3 antagonizes myelinogenic neuregulin/PI3K/AKT signaling axis. Moreover, genome-wide profiling analyses reveal that HDAC3 represses pro-myelinating programs through epigenetic silencing, while coordinating with p300 histone acetyltransferase to activate myelination-inhibitory programs that include HIPPO signaling effector TEAD4 to inhibit myelin growth. Schwann-cell-specific deletion of either Hdac3 or Tead4 results in a profound increase in myelin thickness in sciatic nerves. Thus, our findings identify the HDAC3-TEAD4 network as a dual-function switch of cell-intrinsic inhibitory machinery that counters myelinogenic signals and maintains peripheral myelin homeostasis, highlighting the therapeutic potential of transient HDAC3 inhibition for improving peripheral myelin repair.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29431744" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93249" }, "primaryId" : "GEO:GSE93249", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93249" } ] }, "title" : "RNA-Seq analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury", "dateAssigned" : "2017-01-06T00:00:00.000-06:00", "summary" : "Conclusions: Overall, our study provides an unprecedented resource for the study of sub-chronic and chronic SCI that will help the research community identify new molecular targets for future functional investigation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28106101" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93401" }, "primaryId" : "GEO:GSE93401", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93401" } ] }, "title" : "Reseveratrol and Rosiglitazone regulation of epididymal tissue gene expression in ZDF rats", "dateAssigned" : "2017-01-11T00:00:00.000-06:00", "summary" : "The goal of this work was to examine if reserveratrol or rosiglitazone treatment could improve the metabolic status of obese male ZDF rats after 6 weeks. Gene expression was analyzed in several key metabolic tissues, including liver, various white adipose tissue depots, red tibalus muscle, and peripheral blood mononuclear cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93402" }, "primaryId" : "GEO:GSE93402", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93402" } ] }, "title" : "Reseveratrol and Rosiglitazone regulation of blood gene expression in ZDF rats", "dateAssigned" : "2017-01-11T00:00:00.000-06:00", "summary" : "The goal of this work was to examine if reserveratrol or rosiglitazone treatment could improve the metabolic status of obese male ZDF rats after 6 weeks. Gene expression was analyzed in several key metabolic tissues, including liver, various white adipose tissue depots, red tibalus muscle, and whole blood.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28257645" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93403" }, "primaryId" : "GEO:GSE93403", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93403" } ] }, "title" : "Reseveratrol and Rosiglitazone regulation of liver gene expression in ZDF rats", "dateAssigned" : "2017-01-11T00:00:00.000-06:00", "summary" : "The goal of this work was to examine if reserveratrol or rosiglitazone treatment could improve the metabolic status of obese male ZDF rats after 6 weeks. Gene expression was analyzed in several key metabolic tissues, including liver, various white adipose tissue depots, red tibalus muscle, and peripheral blood mononuclear cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28257645" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93404" }, "primaryId" : "GEO:GSE93404", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93404" } ] }, "title" : "Reseveratrol and Rosiglitazone regulation of retroperitoneal tissue gene expression in ZDF rats", "dateAssigned" : "2017-01-11T00:00:00.000-06:00", "summary" : "The goal of this work was to examine if reserveratrol or rosiglitazone treatment could improve the metabolic status of obese male ZDF rats after 6 weeks. Gene expression was analyzed in several key metabolic tissues, including liver, various white adipose tissue depots, red tibalus muscle, and peripheral blood mononuclear cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93405" }, "primaryId" : "GEO:GSE93405", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93405" } ] }, "title" : "Reseveratrol and Rosiglitazone regulation of subcutaneous tissue gene expression in ZDF rats", "dateAssigned" : "2017-01-11T00:00:00.000-06:00", "summary" : "The goal of this work was to examine if reserveratrol or rosiglitazone treatment could improve the metabolic status of obese male ZDF rats after 6 weeks. Gene expression was analyzed in several key metabolic tissues, including liver, various white adipose tissue depots, red tibalus muscle, and peripheral blood mononuclear cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93406" }, "primaryId" : "GEO:GSE93406", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93406" } ] }, "title" : "Reseveratrol and Rosiglitazone regulation of red tibialis anterior (red TA) gene expression in ZDF rats", "dateAssigned" : "2017-01-11T00:00:00.000-06:00", "summary" : "The goal of this work was to examine if reserveratrol or rosiglitazone treatment could improve the metabolic status of obese male ZDF rats after 6 weeks. Gene expression was analyzed in several key metabolic tissues, including liver, various white adipose tissue depots, red tibalus muscle, and peripheral blood mononuclear cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28257645" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93609" }, "primaryId" : "GEO:GSE93609", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93609" } ] }, "title" : "Gene expressions in rat intracranial aneurysms", "dateAssigned" : "2017-01-13T00:00:00.000-06:00", "summary" : "Specimens from aneurysms and control arterial walls were analyzed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28174280" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93645" }, "primaryId" : "GEO:GSE93645", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93645" } ] }, "title" : "Comparative analysis of gene expression profile of pre-defined niches within demyelinated white matter in rats", "dateAssigned" : "2017-01-16T00:00:00.000-06:00", "summary" : "Microenviromental niche characterization by comparative transcriptome profiling. The hypothesis tested in the present study was that unique properties of the perivascular niche within remyelinating white matter would create microenvironment that favor the alternative differentiation of oligodendrocyte precursor cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30222103" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93676" }, "primaryId" : "GEO:GSE93676", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93676" } ] }, "title" : "Viral and Cellular N6-methyladenosine (m6A) Epitranscriptomes in KSHV Life Cycle", "dateAssigned" : "2017-01-16T00:00:00.000-06:00", "summary" : "Tan et al. discovered abundant conserved N6-methyladenosine (m6A) modifications on KSHV transcripts during latent and productive infection in different cell types. They also show that m6A readers YTHDF2 and YTHDF3 mediate KSHV replication, and KSHV optimizes both phases of viral replication by reprograming cellular epitranscriptome to regulate distinct signaling pathways.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93695" }, "primaryId" : "GEO:GSE93695", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93695" } ] }, "title" : "Antidyskinetic effects of MEK inhibitor are associated with multiple neurochemical alterations in the striatum of hemiparkinsonian rats", "dateAssigned" : "2017-01-17T00:00:00.000-06:00", "summary" : "L-DOPA-induced dyskinesia (LID) represents one of the major problems of the long-term therapy of patients with Parkinson's disease (PD). Although the pathophysiologic mechanisms underlying LID are not completely understood, activation of the extracellular signal regulated kinase (ERK) is recognized to play a key role. ERK is phosphorylated by mitogen-activated protein kinase kinase (MEK), and thus MEK inhibitor can prevent ERK activation. Here the effect of the MEK inhibitor PD98059 on LID and the associated molecular changes were examined. Rats with unilateral 6-OHDA lesions of the nigrostriatal pathway received daily L-DOPA treatment for three weeks, and abnormal involuntary movements (AIMs) were assessed every other day. PD98059 was injected in the lateral ventricle daily for 12 days starting from day 10 of L-DOPA treatment. Striatal molecular markers of LID were analyzed together with gene regulation using microarray. The administration of PD98059 significantly reduced AIMs. In addition, ERK activation and other associated molecular changes including ¿FosB were reversed in rats treated with the MEK inhibitor. PD98059 induced significant up-regulation of 418 transcripts and down-regulation of 378 transcripts in the striatum. Tyrosine hydroxylase (Th) and aryl hydrocarbon receptor nuclear translocator (Arnt) genes were down-regulated in lesioned animals and up-regulated in L-DOPA-treated animals. Analysis of protein levels showed that PD98059 reduced the striatal TH. These results support the association of p-ERK1/2, ¿FosB, p-H3 to the regulation of TH and ARNT in the mechanisms of LID, and pinpoint other gene regulatory changes, thus providing clues for identifying new targets for LID therapy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93726" }, "primaryId" : "GEO:GSE93726", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93726" } ] }, "title" : "Transcriptome profile of rat adrenal evoked by gonadectomy and testosterone or estradiol replacement", "dateAssigned" : "2017-01-17T00:00:00.000-06:00", "summary" : "Therefore we performed microarray studies to demonstrate the effect of testosterone and estradiol on the expression of differentially regulated genes in rat adrenal gland.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28261157" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93790" }, "primaryId" : "GEO:GSE93790", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93790" } ] }, "title" : "PIWI-interacting RNAs as novel regulators of pancreatic beta-cell function [p10, adult samples]", "dateAssigned" : "2017-01-18T00:00:00.000-06:00", "summary" : "There is mounting evidence indicating that piRNAs are also present in somatic cells where they may accomplish additional regulatory tasks. The aim of this study was to identify the piRNAs expressed in pancreatic islets and to determine whether they are involved in the control of beta-cell activities. piRNA profiling of rat pancreatic islets was performed by microarray. We detected about 18’000 piRNAs in rat pancreatic islets, many of which were differentially expressed throughout islet postnatal development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93791" }, "primaryId" : "GEO:GSE93791", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93791" } ] }, "title" : "PIWI-interacting RNAs as novel regulators of pancreatic beta-cell function [GK, wistar samples]", "dateAssigned" : "2017-01-18T00:00:00.000-06:00", "summary" : "There is mounting evidence indicating that piRNAs are also present in somatic cells where they may accomplish additional regulatory tasks. The aim of this study was to identify the piRNAs expressed in pancreatic islets and to determine whether they are involved in the control of beta-cell activities. piRNA profiling of rat pancreatic islets was performed by microarray. We detected about 18’000 piRNAs in rat pancreatic islets, many of which were differentially expressed throughout islet of Goto-Kakizaki rats, a well-established model of Type 2 diabetes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93838" }, "primaryId" : "GEO:GSE93838", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93838" } ] }, "title" : "Expression profiling of soleus muscle under the effect of simulated spaceflight", "dateAssigned" : "2017-01-19T00:00:00.000-06:00", "summary" : "A distinct difference between spaceflight-induced muscle atrophy and other forms of atrophy is the additional effect of cosmic rays in outer space. To study spaceflight-induced muscle atrophy, we performed two ground-based models of microgravity in a low dose radiation environment and studied transcriptional changes in rat soleus muscle using microarray technology.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93940" }, "primaryId" : "GEO:GSE93940", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE93940" } ] }, "title" : "Intravesical BCG induces CD4+ T Cell Expansion in a Clinically Relevant Immune Competent Model of Bladder Cancer", "dateAssigned" : "2017-01-23T00:00:00.000-06:00", "summary" : "Intravesical BCG Immunotherapy is the standard of care in treating non-muscle invasive bladder cancer, yet its mechanism of action remains elusive. Both innate and adaptive immune responses have been implicated in BCG activity. While prior research has indirectly demonstrated the importance of T cells and shown a rise in CD4+ T cells in bladder tissue after BCG, T cell subpopulations have not been fully characterized. We investigated the relationship between effector and regulatory T cells in an immune competent, clinically relevant rodent model of bladder cancer. Our data demonstrate that cancer progression in the MNU rat model of bladder cancer is characterized by a decline in the CD8/FoxP3 ratio, consistent with decreased adaptive immunity. By contrast, treatment with intravesical BCG leads to a large, transient rise in the CD4+ T cell population in the urothelium, and is both more effective and immunogenic compared to intravesical chemotherapy. Interestingly, whole transcriptome expression profiling of post-treatment intravesical CD4+ and CD8+ T cells revealed minimal differences in gene expression after BCG treatment. Together, our results suggest that while BCG induces T cell recruitment to the bladder, the T cell phenotype does not markedly change, implying that combining T cell activating agents with BCG might improve clinical activity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28588015" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94008" }, "primaryId" : "GEO:GSE94008", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94008" } ] }, "title" : "Genome-wide identification of glucocorticoid receptor binding sites in the whole hippocampus of adrenalectomised male rats given corticosterone infusion and stressed or non-stressed.", "dateAssigned" : "2017-01-24T00:00:00.000-06:00", "summary" : "We have applied next-generation sequencing technology to obtain high through-put profiling of glucocorticoid receptor (GR) DNA binding in whole hippocampus from male rat brain. By obtaining sequence from immunoprecipitated, sonicated chromatin, we have generated genome-wide binding maps for GR in two contexts, testing whether chromatin is primed for GR binding according to the animal's acute experience. In one context (stressed) adrenalectomised rats are infused with corticosterone while undergoing restraint stress. In the second context (non-stressed control) rats are infused with the same corticosterone profile but restraint stress is omitted. We find that GR binding was highly similar suggesting factors other than GR binding may account for any context-dependent alterations in GR function associated with acute stress. We show that GR is positioned near to genes associated with structural and functional organisation of the hippocampus at largely intergenic and intronic sites. Glucocorticoid response element sequences support a majority of GR binding in this tissue but may be reinforced by NF-1 and/or basic-helix loop helix transcription factors binding their nearby recognition motifs. We found little evidence for tethering of GR to other factors, or for the usage of negative glucocorticoid response elements.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28200020" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94026" }, "primaryId" : "GEO:GSE94026", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94026" } ] }, "title" : "Hepatic gene expression analysis from rats with chronic sleep restriction", "dateAssigned" : "2017-01-24T00:00:00.000-06:00", "summary" : "We report the change in gene expression in rat liver post chronic sleep restriction. Rats were sleep restricted by for 5 days by forced activity protocol. We found changes in genes related to NAD metabolism (Nampt), TCA cycle (Acly) and methionine metabolism (Msrb2 and Mtr)", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94080" }, "primaryId" : "GEO:GSE94080", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94080" } ] }, "title" : "Genome wide identification of gene sets involved in the regulation of hypothalamic pubertal development", "dateAssigned" : "2017-01-25T00:00:00.000-06:00", "summary" : "Gene expression analysis of hypothalami from female animals at different juvenile developmental reproductive stages. Results provide insight into the role of the hypothalamus in controlling the onset of puberty.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29302059" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94392" }, "primaryId" : "GEO:GSE94392", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94392" } ] }, "title" : "Selective estrogen receptor modulator-like gene expression in prepubertal rat testis after soy feeding", "dateAssigned" : "2017-02-01T00:00:00.000-06:00", "summary" : "In this study, we investigated the potential estrogenicity of soy protein isolate (SPI) as opposed to pure isoflavones (i.e., estradiol) in the prepubertal stage of testis development. Bioinformatics analysis of the microarray analysis indicate that rather than acting as a weak estrogen in the developing testis, SPI appears to act as a selective estrogen receptor modulator with little effect on reproductive processes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94473" }, "primaryId" : "GEO:GSE94473", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94473" } ] }, "title" : "An in vitro model of intestinal infection reveals a developmentally regulated transcriptome of Toxoplasma sporozoites and a NF-¿B-like signature in infected host cells", "dateAssigned" : "2017-02-03T00:00:00.000-06:00", "summary" : "Toxoplasmosis is a zoonotic infection affecting approximately 30% of the world’s human population. After sexual reproduction in the definitive feline host, Toxoplasma oocysts, each containing 8 sporozoites, are shed into the environment where they can go on to infect humans and other warm-blooded intermediate hosts. Here, we use an in vitro model to assess host transcriptomic changes that occur in the earliest stages of such infections. We show that infection of rat intestinal epithelial cells with mature sporozoites primarily results in higher expression of genes associated with Tumor Necrosis Factor alpha (TNFa) signaling via NF-¿B. Furthermore, we find that, consistent with their biology, these mature, invaded sporozoites display a transcriptome intermediate between the previously reported day 10 oocysts and that of their tachyzoite counterparts. Thus, this study uncovers novel host and pathogen factors that may be critical for the establishment of a successful intracellular niche following sporozoite-initiated infection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28362800" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94590" }, "primaryId" : "GEO:GSE94590", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94590" } ] }, "title" : "Sox2-dependent fibronectin fibrillogenesis controls directional collective migration of Schwann cells", "dateAssigned" : "2017-02-07T00:00:00.000-06:00", "summary" : "The extracellular matrix is essential for tissue formation and regeneration through the control of cellular behavior. Deregulation of extracellular matrix components is associated to disease, including neurodegeneration. After peripheral nerve injury, Schwann cells guide regrowing axons to their targets. These glial cells migrate collectively and provide an extracellular environment to enable neural repair. How this occurs remains poorly understood. Here, we show that Sox2 controls fibronectin fibrillogenesis in Schwann cells to provide a highly oriented extracellular matrix, which supports their rapid collective migration with a continuous cellular flow. Sox2 directly activates fibronectin expression in Schwann cells, leading to an increase in fibrillogenesis and cellular huddling. Accordingly, loss of fibrillogenesis leads to glial disassembly and disorganized axon regrowth. In vivo, 7 days post nerve injury, we found that pro-regenerative Schwann cells co-express Sox2 and the EIIIA-containing fibronectin splicing isoform. This mechanism is conserved in mammals, including humans, but absent in zebrafish. Taken together, our results demonstrate that Sox2 directly controls fibrillogenesis and provide a novel mechanism for the modification of the environmental architecture by glial cells during neuronal repair.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32029747" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94623" }, "primaryId" : "GEO:GSE94623", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94623" } ] }, "title" : "Whole-transcriptome expression data from neonatal rat ventricular myocytes (NRVM) silenced for KChIP2", "dateAssigned" : "2017-02-07T00:00:00.000-06:00", "summary" : "Loss of KChIP2 during cardiac stress has been suggested to have a transcriptional impact on cardiac ion channels contributing to maladaptive electrical remodeling. Therefore, we tested the consequence of KChIP2 loss, in the absence of cardiac stress, by treating cultured neonatal rat ventricular myocytes with shRNA for KChIP2 and subsequently performed whole-transcriptome microarray analysis to identify gene changes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28263709" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94678" }, "primaryId" : "GEO:GSE94678", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94678" } ] }, "title" : "Acutely Injured Kidneys Release Proteins into the Serum that Cause Oxidative Stress", "dateAssigned" : "2017-02-08T00:00:00.000-06:00", "summary" : "We previously conducted a Phase I Clinical Trial in which Mesenchymal Stem/Stromal Cells (MSCs) were administered to patients at risk for developing acute kidney injury (AKI), and which suggested that MSC therapy is safe and effective in preventing both postoperative AKI and progression to CKD. It is well understood that AKI creates an internal environment that adversely affects not only the kidneys but also the function of distant organs and tissues. To study the consequences of the AKI environment on MSCs and renal cells, we developed an in vitro assay of exposing MSCs or cultured tubular cells (NRK Cells) to serum from animals that had AKI, or SHAM surgeries. Compared to SHAM sera, exposure of cells to AKI serum caused increased intra-cellular resazurin reduction, and activation of anti-oxidant genes,", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94719" }, "primaryId" : "GEO:GSE94719", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94719" } ] }, "title" : "Novel surrogate markers for reflux esophagitis using exosomal microRNAs in rats", "dateAssigned" : "2017-02-09T00:00:00.000-06:00", "summary" : "There is no useful biomarker for reflux esophagitis. The aim of this study is to establish novel diagnosis marker for RE by using miRNA.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94722" }, "primaryId" : "GEO:GSE94722", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94722" } ] }, "title" : "The differential gene expressions of rat mucosa colonized with single or multi-species of MRSA or PA were studied using RNA-sequencing of total transcriptome.", "dateAssigned" : "2017-02-09T00:00:00.000-06:00", "summary" : "The differential gene expressions of rat mucosa colonized with single or multi-species of MRSA or PA were studied using RNA-sequencing of total transcriptome. In multi-species in-vitro biofilms PA partially inhibited SA growth. However, no significant inhibition of MRSA was detected during in-vivo colonization of multi-species in rat bullae. A total of 1797 genes were significantly (p < 0.05) differentially expressed in MRSA or PA or MRSA+PA colonized rat middle ear mucosa with respect to the control. The poly-microbial colonization of MRSA and PA induced the differential expression of a significant number of genes that are involved in immune response, inflammation, signaling, development, and defense; these were not expressed with single species colonization by either MRSA or PA. Genes involved in defense, immune response, inflammatory response, and developmental process were exclusively up-regulated, and genes that are involved in nervous system signaling, development and transmission, regulation of cell growth and development, anatomical and system development, and cell differentiation were down-regulated after multi-species inoculation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28459043" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94738" }, "primaryId" : "GEO:GSE94738", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94738" } ] }, "title" : "Expression data from rat liver", "dateAssigned" : "2017-02-09T00:00:00.000-06:00", "summary" : "We used microarrays to evaluate gene expression profiling in rat liver at the early phase of treatment with epsilon-momfluorothrin.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28520973" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94770" }, "primaryId" : "GEO:GSE94770", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94770" } ] }, "title" : "Effect of 2-ITX on mRNA expression in the liver of male Wistar rats", "dateAssigned" : "2017-02-10T00:00:00.000-06:00", "summary" : "2-Isopropylthioxanthone (2-ITX), a photoinitiator used in ink for printing of food packaging materials, has been detected in products like milk and fruit beverages. Previous in vitro research demonstrated 2-ITX to 1) exert agonistic effects on the aryl hydrocarbon receptor (AhR), 2) exert antagonistic effects on both the androgen (AR) and estrogen receptor (ER), and 3) to increase aromatase activity. To validate these findings in vivo, male rats were treated by gavage with 50, 150 or 500 mg 2-ITX/kg b.w. per day from postnatal day 23 to 53. For comparison, other groups were treated with 50 ng TCDD/kg b.w./day (AhR agonist), 30 mg bicalutamide/kg b.w./day (Casodex, AR antagonist) or 50 mg flutamide/kg b.w./day (AhR agonist and AR antagonist). 2-ITX, from the lowest dose onwards, decreased the weight of the ventral prostate, and from the middle dose onwards the weight of the seminal vesicles and coagulating gland. The highest dose of 2-ITX reduced the number of spermatozoa in the cauda of the epididymis. Similar effects, but more severe, were induced by flutamide and bicalutamide. Epididymal weight, caput sperm count and preputial separation were negatively affected by Casodex and flutamide but not by 2-ITX. The two highest doses of 2-ITX as well as TCDD increased liver weight. Whole genome mRNA expression profiling of the liver revealed similarity between the effects of 2-ITX and flutamide. In addition, many genes induced by TCDD were also induced by 2-ITX and flutamide. These results demonstrate 2-ITX to express AhR agonistic and AR antagonistic activities, both in vitro and in vivo.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94780" }, "primaryId" : "GEO:GSE94780", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94780" } ] }, "title" : "Gene expression in rat striatum following carbon monoxide poisoning and hypoxic hypoxia", "dateAssigned" : "2017-02-10T00:00:00.000-06:00", "summary" : "We have proposed the existence of a threshold for brain damage, in terms of hydroxyl radical production in rat striatum, between poisoning of carbon monoxide (CO) at 1000 ppm and 3000 ppm, where blood CO-hemoglobin levels reach approximately 50% and over 70%, respectively. To search for factors involved in brain damage, we examined the effects of air, 1000 ppm CO, 3000 ppm CO and 5% O2 (hypoxic conditions comparable with those by 3000 ppm CO) on gene expression in rat striatum, using microarray analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94825" }, "primaryId" : "GEO:GSE94825", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94825" } ] }, "title" : "Effect of corticision on orthodontic tooth movement in a rat model as assessed by RNA sequencing", "dateAssigned" : "2017-02-13T00:00:00.000-06:00", "summary" : "Corticision is a common technique to accelerate orthodontic tooth movement; however, not much is known about the underlying mechanisms. In this study, we investigated the mechanism of alveolar tissue remodeling after corticision in a rat model of tooth movement (TM) by analyzing the differential transcriptome", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94988" }, "primaryId" : "GEO:GSE94988", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94988" } ] }, "title" : "Expression data from Chronic Unpredict Mild Stress-induced depression in GK rats‘ liver", "dateAssigned" : "2017-02-16T00:00:00.000-06:00", "summary" : "The expression profile in GK rats' livers were screened using Affymetrix Rat 230 2.0 Array.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28574832" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94990" }, "primaryId" : "GEO:GSE94990", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE94990" } ] }, "title" : "A Reciprocal Regulatory Loop Between TAZ/YAP and G protein Gas Regulates Schwann Cell Proliferation and Differentiation", "dateAssigned" : "2017-02-16T00:00:00.000-06:00", "summary" : "Schwann cell (SC) myelination in the peripheral nervous system is essential for motor function, and uncontrolled SC proliferation occurs in cancer. Here, we show that a dual direct role for Hippo effectors TAZ and YAP in regulation of SC proliferation and myelination through modulating G protein expression and interacting with SOX10, respectively. Developmentally-regulated mutagenesis indicates that TAZ/YAP are critical for SC proliferation yet also required for their differentiation and myelination. Genome-wide occupancy mapping and transcriptome profiling reveal that nuclear TAZ and YAP promote SC proliferation by activating cell cycle regulators, while targeting critical differentiation regulators in cooperation with SOX10 for myelination. We further identified that TAZ targets and represses Gnas, encoding Gas-protein, which opposes TAZ/YAP activities to decelerate proliferation. Gnas deletion expands SC precursor pools and blocks myelination in the sciatic nerve. Thus, our study revealed that the Hippo/TAZ/YAP and Gas-protein feedback circuit functions as a fulcrum balancing SC proliferation and differentiation, providing insights into molecular programming of SC lineage progression and homeostasis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28443644" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95067" }, "primaryId" : "GEO:GSE95067", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95067" } ] }, "title" : "Regulation of Angiotensin II Actions by Enhancers and Super-enhancers in Vascular Smooth Muscle Cells", "dateAssigned" : "2017-02-19T00:00:00.000-06:00", "summary" : "We have profiled Ang II regulated enhancer and super-enhancers in Rat Vascular smooth muscle cells using genomewide analysis of enhancer marks H3K27ac, H3K4me1 and super-enhancer mark BRD4.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29133788" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95214" }, "primaryId" : "GEO:GSE95214", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95214" } ] }, "title" : "Ventral prostate in male F344 rats: Control vs. PhIP treatment", "dateAssigned" : "2017-02-22T00:00:00.000-06:00", "summary" : "The gene expression profling between Control and 300 mg/kg PhIP treatment in ventral prostate lobe of male F344 rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29877212" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95231" }, "primaryId" : "GEO:GSE95231", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95231" } ] }, "title" : "Biological sex influences gene expressions in cardiac myocytes", "dateAssigned" : "2017-02-22T00:00:00.000-06:00", "summary" : "Results: We identified ~ 600 transcripts that were differentially expressed in cardiac myocytes from either sex. We also observed that enriched pathways from this data set were sexually dimorphic", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29030402" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95274" }, "primaryId" : "GEO:GSE95274", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95274" } ] }, "title" : "The effect of TAZ-K in neonatal rat cardiomyocytes", "dateAssigned" : "2017-02-23T00:00:00.000-06:00", "summary" : "Accumulating evidence suggests that new cardiomyocytes are generated from existing cardiomyocytes at a low rate throughout life. This limited regenerative capacity is unable to restore cardiac function after substantial cardiac damage; thus, small molecules have been examined for their ability to enhance the replication of existing cardiomyocytes. A novel compound TAZ-K promoted cardiomyocyte proliferation, therefore, we analyzed the effect of TAZ-K on gene expression in neonatal rat cardiomyocytes. Gene expression involved in cell cycle, anti-oxidant and anti-apoptosis was up-regulated. Thus, TAZ-K may have multifaceted effects and provide a treatment strategy that complements current therapies for patients with myocardial infarction.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95403" }, "primaryId" : "GEO:GSE95403", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95403" } ] }, "title" : "Next Generation Sequencing of miRNAs in rat hepatic macrophage Kupffer cells.", "dateAssigned" : "2017-02-27T00:00:00.000-06:00", "summary" : "We report the application of single-end-based sequencing technology for high-throughput profiling of miRNAs in Kupffer Cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29142263" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95420" }, "primaryId" : "GEO:GSE95420", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95420" } ] }, "title" : "Adult Cardiac Stem Cells are Multipotent and Robustly Myogenic: c-kit Expression is Necessary but not Sufficient for their Identification", "dateAssigned" : "2017-02-27T00:00:00.000-06:00", "summary" : "Multipotent adult resident cardiac stem cells (CSCs) originally were identified by the expression of c-kit, the stem cell factor receptor. However, in the adult myocardium c-kit alone distinguish CSCs from other c-kit-expressing cardiac cells because the adult heart contains a heterogeneous mixture of c-kitpos cells, mainly composed of mast and endothelial/progenitor cells. This heterogeneity of cardiac c-kitpos cells has not been considered in recent c-kit-expressing cell fate mapping publications, which have equated the contribution of the whole heterogeneous c-kitpos population to cardiomyocyte generation in adulthood, which is minimal, to that of the CSCs, a result at odds with previous publications. To shed light on this issue, we have assessed the identity, abundancy and myogenic potential of true multipotent CSCs within the total c-kitpos cardiac cell cohort. Blood lineage-committed c-kitpos cells were removed by CD45 negative sorting to obtain a CD45negc-kitpos cell population (<10% of the total c-kitpos cells), which is enriched for cells that express c-kit at low levels and possess all properties of multipotent stem/progenitor cells in vitro. These characteristics are absent from the c-kitneg and the lineage-committed c-kitpos cardiac cells. Single Linnegc-kitpos cell-derived CSC clones, representing 1-2% of total c-kitpos cells, when instructed by TGF-b/Wnt molecules, acquire full transcriptome expression, sarcomere organization, spontaneous contraction and electrophysiological properties of differentiated cardiomyocytes. Significantly, clonogenic CSCs have a potent cardio-regenerative/repair capacity in vivo after acute myocardial infarction. CSC myogenic regenerative capacity is dependent on cardiomyocyte commitment through activation of the SMAD2 pathway. Such regeneration was not apparent when freshly-isolated total c-kitpos cardiac cells were administered. In conclusion, only a very small fraction of cardiac c-kitpos cells (~1-2%) have the characteristics of multipotent CSCs but these exhibit robust myogenic properties. ¿", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95449" }, "primaryId" : "GEO:GSE95449", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95449" } ] }, "title" : "Experience-dependent Epigenomic Reorganization in the Hippocampus", "dateAssigned" : "2017-02-27T00:00:00.000-06:00", "summary" : "To further investigate epigenetic regulation of memory, we utilized whole-genome sequencing tools to systematically characterize memory-related changes in gene expression and DNA methylation status following memory acquisition.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28620075" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95470" }, "primaryId" : "GEO:GSE95470", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95470" } ] }, "title" : "Expression data of liver tissues from rats with and without methapyrilene treatment", "dateAssigned" : "2017-02-28T00:00:00.000-06:00", "summary" : "We investigated a drug-induced liver injury (DILI) model in rats induced by methapyrilene (MPy) administration. MPy, a former antihistamine and anticholinergic drug, was withdrawn in the 1970ties due to its ability to initiate hepatocarcinogenesis and is now used to induce hepatobiliary injury and biliary epithelial cell hyperplasia. Male Wistar rats (8–10 weeks old, weighing 170–200 g) were randomly assigned to three dosing groups (n=6 per group and time-point) and dosed with MPy at 0, 30 and 80 mg/kg/day by oral gavage. After 4, 8 or 15 days, or after 14 days followed by a recovery period of 10 days (day 24) rats were sacrificed. Increased levels of ALAT, ASAT, AP and ɣ-GT as well as bili-t and total bile acids indicated liver damage (AP and ɣGT indicating biliary effects). They were detectable on day 7 at the high dose of 80 mg/kg MPy and persisted until day 15 at end of treatment. Histopathologically, vacuolation and necrosis of the hepatocytes (predominantly in the periportal region) were seen starting on day 3 - especially in animals treated with 80 mg/kg MPy. These findings were accompanied by periportal mononuclear inflammatory cell filtration. Bile duct proliferation, bile duct hyperplasia and increased numbers of mitoses of hepatocytes were evident at all treatment time points. The frequency and severity of these findings increased with dose and duration of the treatment. Gene expression analysis in liver tissues revealed highly significant transcriptional changes in the high dose group, detectable on day 4 and intensifying over time. Besides genes associated with apoptosis (CASP4, CASP12), detoxification (CYB4B) and proliferation (p21, CCNG1) several were related to bile acid metabolism or transport. For example, bile acid exporters OATP1, NTCP, OATP4 and MOAT1/ OATPB as well as the putative bile acid metabolizing enzymes AMACR, BAAT and ACOX2 were found down regulated in response to MPy treatment. In contrast, mRNAs encoding putative bile acid importers MRP2 and ABCC4 / MRP4 were found up regulated. Most of the deregulated levels returned to control values during the recovery phase except OATP1, MOAT1/ OATPB, which remained slightly elevated. Interestingly, OATP4 followed an inverse trend of deregulation after 10 days of recovery, presumably due to overcompensation. Overall, the expression changes found associated with bile acid metabolism or transport could be linked to detected bile acid level alterations in liver and plasma.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28529062" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95475" }, "primaryId" : "GEO:GSE95475", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95475" } ] }, "title" : "Gene expression analysis in rat liver after exposure to pregnenolone-16α-carbonitrile", "dateAssigned" : "2017-02-28T00:00:00.000-06:00", "summary" : "We used microarrays to evaluate gene expression profiling in rat liver at the early phase of treatment with PCN.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28825834" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95490" }, "primaryId" : "GEO:GSE95490", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95490" } ] }, "title" : "mRNA expression in Extensor Digitorum longus (EDL) muscle of adult F2 female offspring from F0-fathers fed a chow or high-fat diet", "dateAssigned" : "2017-02-28T00:00:00.000-06:00", "summary" : "EDL muscle mRNA expression profiling of F2-female offspring from F0-founders fed either a chow or a chronic HFD challenged. Adult females were challenge or not a high-fat diet for 12 weeks. EDL muscle was dissected at an endpoint experiment. Rats were subjected to 4 hours fasting prior to anesthesia with pentobarbital and tissue collection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28702319" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95522" }, "primaryId" : "GEO:GSE95522", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95522" } ] }, "title" : "BEX1 is an RNA-dependent mediator of cardiomyopathy [RIP-Seq]", "dateAssigned" : "2017-02-28T00:00:00.000-06:00", "summary" : "Regulation of mRNA splicing, processing and stability is increasingly recognized as a critical control point in dynamically altering gene expression during stress or disease states. Very little is understood of this process in the heart despite the wide ranging changes in gene expression that occurs during heart failure; a disease of epidemic proportions in the western world. Here we identified BEX1 as a heart-failure-induced gene and identified its function as an mRNA binding protein responsible for enhancing expression of a subset of cardiac disease promoting genes. Modeling this increase in BEX1 that occurs in disease, BEX1 cardiac-specific overexpressing transgenic mice were generated and shown to have worse cardiac disease with stress stimulation while Bex1 gene-deleted mice were protected from insults that would otherwise promote heart failure. Since BEX1 was of unknown molecular function we performed a series of proteomic and interactive screening assays, which identified Bex1 as part of a large ribonucleoprotein processing complex involved in regulating pro-inflammatory mRNA expression in the heart. Specifically, induction of BEX1 augmented the stability and expression of AU-rich element containing mRNAs typically found within pro-inflammatory genes. Thus, BEX1 functions as an mRNA modulatory effector that augments pathology promoting gene expression during heart failure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29192139" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95523" }, "primaryId" : "GEO:GSE95523", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95523" } ] }, "title" : "BEX1 is an RNA-dependent mediator of cardiomyopathy [RNA-Seq]", "dateAssigned" : "2017-02-28T00:00:00.000-06:00", "summary" : "Regulation of mRNA splicing, processing and stability is increasingly recognized as a critical control point in dynamically altering gene expression during stress or disease states. Very little is understood of this process in the heart despite the wide ranging changes in gene expression that occurs during heart failure; a disease of epidemic proportions in the western world. Here we identified BEX1 as a heart-failure-induced gene and identified its function as an mRNA binding protein responsible for enhancing expression of a subset of cardiac disease promoting genes. Modeling this increase in BEX1 that occurs in disease, BEX1 cardiac-specific overexpressing transgenic mice were generated and shown to have worse cardiac disease with stress stimulation while Bex1 gene-deleted mice were protected from insults that would otherwise promote heart failure. Since BEX1 was of unknown molecular function we performed a series of proteomic and interactive screening assays, which identified Bex1 as part of a large ribonucleoprotein processing complex involved in regulating pro-inflammatory mRNA expression in the heart. Specifically, induction of BEX1 augmented the stability and expression of AU-rich element containing mRNAs typically found within pro-inflammatory genes. Thus, BEX1 functions as an mRNA modulatory effector that augments pathology promoting gene expression during heart failure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29192139" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95554" }, "primaryId" : "GEO:GSE95554", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95554" } ] }, "title" : "Mammary transcriptome of rats treated with low-dose environmental chemicals from birth to adulthood", "dateAssigned" : "2017-03-01T00:00:00.000-06:00", "summary" : "We used affymetrix arrays to assess the influence of diethyl phthalate (DEP), methyl paraben (MPB), triclosan (TCS) and their mixture (MIX) on global gene expression profiles in rat mammary tissues, using doses comparable to human exposure. Exposure was from birth to adulthood (postnatal day 1 – 180) in parous and nulliparous rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32341500" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95569" }, "primaryId" : "GEO:GSE95569", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95569" } ] }, "title" : "Transcriptional profiling reveals differential changes in the respective expression of oxytocin and CART mRNA levels in the nucleus accumbens and dorsal striatum of compulsive methamphetamine taking rats (nucleus accumbens)", "dateAssigned" : "2017-03-01T00:00:00.000-06:00", "summary" : "Methamphetamine addiction is mimicked in rats that self-administer the drug and accelerate their intake when given long access to it. Self-administration (SA) models do not include adverse consequences that are necessary to reach a diagnosis of addiction in humans. Here, we studied transcriptional consequences of methamphetamine SA and repeated foot-shocks in rat brain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28827541" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95570" }, "primaryId" : "GEO:GSE95570", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95570" } ] }, "title" : "Transcriptional profiling reveals differential changes in the expression of oxytocin and CARTpt  mRNAs in the nucleus accumbens and dorsal striatum of rats (striatum)", "dateAssigned" : "2017-03-01T00:00:00.000-06:00", "summary" : "Methamphetamine addiction is mimicked in rats that self-administer the drug and accelerate their intake when given long access to it. Self-administration (SA) models do not include adverse consequences that are necessary to reach a diagnosis of addiction in humans. Here, we studied transcriptional consequences of methamphetamine SA and repeated foot-shocks in rat brain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28827541" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95660" }, "primaryId" : "GEO:GSE95660", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95660" } ] }, "title" : "Genome wide identification of chromatin modifications in the hypothalamus during pubertal development", "dateAssigned" : "2017-03-03T00:00:00.000-06:00", "summary" : "Histone modification analysis of hypothalami from female animals at different juvenile developmental reproductive stages. Results provide insight into the role of the hypothalamus in controlling the onset of puberty.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29302059" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95783" }, "primaryId" : "GEO:GSE95783", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95783" } ] }, "title" : "Expression data from the uterus of ovariectomized young adult rats treated for three days with E2, 3-MC, E2+3-MC", "dateAssigned" : "2017-03-07T00:00:00.000-06:00", "summary" : "The study was designed to see the overall gene-expression change in the uterus induced by E2, the AHR ligand 3-MC alone and in combination with E2.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28285017" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95790" }, "primaryId" : "GEO:GSE95790", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95790" } ] }, "title" : "miRNA Expression data from the uterus of ovariectomized young adult rats treated for three days with E2", "dateAssigned" : "2017-03-07T00:00:00.000-06:00", "summary" : "The study was designed to see the overall ncRNA-expression change in the uterus induced by E2", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95850" }, "primaryId" : "GEO:GSE95850", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95850" } ] }, "title" : "Quantitative Analysis of Wild Type and miR-203 KO transcriptomes in the rat endometrial adenocarcinoma cell line RUCA-I", "dateAssigned" : "2017-03-08T00:00:00.000-06:00", "summary" : "Results: Using an optimized data analysis workflow, we mapped between 30 and 50 million sequence reads per sample to the rat genome (build rn6) and identified 26751 transcripts of which 1591 are differentially expressed in WT and miR-203 KO cells (p<0.05).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95855" }, "primaryId" : "GEO:GSE95855", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE95855" } ] }, "title" : "miRNA Expression Profile and Effect of Wenxin Granule in Rats with Ligation-Induced Myocardial Infarction", "dateAssigned" : "2017-03-09T00:00:00.000-06:00", "summary" : "miRNAs are small (approximately 22 nucleotides) noncoding RNAs which post-transcriptionally regulate gene expression by binding complementary sequences within messenger RNA transcripts. miRNAs are likely to regulate many complex processes in the body, indeed aberrant expression of various miRNAs has been implicated in numerous disease states. They have been shown to participate in cardiovascular disease pathogenesis including atherosclerosis, coronary artery disease, myocardial infarction (MI), heart failure and cardiac arrhythmias. To investigate the expression profiles of miRNA in MI, left ventricular tissues from 3 MI rats and 3 non-MI rats (control) that were collected for miRNA expression microarray analyses to explore the role of miRNA in the pathogenesis of MI. To assess the pathways predicted to be targeted by differentially expressed miRNAs in MI, we performed pathway analysis using the online DIANA miRPATH tool. The miR-1 and miR-133, the most abundant miRNAs in the heart, were chosen for further validation by the quantitative real-time polymerase chain reaction, and their expression trends were consistent with the microarray data. Additionally, the effect of Wenxin Granule on miR-1 and miR-133 expression was observed in present study.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28894747" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96079" }, "primaryId" : "GEO:GSE96079", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96079" } ] }, "title" : "Transcriptome-based analysis of developing dorsal and ventral hippocampus", "dateAssigned" : "2017-03-10T00:00:00.000-06:00", "summary" : "We report the differentiation of dorsal and ventral hippocampus in developing rats by performing and analyzing transcriptome profiling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29085281" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96085" }, "primaryId" : "GEO:GSE96085", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96085" } ] }, "title" : "Global gene expression profiling of radiation-induced rat mammary carcinomas", "dateAssigned" : "2017-03-10T00:00:00.000-06:00", "summary" : "To investigate gene expression patterns in rat mammary carcinomas induced by ionizing radiation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29435983" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96520" }, "primaryId" : "GEO:GSE96520", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96520" } ] }, "title" : "Maternal Western-style diet alters the transcriptome of chemically induced mammary tumors in female offspring rats", "dateAssigned" : "2017-03-12T00:00:00.000-06:00", "summary" : "Some previous experimental studies have shown that early in life intake of high-fat or Western-style diets did alter the development of mammary cancer in adulthood female rats. Thus, the present study investigated the distinct gene expression patterns of chemically induced mammary tumors derived from female offspring whose dams intake control diet (CD) or Western-style diet (WD). During gestational days (GD) 12-21 and post-natal days (PND) 1-21, pregnant Sprague-Dawley (SD) rats were fed a CD diet or WD (high-fat and low-fiber and oligoelements) diet. On postnatal day (PND) 21, the female offspring received a single dose of carcinogen N-Methyl-N-Nitrosourea (MNU, 50 mg/kg) and CD diet for 12 weeks. Latency, incidence and tumor burden were registered. Mammary tumors samples were collected and histopathology and gene expression analysis were performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30683438" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96565" }, "primaryId" : "GEO:GSE96565", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96565" } ] }, "title" : "Global DNA methylation profiling of radiation-induced rat mammary carcinomas", "dateAssigned" : "2017-03-13T00:00:00.000-05:00", "summary" : "To investigate DNA methylation patterns in rat mammary carcinomas induced by ionizing radiation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29435983" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96587" }, "primaryId" : "GEO:GSE96587", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96587" } ] }, "title" : "Gene expression profiles in the liver of spontaneously hypertensive rats at different stages of hypertension", "dateAssigned" : "2017-03-14T00:00:00.000-05:00", "summary" : "The objective of this study was to characterize differences in the global gene expression profiles of spontaneously hypertensive rats (SHR) and Wistar Kyoto rats (WKY) at different stages of hypertension. Using RNA isolated from liver of SHR and WKY rats, we compared the gene expression profiles by microarrays. Differential gene expression was detected in the liver of SHR rats compared to WKY control rats, possibly contributing to hypertension", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96610" }, "primaryId" : "GEO:GSE96610", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96610" } ] }, "title" : "Gene expression data in aortic tissue from rats with experimental preeclampsia, healthy pregnancy and non pregnant rats", "dateAssigned" : "2017-03-14T00:00:00.000-05:00", "summary" : "Whole aortic tissue was isolated from rats with low-dose LPS-induced preeclampsia, healthy pregnant and non-pregnant rats. Gene expression was measured by a whole genome microarray.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29093568" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96765" }, "primaryId" : "GEO:GSE96765", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96765" } ] }, "title" : "Whole transcriptome expression of trigeminal ganglia compared to dorsal root ganglia in Rattus norvegicus", "dateAssigned" : "2017-03-17T00:00:00.000-05:00", "summary" : "RNA-Sequencing of the trigeminal ganglia and dorsal root ganglia in male naive rats (Wistar Han) of 10 weeks old.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28359950" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96850" }, "primaryId" : "GEO:GSE96850", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96850" } ] }, "title" : "Generational Comparisons (F1 versus F3) of Vinclozolin Induced Epigenetic Transgenerational Inheritance of Sperm Differential DNA Methylation Regions (Epimutations) Using MeDIP-Seq", "dateAssigned" : "2017-03-21T00:00:00.000-05:00", "summary" : "The agricultural fungicide vinclozolin exposure of a gestating female rat has previously been shown to promote transgenerational disease and epimutations in F3 generation (great-grand-offspring) animals. The current study was designed to investigate the actions of direct fetal exposure on the F1 generation rat sperm DMRs compared to the F3 transgenerational sperm DMRs. The F1 generation DMRs were found to be fewer in number and for the most part distinct from the F3 generation epimutations. Therefore, the direct exposure induced F1 generation DMRs appear to promote alterations in germ cell development that lead to the programming of the F3 generation epimutations, but are distinct between the generations.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96886" }, "primaryId" : "GEO:GSE96886", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96886" } ] }, "title" : "Global effect of H2A.Z hypervariant knockdown on basal expression of neuronal genes", "dateAssigned" : "2017-03-21T00:00:00.000-05:00", "summary" : "Variant histone H2A.Z is an essential and conserved regulator of eukaryotic gene transcription. However, the exact role of this histone in the process remains perplexing. In vertebrates, H2A.Z has two hypervariants – H2A.Z.1 and H2A.Z.2 – that have almost identical amino-acid sequences excepting three residues. Due to such similarity, functional specificity of these hypervariants in neurobiological processes, if any, remain largely unknown. In this study with dissociated mature cortical neurons, we asked if H2A.Z hypervariants have functional specificity in regulating basal and activity-induced gene transcription. Hypervariant-specific RNAi and microarray analyses revealed that H2A.Z.1 and H2A.Z.2 regulate basal expression of largely non-overlapping gene-sets, including genes that code for several synaptic proteins. In response to neuronal activity, depletion of H2A.Z hypervariants impairs transcription of our model gene Arc differentially. As part of the +1 nucleosome, H2A.Z.2, not H2A.Z.1, is necessary for rapid immediate-early transcription by facilitating RNA Pol II promoter proximal pausing. In contrast, H2A.Z.1 plays complicated and perhaps indirect roles that affect Arc transcription kinetics context-dependently. Context-dependent roles of H2A.Z hypervariants are also evident amongst several other immediate early genes where their regulatory roles vary from gene to gene under different conditions. Together, our data suggest that H2A.Z hypervariants have context-specific roles that complement each other to mediate activity-induced neuronal gene transcription.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28856239" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96992" }, "primaryId" : "GEO:GSE96992", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96992" } ] }, "title" : "Microarray expression profiling in the denervated hippocampus identifies long noncoding RNAs functionally involved in neurogenesis", "dateAssigned" : "2017-03-24T00:00:00.000-05:00", "summary" : "RNA samples were extracted from the paired rat untreated hippocampus 7 days after the FF transection. The general RNA quality was evaluated by RIN. RNA quantity and purity were assessed using K5500 micro-spectrophotometer. A260/A280 =1.5 and A260/A230 =1 indicated acceptable RNA purity, and RIN value =7 using the Agilent 2200 RNA assay indicated acceptable RNA integrity (Table. S1). Genomic DNA contamination was evaluated by gel electrophoresis .Three independent samples were assayed to evaluate the reproducibility of the experimental procedure. Using the microarray expression profiles, 103 (74 activated and 29 repressed) lncRNAs differentially expressed in the hippocampus after the FF transection were identified.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96995" }, "primaryId" : "GEO:GSE96995", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE96995" } ] }, "title" : "Diverse requirements for microglial survival, specification, and function revealed by defined-medium cultures", "dateAssigned" : "2017-03-24T00:00:00.000-05:00", "summary" : "Microglia, the resident macrophages of the central nervous system (CNS), engage in various CNS-specific functions that are critical for development and health. To better study the properties that distinguish microglia from other tissue macrophage populations, we have optimized serum-free culture conditions to permit robust survival of highly purified adult microglia under defined-medium conditions. We find that astrocyte-derived factors prevent microglial death ex vivo and that this activity results from three primary components (CSF-1/IL-34, TGF-b2, and cholesterol). Using microglial cultures that have never been exposed to serum, we demonstrate a dramatic change in intrinsic phagocytic capacity after serum exposure. Finally, we find that mature microglia rapidly lose signature gene expression profiles after isolation, and that this loss can be reversed by engrafting cells back into an intact CNS environment. These data indicate that the specialized gene expression profile of mature microglia require continuous instructive signaling from the intact CNS. This RNA-seq dataset describes changes in rat microglial transcriptome in culture with or without serum exposure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97040" }, "primaryId" : "GEO:GSE97040", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97040" } ] }, "title" : "The role of Tmub1 protein in the regulation of hepatic cell transcription", "dateAssigned" : "2017-03-26T00:00:00.000-05:00", "summary" : "Tmub1 is involved in liver regeneration and functions as a bridging protein in tumor cell proliferation. To investigate the transcriptional profile and potential biological processes affected by Tmub1 expression in normal rat hepatocytes, microarray and bioinformatics experiments were used to identify 127 mRNAs differentially expressed between Tmub1-overexpression, Tmub1-knockdown and normal BRL-3A cells (fold change = 2.5, P < 0.05).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97044" }, "primaryId" : "GEO:GSE97044", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97044" } ] }, "title" : "Dynamic Changes in the Expressions of Elastogenesis- and Elastinolysis-Associated Genes and Remodeling of the Elastin Network in Volume-Overloaded Heart", "dateAssigned" : "2017-03-27T00:00:00.000-05:00", "summary" : "Conclusions: In the volume-overloaded heart, upregulation of potent elastases during the early phase and persistent upregulation of elastogenesis-related genes result in early degradation followed by repair and reinforcement of the elastin network of the LV. Remodeling of the elastin network may contribute to changes in the mechanical property of the volume-overloaded heart.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97047" }, "primaryId" : "GEO:GSE97047", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97047" } ] }, "title" : "Wound regeneration deficit in rats correlates with low morphogenetic potential and distinct transcriptome profile of epidermis", "dateAssigned" : "2017-03-27T00:00:00.000-05:00", "summary" : "We report whole tissue transcriptomes from rat and mouse wounds, as well as rat inter-follicular epidermis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29317265" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97083" }, "primaryId" : "GEO:GSE97083", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97083" } ] }, "title" : "An integrative model of cirrhosis-associated hepatocarcinogenesis in rat: histological, biochemical and molecular approaches", "dateAssigned" : "2017-03-27T00:00:00.000-05:00", "summary" : "The present study aimed at proposing a novel chemically-induced cirrhosis-associated rat hepatocarcinogenesis model, involving the characterization of histological, biochemical and molecular features. Male Wistar rats received a single dose of diethylnitrosamine (DEN, 200 mg/Kg body weight [b.wt.]), and were submitted to several cycles of thioacetamide (TAA, 200 mg/Kg b.wt.), during 23 weeks. Blood and liver were collected from untreated and DEN/TAA-treated groups. Liver samples were processed for global gene expression (cDNA microarray), histopathological (HE) and collagen content (picrosirius red) evaluations, immunohistochemical (Ki-67, GST-P and α-SMA), biochemical (catalase, glutathione peroxidase and glutathione-S-transferase) and gelatin zymography (MMP-2 and 9) analysis. Using a very stringent analysis (FDR<0.01 and fold change>3), gene expression array evidenced 359 differentially expressed genes upon DEN/TAA regimen. Gene Ontology and functional analyses showed several upregulated genes involved in extracellular matrix organization, mainly collagen type I α1 and 2 (Col1α1, Col1α2) and tissue inhibitor of metalloproteinase 1 and 2 (Timp1 and Timp2) genes. In addition, glutathione S-transferase, pi 1 and 2 (Gstp1 and Gstp2) genes were markedly upregulated. In contrast, functional analyses also revealed the downregulation of antioxidant response genes, as catalase, glutathione peroxidase 1 and glutathione S-transferase mu type 3 (Cat, Gpx1 and Gstm3). In agreement with gene expression data, our model presented extensive liver cirrhosis with increased α-SMA expression and collagen deposition, as well as marked development of preneoplastic GST-P positive hyperplastic lesions and some neoplasms. Besides, we observed a decrease in total glutathione peroxidase, total glutatione-S-tranferase and catalase activities. The characterization of a suitable cirrhosis-associated hepatocarcinogenesis model could provide insights into molecular characteristics of the human disease and be applied to evaluate potential preventive and therapeutic approaches.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28943392" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97229" }, "primaryId" : "GEO:GSE97229", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97229" } ] }, "title" : "MicroRNA expression in male rat hepatocytes and liver sinusoidal endothelial cells (LSECs)", "dateAssigned" : "2017-03-30T00:00:00.000-05:00", "summary" : "We determined the microRNA expression profiles of the hepatocytes and liver sinusoidal endothelial cells (LSECs) isolated from nontreated rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97299" }, "primaryId" : "GEO:GSE97299", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97299" } ] }, "title" : "Defining the microglial transcriptome in the rat subventricular zone (SVZ) after neonatal hypoxia-ischemia (HI).", "dateAssigned" : "2017-03-31T00:00:00.000-05:00", "summary" : "Purpose: Recent findings indicate a regulatory role of microglia on neurogenesis in the SVZ in health and disease. Microglia in the early postnatal SVZ are not fully maturated and may react differently than adult microglia to injury. We sought to investigate the impact of cortico-striatal neonatal HI injury on the microglial phenotype in the early postnatal SVZ. Results: In comparison to sham SVZ microglia, HI SVZ microglia upregulate both pro- and anti-inflammatory genes as well as neurotrophic genes. HI SVZ microglia do not adopt a M1 or M2 polarization state, but instead share commonly expressed genes with microglia in rodent models of neurodegenerative diseases.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97376" }, "primaryId" : "GEO:GSE97376", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97376" } ] }, "title" : "A memory of early life physical activity is retained in bone marrow of adult rats but does not prevent reversal to obese phenotype", "dateAssigned" : "2017-04-04T00:00:00.000-05:00", "summary" : "Studies have reported opposing effects of high-fat diet and mechanical stimulation on lineage commitment of the bone marrow stem cells. Yet, how the bone marrow modulates its gene expression in response to the combined effects of mechanical loading and a high-fat diet has not yet been addressed. We investigated whether early-life voluntary physical activity can modulate the effects of a high-fat diet on body composition, bone phenotype and bone marrow gene expression in male Sprague Dawley rats. We show that early-life high-fat diet positively affected body weight, total fat percentage and bone mass indices. In the bone marrow, early-life high-fat diet resulted in adipocyte hypertrophy and a pro-inflammatory and pro-adipogenic gene expression profile. Crucially, the bone marrow of the rats that undertook wheel exercise while on a high-fat diet retained a memory of the early-life exercise. This memory lasted at least 60 days after the cessation of the voluntary exercise and was manifest by: 1) the bone marrow adipocyte size of the exercised rats not exhibiting hypertrophy; and 2) genes associated with mature adipocyte function being down-regulated. Our results are consistent with the marrow adipose tissue having a unique and long-lasting response to high-fat feeding in the presence or absence of exercise.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28736532" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97429" }, "primaryId" : "GEO:GSE97429", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97429" } ] }, "title" : "Gene expression in the liver remnant is significantly affected by the size of partial hepatectomy - an experimental rat study", "dateAssigned" : "2017-04-05T00:00:00.000-05:00", "summary" : "Conclusion: With decreasing size of the future liver remnant, the liver tended to prioritize expression of genes involved in cell proliferation and differentiation at the expense of genes involved in metabolism and body homeostasis. This prioritizing may be an essential molecular explanation for post-hepatectomy liver failure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28488569" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97470" }, "primaryId" : "GEO:GSE97470", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97470" } ] }, "title" : "Expression data from control or rat Giver knock-down cells treated w/o Ang II for 3 hours", "dateAssigned" : "2017-04-06T00:00:00.000-05:00", "summary" : "We used microarrays to detail Giver-mediated global gene expression and identified distinct classes of up- and down-regulated genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97496" }, "primaryId" : "GEO:GSE97496", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97496" } ] }, "title" : "TonEBP/NFAT5 controls inflammatory transcriptional response to TNF-a in nucleus pulposus cells", "dateAssigned" : "2017-04-07T00:00:00.000-05:00", "summary" : "RNA sequencing of nucleus pulposus cells transduced with shRNA (control or TonEBP-targeted) and either untreated or treated with TNF-a (24h)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28842479" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97532" }, "primaryId" : "GEO:GSE97532", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97532" } ] }, "title" : "Expression data from MCAO or Sham operated rat blood [miRNA]", "dateAssigned" : "2017-04-07T00:00:00.000-05:00", "summary" : "By using microarray analysis and comparing with Sham operated rats, we extracted the miRNAs whose expressions are alterated by stroke.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29113076" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97533" }, "primaryId" : "GEO:GSE97533", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97533" } ] }, "title" : "Expression data from MCAO or Sham operated rat blood [mRNA]", "dateAssigned" : "2017-04-07T00:00:00.000-05:00", "summary" : "Using microarray analysis, we aimed to grasp the overall expression alteration of mRNA in blood after stroke.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29113076" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97537" }, "primaryId" : "GEO:GSE97537", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97537" } ] }, "title" : "Expression data from MCAO or Sham operated rat brain [mRNA]", "dateAssigned" : "2017-04-07T00:00:00.000-05:00", "summary" : "Using microarray analysis, we aimed to grasp the overall expression alteration of mRNA in brain after stroke.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97608" }, "primaryId" : "GEO:GSE97608", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97608" } ] }, "title" : "Hippocampal subfield transcriptomic profiles: Regional vulnerability to age and cognitive impairment", "dateAssigned" : "2017-04-10T00:00:00.000-05:00", "summary" : "The current study employed next-generation RNA sequencing to examine gene expression related to brain aging and cognitive decline. Young and aged rats were trained on a spatial episodic memory task. Hippocampal regions CA1, CA3 and the dentate gyrus (DG) were isolated. Poly-A mRNA was examined using two different platforms, Illumina and Ion Proton. The Illumina platform was used to generate lists of genes that were differentially expressed across regions, ages, and in association with cognitive function. The gene lists were then retested using the Ion Proton platform. The results describe regional differences in gene expression and point to regional differences in vulnerability to aging. Aging was associated with increased expression of immune response related genes, particularly in the dentate gyrus. Finally, for the memory task used, impaired performance of aged animals was linked to the regulation of Ca2+ and synaptic function in region CA1.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29276487" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97612" }, "primaryId" : "GEO:GSE97612", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97612" } ] }, "title" : "DNA Methylation of Synaptic Genes in the Prefrontal Cortex is Associated with Aging and Age-Related Cognitive Impairment", "dateAssigned" : "2017-04-10T00:00:00.000-05:00", "summary" : "The results indicate that differential methylation was linked to the expression of genes within functional categories which may mediate impaired cognition in aging. Differences in aging included hypermethylation of genes linked to synaptic function and GTPase activity. Further, age-related cognitive flexibility impairment was correlated to hypermethylation of synaptic, postsynaptic density and ion channel activity genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28824413" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97623" }, "primaryId" : "GEO:GSE97623", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97623" } ] }, "title" : "Transcriptome analysis of hypothalamuses from prepubertal and pubertal rats", "dateAssigned" : "2017-04-11T00:00:00.000-05:00", "summary" : "We applied RNA sequencing analysis to hypothalamuses from prepubertal and pubertal rats. The significant differential expression transcripts were screened out. In order to validate the RNA-seq data, the expression patterns in the samples of lncRNAs and mRNA genes were confirmed by qRT-PCR. This research provides an expression profile of lncRNAs to further research on puberty.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97740" }, "primaryId" : "GEO:GSE97740", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97740" } ] }, "title" : "Rat muscle atrophy", "dateAssigned" : "2017-04-13T00:00:00.000-05:00", "summary" : "Transcriptional profiling of castrated rat cells (C3d) treated or not with testosterone for 8h (C3dpt8h) or 24h (C3dpt24h).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97852" }, "primaryId" : "GEO:GSE97852", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97852" } ] }, "title" : "Transcriptomic study of NR8383 cells following exposure to zinc oxide nanoparticles NM110", "dateAssigned" : "2017-04-16T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanoparticle exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 2 µg/mL of NP ZnO (20 % cell viability). This project (SmartNanoTox) has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 686098.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31352547" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97897" }, "primaryId" : "GEO:GSE97897", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97897" } ] }, "title" : "Engraftment and Repopulation Potential of Late Gestation Fetal Rat Hepatocytes", "dateAssigned" : "2017-04-17T00:00:00.000-05:00", "summary" : "Conclusions: Our studies show that late gestation fetal hepatocytes, despite their being far along in the differentiation process, possess the capacity for extensive liver repopulation. This is likely related to the unexpected presence of a significant proportion of hepatocyte marker-positive cells maintaining a less well differentiated phenotype.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28749819" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97950" }, "primaryId" : "GEO:GSE97950", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97950" } ] }, "title" : "Molecular Mediators of Cardiac Pathology in Cardiorenal Syndrome Type 4", "dateAssigned" : "2017-04-18T00:00:00.000-05:00", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97966" }, "primaryId" : "GEO:GSE97966", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97966" } ] }, "title" : "Rat embryonic stem cells produce fertile offspring through tetraploid complementation [RNA-Seq]", "dateAssigned" : "2017-04-19T00:00:00.000-05:00", "summary" : "Pluripotency of embryonic stem cells (ESCs) can be functionally assessed according to their developmental potency. Tetraploid complementation, through which an entire organism is produced from donor pluripotent cells, is taken as the most stringent test for pluripotency. It remains unclear whether ESCs from other species besides mice can pass this test. Here we show that the rat ESCs at very early passages are also capable to produce fertile offspring by tetraploid complementation, however, this capacity is rapidly lost during culture due to the loss of genomic imprinting. Our findings support that the naïve ground state pluripotency exists in rat and can be captured in rat ESCs, yet may be subjected to species-specific regulations, which have implications for the derivation and application of naïve pluripotent stem cells in other species including human.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29078333" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97968" }, "primaryId" : "GEO:GSE97968", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE97968" } ] }, "title" : "Rat embryonic stem cells produce fertile offspring through tetraploid complementation [RRBS]", "dateAssigned" : "2017-04-19T00:00:00.000-05:00", "summary" : "Pluripotency of embryonic stem cells (ESCs) can be functionally assessed according to their developmental potency. Tetraploid complementation, through which an entire organism is produced from donor pluripotent cells, is taken as the most stringent test for pluripotency. It remains unclear whether ESCs from other species besides mice can pass this test. Here we show that the rat ESCs at very early passages are also capable to produce fertile offspring by tetraploid complementation, however, this capacity is rapidly lost during culture due to the loss of genomic imprinting. Our findings support that the naïve ground state pluripotency exists in rat and can be captured in rat ESCs, yet may be subjected to species-specific regulations, which have implications for the derivation and application of naïve pluripotent stem cells in other species including human.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29078333" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98064" }, "primaryId" : "GEO:GSE98064", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98064" } ] }, "title" : "Iron-Deficiency in Pregnancy: Effects on the Rat Hippocampus", "dateAssigned" : "2017-04-21T00:00:00.000-05:00", "summary" : "Whole-genome bisulfite sequencing on the rat hippocampus identifies DMRs near genes concerning neuronal development and plasticity which are affected by an iron-deficient diet in pregnancy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98105" }, "primaryId" : "GEO:GSE98105", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98105" } ] }, "title" : "Wound Healing Protects Against Chemotherapy-induced Alopecia in Young Rats via Up-regulating Interleukin-1ß-mediated Signaling", "dateAssigned" : "2017-04-24T00:00:00.000-05:00", "summary" : "Wound healing is a complex process regulated by various cell types and a plethora of mediators. While interactions between wounded skin and the hair follicles (HFs) could induce HF neogenesis or promote wound healing, it remains unknown whether the wound healing-associated signaling milieu can be manipulated to protect against alopecia, such as chemotherapy-induced alopecia (CIA). Utilizing a well-established neonatal rat model of CIA, we show here that skin wounding protects from alopecia caused by several clinically relevant chemotherapeutic regimens, and that protection is dependent on the time of wounding and hair cycle stage. Gene expression profiling unveiled a significant increase in interleukin-1 beta (IL-1ß) mediated signaling by skin wounding. Subsequently, we showed that IL-1ß is sufficient and indispensable for mediating the CIA-protective effect. Administration of IL-1ß alone to unwounded rats exhibited local CIA protection while IL-1ß neutralization abrogated CIA protection by wounding. Mechanistically, IL-1ß retarded postnatal HF morphogenesis, making HFs at the wound sites or IL-1ß treated areas damage-resistant while the rats developed total alopecia elsewhere. We conclude that wound healing switches the cutaneous cytokine milieu to an IL-1ß-dominated state thus retarding HF growth progression and rendering the HFs resistant to chemotherapy agents. In the future, manipulation of HF progression through interfering with the IL-1ß signaling milieu may provide therapeutic benefits to a variety of conditions, from prevention of CIA to inhibition of hair growth and treatment of hirsutism. In this experiment, we used the Rat MI-Ready array comprised of over 34,000 transcript probes for gene and alternative splice products in ENSEMBL release 37 to profile gene expression changes during acute wound healing in rat skin. 16,198 Selected rat probes were above threshold in at least one group. 3,239 significant genes were found (FDR < 0.1).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28607955" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98116" }, "primaryId" : "GEO:GSE98116", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98116" } ] }, "title" : "Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin, and preferentially associates with LINE L1 elements", "dateAssigned" : "2017-04-24T00:00:00.000-05:00", "summary" : "Conclusion: Present study revealed that HILS1 is preferentially associated Line L1 elements in rat spermatids.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98152" }, "primaryId" : "GEO:GSE98152", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98152" } ] }, "title" : "Expression data from two rat strains comparing naïve vs 24h picornavirus infection.", "dateAssigned" : "2017-04-25T00:00:00.000-05:00", "summary" : "Allergic (Th2high immunophenotype) asthmatics have a heightened susceptibility to common respiratory viral infections such as human rhinovirus. Evidence suggests that the innate interferon response is deficient in asthmatic/atopic individuals, whilst other studies show no differences in antiviral response pathways. Unsensitized and OVA-sensitized/challenged Th2high (BN rats) and Th2low immunophenotype (PVG rats) animals were inoculated intranasally with attenuated mengovirus (vMC0). Sensitized animals were exposed/unexposed during the acute viral response phase. Cellular and transcriptomic profiling was performed on bronchoalveolar lavage cells. In unsensitized PVG rats, vMC0 elicits a prototypical antiviral response (neutrophilic airways inflammation, upregulation of Th1/type I interferon-related pathways). In contrast, response to infection in the Th2high BN rats was associated with a radically altered intrinsic host response to respiratory viral infection, characterized by macrophage influx/Th2-associated pathways. In sensitized animals, response to virus infection alone was not altered compared to unsensitized animals. However, allergen exposure of sensitized animals during viral infection unleashes a notably exaggerated airways inflammatory response profile orders of magnitude higher in BN versus PVG rats despite similar viral loads. The coexposure responses in the Th2high BN incorporated type I interferon/Th1, alternative macrophage activation/Th2 and Th17 signatures. Similar factors may underlie the hyper-susceptibility to infection-associated airways inflammation characteristic of the human Th2high immunophenotype.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30150981" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98272" }, "primaryId" : "GEO:GSE98272", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98272" } ] }, "title" : "Temporal Transcriptome Analysis of Pancreatic β-Cells in Response to Lipotoxicity and Glucolipotoxicity.", "dateAssigned" : "2017-04-27T00:00:00.000-05:00", "summary" : "The pancreatic beta cell function failure is the core event of type 2 diabetes mellitus. High levels of free fatty acid and glucose are two main factor that induced pancreatic beta cell function failure. Long term exposure to palmitate can induced pancreatic beta cell apoptoss and impaired insulin secretion in vivo and in vitro, called lipotoxicity. The lipotoxicity often coupled with high glucose, their combination form called glucolipotoxcity. We carried out temporal transcriptome and proteome studies investigating the evolution of molecular events in Ins1 cells stimulated by palmitate for different times. And through compared the transcriptome and proteome between lipotoxicity and glucolipotoxicity explain the mechanism of glucolipotoxicity more harmfull to beta cell.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30082485" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98520" }, "primaryId" : "GEO:GSE98520", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98520" } ] }, "title" : "Molecular Mediators of Cardiac Pathology in Cardiorenal Syndrome Type 4 [mRNA]", "dateAssigned" : "2017-05-03T00:00:00.000-05:00", "summary" : "We report the changes in left ventricle mRNA abundance in response to 5/6 nephrectomy surgery", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98521" }, "primaryId" : "GEO:GSE98521", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98521" } ] }, "title" : "Molecular Mediators of Cardiac Pathology in Cardiorenal Syndrome Type 4 [miRNA]", "dateAssigned" : "2017-05-03T00:00:00.000-05:00", "summary" : "We report the changes in left ventricle miRNA abundance in response to 5/6 nephrectomy surgery", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98522" }, "primaryId" : "GEO:GSE98522", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98522" } ] }, "title" : "Molecular Mediators of Cardiac Pathology in Cardiorenal Syndrome Type 4 [anti-miR-21]", "dateAssigned" : "2017-05-03T00:00:00.000-05:00", "summary" : "We report the changes in left ventricle mRNA abundance in response to miR-21-5p suppression in 5/6 nephrectomized rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98535" }, "primaryId" : "GEO:GSE98535", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98535" } ] }, "title" : "Transcriptional Changes in Rat Dorsal Root Ganglia Neurons During Stretch-Mediated Axon Growth", "dateAssigned" : "2017-05-04T00:00:00.000-05:00", "summary" : "The development of meter-long axons within the nervous system is a remarkable, yet unresolved biological process. The most widely studied aspects of neuronal growth focus on the extension and chemotropism of growth cones. However, over the course of organismal development, short axons elongate up to one meter in length with the systemic expansion of mitotic tissues. The preeminent regulatory mechanism for such synchronized growth between the nervous system and the tissues it spans, is the biomechanical stretch of axons, a known stimulus of axon growth. Here, we reveal the transcriptional profile of stretch-mediated axon growth as found using embryonic rat dorsal root ganglia neurons stretch-grown in vitro.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98546" }, "primaryId" : "GEO:GSE98546", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98546" } ] }, "title" : "Characterization of neuroendocrine tumors in heterozygous mutant MENX rats: a novel model of invasive medullary thyroid carcinoma [thyroid]", "dateAssigned" : "2017-05-04T00:00:00.000-05:00", "summary" : "Transcriptome profiling of rat NETs having different p27 dosages revealed a tissue-specific, dose-dependent effect of p27 on gene expression. In p27+/mut rats, thyroid neoplasms progress to invasive and metastatic medullary thyroid carcinomas (MTCs) accompanied by increased calcitonin levels, as in humans. Comparison of expression signatures of late-stage versus early-stage MTCs from p27+/mut rats identified genes potentially involved in tumor aggressiveness. The expression of a subset of these genes was evaluated in human MTCs, and found associated with aggressive RET-M918T-positive tumors. Altogether, p27 haploinsufficiency in MENX rats uncovered a novel, representative model of invasive/metastatic MTC, exploitable for translational studies of this aggressive and often incurable cancer.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29142006" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98575" }, "primaryId" : "GEO:GSE98575", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98575" } ] }, "title" : "REV-ERBα Ameliorates Heart Failure Through Transcription Repression", "dateAssigned" : "2017-05-04T00:00:00.000-05:00", "summary" : "Heart failure remains a major unmet clinical need and current therapies targeting neurohomonal and hemodynamic regulation have limited efficacy. We report that pharmacological activation of the transcriptional repressor REV-ERBa prevents expression of a pathological gene program and cardiomyocyte hypertrophy. In vivo, REV-ERBa agonism prevents development and halts progression of heart failure in mouse models. Thus, modulation of gene networks by targeting REV-ERBa represents a novel approach to heart failure therapy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28878135" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98621" }, "primaryId" : "GEO:GSE98621", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98621" } ] }, "title" : "4 or 14-Day Food Restriction Study in Sprague Dawley Rats", "dateAssigned" : "2017-05-08T00:00:00.000-05:00", "summary" : "This study is designed to determine effects on parameters routinely measured in toxicology studies", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31285465" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98636" }, "primaryId" : "GEO:GSE98636", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98636" } ] }, "title" : "Gene expression change by miR-17-92 in the dorsal root ganglion", "dateAssigned" : "2017-05-08T00:00:00.000-05:00", "summary" : "Gene expression profile of L5 DRG was examined to analyze a role of miR-17-92 in the DRG.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98656" }, "primaryId" : "GEO:GSE98656", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98656" } ] }, "title" : "Expression data from C6 glioma and small molecule induced cells (SMiN)", "dateAssigned" : "2017-05-08T00:00:00.000-05:00", "summary" : "Gene ontology and gene expression profiles related to cell division, gliogenesis, and angiogenesis were significantly down-regulated in SMiNs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98683" }, "primaryId" : "GEO:GSE98683", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98683" } ] }, "title" : "Atrazine Induced Epigenetic Transgenerational Inheritance of Disease, Lean Phenotype and Sperm Epimutation Pathology Biomarkers", "dateAssigned" : "2017-05-08T00:00:00.000-05:00", "summary" : "This study examined the potential transgenerational actions of the herbicide atrazine. The F1 generation offspring (directly exposed as a fetus) derived from the F0 generation exposed gestating female rats did not develop disease, but weighed less compared to controls. The F2 generation (grand-offspring) was found to have increased frequency of testis disease, increased frequency of tumor development in males and females (predominately mammary tumors), early onset puberty in males, and decreased body weight in females compared to controls. The transgenerational F3 generation rats were found to have increased frequency of testis disease, early onset puberty in females, behavioral alterations and a lean phenotype in males and females involving a reduced adipocyte size, decreased body mass index (BMI) and reduced adiposity. The frequency of multiple diseases was significantly higher in the transgenerational F3 generation atrazine lineage males and females. The sperm differential DNA methylation regions (DMRs), termed epimutations, induced by atrazine were identified. A comparison of control versus atrazine lineage sperm identified 519 DMRs (p<10-6) for the F1 generation, 431 DMR (p<10-5) for the F2 generation, and 958 DMR (p<10-9) for the transgenerational F3 generation sperm.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28931070" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98745" }, "primaryId" : "GEO:GSE98745", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98745" } ] }, "title" : "RNA-seq of Wistar-rat liver from young and old animals", "dateAssigned" : "2017-05-10T00:00:00.000-05:00", "summary" : "Comparison of gene expression level by Illumina sequencing of rat liver from young and old animals. We identified differentially expressed genes and provide functional profiles, which give insights into the aging process of short-lived rodents.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28916632" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98777" }, "primaryId" : "GEO:GSE98777", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98777" } ] }, "title" : "Amygdala transcriptome in rats prenatally exposed to valproic acid", "dateAssigned" : "2017-05-10T00:00:00.000-05:00", "summary" : "The amygdala controls socioemotional behavior and has consistently been implicated in the etiology of Autism Spectrum Disorder (ASD). Precocious amygdala development is commonly reported in ASD youth with the degree of overgrowth positively correlated to the severity of ASD symptoms. However, surprisingly little is known about the cellular, molecular, or genetic changes that occur in the amygdala over development in ASD individuals or rodent models. We examined abnormalities in gene expression in the amygdala and socioemotional behavior across development in the valproic acid (VPA) rat model of ASD.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98851" }, "primaryId" : "GEO:GSE98851", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98851" } ] }, "title" : "Regulatory Mechanisms Mediated by DNA methyltransferase 1 link the maternal Environment with the Development of the Embryo", "dateAssigned" : "2017-05-12T00:00:00.000-05:00", "summary" : "Epidemiological as well as animal model studies have demonstrated the close relationship that exists between the early maternal developmental environment and the risk of developing metabolic diseases in adulthood. Small birth weight has been shown to be an important marker for this although the molecular mechanisms which mediate these changes are not well understood", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29434026" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98855" }, "primaryId" : "GEO:GSE98855", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98855" } ] }, "title" : "Immune repertoire after immunization as seen by next generation sequencing and proteomics", "dateAssigned" : "2017-05-12T00:00:00.000-05:00", "summary" : "We study the repertoire of immunoglobulin sequences after immunization in a cohort of rats. Animals were immunized with dinitrophenol modified KLH or with recombinant human HuD. In the immune reprtoire, and also in the matching proteomics data, we observe that the animals produce a repertoire that has many shared motifs for those immunized with the same antigen. Cluster analysis allows the samples to be segregated according to the immunogen used.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29085363" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98858" }, "primaryId" : "GEO:GSE98858", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE98858" } ] }, "title" : "The Effect of RBM5 Gene Manipulation on Expression Data from Day In Vitro 6 Primary Rat Cortical Neurons", "dateAssigned" : "2017-05-12T00:00:00.000-05:00", "summary" : "We used microarrays to examine genes that are up-regulated vs. down-regulation in cortical neurons after RBM5 knockdown vs. overexpression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28818525" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99021" }, "primaryId" : "GEO:GSE99021", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99021" } ] }, "title" : "Blood transcriptional signatures for disease progression in a rat model of osteoarthritis", "dateAssigned" : "2017-05-17T00:00:00.000-05:00", "summary" : "Biomarkers of osteoarthritis (OA) that can accurately diagnose the disease at the earliest stage would significantly support efforts to develop treatments for prevention and early intervention. The different stages of disease progression are described by the complex pattern of transcriptional regulations. The dynamics in pattern alterations were monitored in each individual animal during the time-course of OA progression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99119" }, "primaryId" : "GEO:GSE99119", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99119" } ] }, "title" : "RNA binding protein DDX1 is responsible for fatty acid mediated repression of insulin translation", "dateAssigned" : "2017-05-21T00:00:00.000-05:00", "summary" : "Previous studies have focused on the combined glucolipoxicity that is presence of high glucose and free fatty acid levels effect on insulin gene expression, but the effect of high FFA and normal glucose level on insulin expression is unkown. Here we observed that palmitate can inhibit insulin translation. And we identified a novel insulin mrna binding protein DDX1 that is responsible for fatty acid mediated insulin translation inhibition. Palmitate treatment causes phosphorylation of DDX1 at S295 and dissociation from insulin mRNA, which decreases insulin translation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30295850" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99203" }, "primaryId" : "GEO:GSE99203", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99203" } ] }, "title" : "DNA array analysis in OLETF, a type 2 diabetic rats, and LETO, a non-diabetic control rats", "dateAssigned" : "2017-05-23T00:00:00.000-05:00", "summary" : "AMP deaminase (AMPD) plays a crucial role in adenine nucleotide metabolism, and its upregulated activity contributes to diastolic dysfunction of the heart caused by type 2 diabetes mellitus (T2DM) via reduction of the adenine nucleotide pool. Here we examined the mechanism of AMPD upregulation by T2DM. The protein level of 90-kDa full-length AMPD3 was increased in whole myocardial lysates and in the sarcoplasmic reticulum (SR) fraction by 55% and 123%, respectively, in OLETF, a rat model of T2DM, compared to those in LETO, a non-diabetic control, though AMPD mRNA level was unchanged in OLETF. MicroRNA array analysis revealed downregulation (>50%) of 57 microRNAs in OLETF compared to those in LETO, among which miR-301b was predicted to interact with the 3’UTR of AMPD3 mRNA. The 90-kDa AMPD3 level was significantly increased by miR-301b inhibitor, but decreased by a miR-301b mimetic in H9c2 cells. A luciferase reporter assay indicated binding of miR-301b to the 3’UTR of AMPD3 mRNA. The results indicate that translational regulation by miR-301b mediates AMPD3 upregulation in the diabetic heart. Since ATP generated by SR-associated glycolytic enzymes contributes to Ca2+ uptake by SERCA2a, upregulated AMPD3 in the vicinity of the SR may be a therapeutic target for diabetic cardiomyopathy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99206" }, "primaryId" : "GEO:GSE99206", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99206" } ] }, "title" : "Perivascular macrophages proliferate in the CNS, but also contributed by bone-marrow precursors in response to cerebral ischemia", "dateAssigned" : "2017-05-23T00:00:00.000-05:00", "summary" : "Immune response following CNS disease and injury comprises three different compartments, parenchymal, perivascular and blood involving specialized immune cells. Microglia are the major immune cell residing in the CNS parenchymal compartment but together with other macrophages which are residing in the non-parenchymal structures such as perivascular spaces, leptomeninges and choroid plexus constitute the total macrophage population of the CNS. While the homeostatic functions of these specialized macrophages in not very well understood, evidence shows that these macrophages at the blood-brain interface might involve immune-surveillance and establish a gate way for the recruitment of peripheral immune cells in to the CNS in response to the pathological stimuli. In humans and rats these macrophages identified exclusively by the high levels of scavenger receptor CD163", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99214" }, "primaryId" : "GEO:GSE99214", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99214" } ] }, "title" : "RNA editing in the Rat brain", "dateAssigned" : "2017-05-23T00:00:00.000-05:00", "summary" : "Adenosine-to-inosine (A-to-I) RNA editing is an epigenetic modification catalyzed by adenosine deaminases acting on RNA (ADARs), and is especially prevalent in the brain.Using microfluidics-based multiplex PCR sequencing (mmPCR-seq) to assess A-to-I editing at 146 pre-selected, conserved sites, we found that editing was generally higher in adult compared to neonatal rat brain, and that at birth, global editing was lower in prefrontal cortex than in amygdala. Prereproductive stress (PRS) affected editing at the serotonin receptor 2c, and editing at this site was significantly altered in offspring of PRS rats across two generations. Changes in ADAR expression did not correlate with editing changes induced by development or stress. Our findings indicate that mmPCR-seq can accurately detect RNA editing in rat brain samples, and confirm previous accounts of a developmental increase in RNA editing rates. Altered RNA editing rates in offspring of stress-exposed rats complements growing literature on the transgenerational effects of stress.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99272" }, "primaryId" : "GEO:GSE99272", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99272" } ] }, "title" : "Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care [BiSulfite-seq]", "dateAssigned" : "2017-05-24T00:00:00.000-05:00", "summary" : "The quality of maternal care in early-life plays a crucial role in mammalian neurodevelopment. Augmented maternal care (AMC) is a well-established rodent model of enhanced neonatal care. Rats that have undergone AMC have improved stress resilience and cognition compared with rats that have experienced normal levels of maternal care or adverse neonatal stress. However, the epigenomic basis of long-lived responses to AMC has not been previously explored. Thus, we employed whole-genome bisulfite sequencing (WGBS), RNA-sequencing (RNA-seq), and a multiplex microRNA (miRNA) assay to assess DNA cytosine methylation, gene expression, and miRNA expression, respectively. The integrated results identify a suite of 20 prioritized candidates impacted by AMC. Overall, these results identified AMC-induced regulatory differences in genes related to neurotransmission, neurodevelopment, protein synthesis, and oxidative phosphorylation in addition to the expected stress response genes. Together, these unbiased results represent a key progression in understanding the complex mechanisms underlying the early-life mechanisms for AMC programming stress resiliency.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29613827" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99278" }, "primaryId" : "GEO:GSE99278", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99278" } ] }, "title" : "Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care [RNA-seq]", "dateAssigned" : "2017-05-24T00:00:00.000-05:00", "summary" : "The quality of maternal care in early-life plays a crucial role in mammalian neurodevelopment. Augmented maternal care (AMC) is a well-established rodent model of enhanced neonatal care. Rats that have undergone AMC have improved stress resilience and cognition compared with rats that have experienced normal levels of maternal care or adverse neonatal stress. However, the epigenomic basis of long-lived responses to AMC has not been previously explored. Thus, we employed whole-genome bisulfite sequencing (WGBS), RNA-sequencing (RNA-seq), and a multiplex microRNA (miRNA) assay to assess DNA cytosine methylation, gene expression, and miRNA expression, respectively. The integrated results identify a suite of 20 prioritized candidates impacted by AMC. Overall, these results identified AMC-induced regulatory differences in genes related to neurotransmission, neurodevelopment, protein synthesis, and oxidative phosphorylation in addition to the expected stress response genes. Together, these unbiased results represent a key progression in understanding the complex mechanisms underlying the early-life mechanisms for AMC programming stress resiliency.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29613827" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99281" }, "primaryId" : "GEO:GSE99281", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99281" } ] }, "title" : "Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care [miRNA]", "dateAssigned" : "2017-05-24T00:00:00.000-05:00", "summary" : "The quality of maternal care in early-life plays a crucial role in mammalian neurodevelopment. Augmented maternal care (AMC) is a well-established rodent model of enhanced neonatal care. Rats that have undergone AMC have improved stress resilience and cognition compared with rats that have experienced normal levels of maternal care or adverse neonatal stress. However, the epigenomic basis of long-lived responses to AMC has not been previously explored. Thus, we employed whole-genome bisulfite sequencing (WGBS), RNA-sequencing (RNA-seq), and a multiplex microRNA (miRNA) assay to assess DNA cytosine methylation, gene expression, and miRNA expression, respectively. The integrated results identify a suite of 20 prioritized candidates impacted by AMC. Overall, these results identified AMC-induced regulatory differences in genes related to neurotransmission, neurodevelopment, protein synthesis, and oxidative phosphorylation in addition to the expected stress response genes. Together, these unbiased results represent a key progression in understanding the complex mechanisms underlying the early-life mechanisms for AMC programming stress resiliency.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29613827" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99380" }, "primaryId" : "GEO:GSE99380", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99380" } ] }, "title" : "Expression data from rat endosalpinx at 3 hours after mating", "dateAssigned" : "2017-05-29T00:00:00.000-05:00", "summary" : "Herein, we used Affymetrix microarrays to conduct a transcriptomic analysis of the endosalpinx at 3 h after mating and used Qiagen´s Ingenuity Pathway Analysis to perform network modeling to identify the main mating-activated cellular processes in the endosalpinx and the possible upstream regulators of the mating-induced transcriptional response.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99398" }, "primaryId" : "GEO:GSE99398", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99398" } ] }, "title" : "Epigenetic effects of vitamin C on differentiation of neural stem cells", "dateAssigned" : "2017-05-30T00:00:00.000-05:00", "summary" : "Vitamin C, is an antioxidant that maintains the activity of iron and alpha-ketoglutarate-dependent dioxygenase. Vitamin C has been shown to enhance neuronal yields from cultured stem cells but the underlying molecular mechanisms are not yet elucidated. Interestingly, a few recent studies have shown that vitamin C induces widespread demethylation by activating Tet methylcytosine dioxygenase and jumonji C (JmjC) domain containing histone demethylase, suggesting an epigenetic regulation by vitamin C.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30005139" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99410" }, "primaryId" : "GEO:GSE99410", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99410" } ] }, "title" : "Micro RNA array analysis in OLETF, a type 2 diabetic rats, and LETO, a non-diabetic control rats", "dateAssigned" : "2017-05-30T00:00:00.000-05:00", "summary" : "AMP deaminase (AMPD) plays a crucial role in adenine nucleotide metabolism, and its upregulated activity contributes to diastolic dysfunction of the heart caused by type 2 diabetes mellitus (T2DM) via reduction of the adenine nucleotide pool. Here we examined the mechanism of AMPD upregulation by T2DM. The protein level of 90-kDa full-length AMPD3 was increased in whole myocardial lysates and in the sarcoplasmic reticulum (SR) fraction by 55% and 123%, respectively, in OLETF, a rat model of T2DM, compared to those in LETO, a non-diabetic control, though AMPD mRNA level was unchanged in OLETF. MicroRNA array analysis revealed downregulation (>50%) of 57 microRNAs in OLETF compared to those in LETO, among which miR-301b was predicted to interact with the 3’UTR of AMPD3 mRNA. The 90-kDa AMPD3 level was significantly increased by miR-301b inhibitor, but decreased by a miR-301b mimetic in H9c2 cells. A luciferase reporter assay indicated binding of miR-301b to the 3’UTR of AMPD3 mRNA. The results indicate that translational regulation by miR-301b mediates AMPD3 upregulation in the diabetic heart. Since ATP generated by SR-associated glycolytic enzymes contributes to Ca2+ uptake by SERCA2a, upregulated AMPD3 in the vicinity of the SR may be a therapeutic target for diabetic cardiomyopathy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99436" }, "primaryId" : "GEO:GSE99436", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99436" } ] }, "title" : "Transcriptomic study of NR8383 cells following exposure to multi-walled carbon nanotubes (NM401)", "dateAssigned" : "2017-05-30T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 0.17 µg/mL of multi-walled carbon nanotubes (NM401) (100 % cell viability). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99633" }, "primaryId" : "GEO:GSE99633", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99633" } ] }, "title" : "In vivo hyperoxia versus normoxia neonatal rat lung MSCs", "dateAssigned" : "2017-06-02T00:00:00.000-05:00", "summary" : "Background: Bronchopulmonary dysplasia (BPD), the most common complication of extreme preterm birth, can be caused by oxygen-related lung injury and is characterized by impaired alveolar and vascular development. Mesenchymal stromal cells (MSCs) have lung protective effects. Conversely, BPD is associated with increased MSCs in tracheal aspirates. Objective: To determine whether endogenous lung (L-)MSCs are perturbed in a well-established oxygen-induced rat model mimicking BPD features. Methods: Rat pups were exposed to room air or 95% oxygen from birth to postnatal day 10. On day 12, CD146+ L-MSCs were isolated and characterized according to the International Society for Cellular Therapy criteria. Epithelial and vascular repair potential were tested by scratch assay and endothelial network formation respectively, immune function by mixed lymphocyte reaction assay. Microarray analysis was performed using the Affymetrix GeneChip and gene set enrichment analysis (GSEA) software. Results: CD146+ L-MSCs isolated from rat pups exposed to hyperoxia had decreased CD73 expression and inhibited lung endothelial network formation. CD146+ L-MSCs indiscriminately promoted epithelial wound healing and limited T-cell proliferation. Expression of potent anti-angiogenic genes of the axonal guidance cue and CDC42 pathways was increased after in vivo hyperoxia, whereas genes of the anti-inflammatory JAK/STAT and lung/vascular growth promoting Fibroblast Growth Factor (FGF) pathways were decreased. Conclusions: In vivo hyperoxia exposure alters the pro-angiogenic effects and FGF expression of L-MSCs. Additionally, decreased CD73 and JAK/STAT expression suggest decreased immune function. L-MSC function may be perturbed and contribute to BPD pathogenesis. These findings may lead to improvements in manufacturing exogenous MSCs with superior repair capabilities.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99748" }, "primaryId" : "GEO:GSE99748", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99748" } ] }, "title" : "MEF2C Protein Isoform Transition to a Repressor Variant is Linked to Development of Heart Failure", "dateAssigned" : "2017-06-07T00:00:00.000-05:00", "summary" : "Objective: To identify if MEF2Cγ+ repressor variant has a role in the cardiac detrimental effects of MEF2C. Conclusions: We conclude that upregulation of MEF2Cγ+ in adult hearts causes cardiac pathogenic features through dysregulation of cell cycle and dedifferentiation of cardiomyocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31911274" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99997" }, "primaryId" : "GEO:GSE99997", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE99997" } ] }, "title" : "TiO2-induced gene expression profiles in rat lung: a subacute inhalation study.", "dateAssigned" : "2017-06-13T00:00:00.000-05:00", "summary" : "In this work we study the pulmonary toxicological properties of titanium dioxide using conventional and molecular toxicological approaches. For this, we exposed Fischer 344 rats by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks to a nanoaerosol of TiO2 (10 mg/m3). Lung samples have been collected up to 180 days after the end of exposure. Biochemical and cytological analyses of the broncho-alveolar lavage fluid (BALF) were performed. In addition, transcriptomic and proteomic approaches were realised in the lung and BALF respectively.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100021" }, "primaryId" : "GEO:GSE100021", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100021" } ] }, "title" : "IGF-1 gene therapy in aging rats modulates hippocampal genes relevant to memory function", "dateAssigned" : "2017-06-14T00:00:00.000-05:00", "summary" : "In rats, learning and memory performance decline during normal aging, which makes this rodent species a suitable model to evaluate therapeutic strategies. In aging rats, insulin-like growth factor-I (IGF-I), is known to significantly improve spatial memory accuracy as compared to control counterparts. A constellation of gene expression changes underlie the hippocampal phenotype of aging but no studies on the effects of IGF-I on the hippocampal transcriptome of old rodents have been documented. Here, we assessed the effects of IGF-I gene therapy on spatial memory performance in old female rats and compared them with changes in the hippocampal transcriptome.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28645186" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100122" }, "primaryId" : "GEO:GSE100122", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100122" } ] }, "title" : "Sex differences in gene regulation in the dorsal root ganglion after nerve injury", "dateAssigned" : "2017-06-16T00:00:00.000-05:00", "summary" : "Pain is a subjective experience derived from complex interactions among biological, environmental, and psychosocial pathways. Sex differences in pain sensitivity and chronic pain prevalence are well established. However, the molecular causes underlying these sex dimorphisms are poorly understood particularly with regard to the role of the peripheral nervous system. Here we sought to identify shared and distinct gene networks functioning in the peripheral nervous systems that may contribute to sex differences of pain after nerve injury. We performed RNA-seq on dorsal root ganglia following chronic constriction injury of the sciatic nerve in male and female rats. Analysis from paired naive and injured tissues showed that 1456 genes were differentially expressed between sexes. Appreciating sex-related gene expression differences and similarities in neuropathic pain models may help to improve the translational relevance to clinical populations and efficacy of clinical trials of this major health issue.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30782122" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100173" }, "primaryId" : "GEO:GSE100173", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100173" } ] }, "title" : "Hepatoprotective Effects of the Ethanolic Extracts of Propolis (EEP) on Alcohol induced Steatosis via Inhibition of Lipogenesis and Stimulation of Fatty Acid Oxidation in Rats", "dateAssigned" : "2017-06-19T00:00:00.000-05:00", "summary" : "Gene expression Array analysis has been an effective technique for exploring treatment-associated transcriptional changes in tissues. The main goal of this study is to explore the expression changes of transcripts in the liver tissue of rats which were treated with the ethanolic extraction of propolis (EEP) as well as alcohol. We aim to find a subset of genes which responded to the treatment of EEP and may be useful candidate genes in explaining the protective effects of EEP on fatty liver.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100177" }, "primaryId" : "GEO:GSE100177", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100177" } ] }, "title" : "Gene expression profiles in rat alveolar macrophages exposure to exfoliated graphene (EGr)", "dateAssigned" : "2017-06-19T00:00:00.000-05:00", "summary" : "To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the transcriptional level, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish characterization of physicochemical properties of exfoliated graphene (EGr).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100189" }, "primaryId" : "GEO:GSE100189", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100189" } ] }, "title" : "Gender differences of gene expression profiles in brain cardiovascular centers of SHRs [nucleus of solitarii tract]", "dateAssigned" : "2017-06-19T00:00:00.000-05:00", "summary" : "Arterial pressure (AP) is lower in pre-menopausal women than in men of similar age. Pre-menopausal women exhibit a lower sympathetic outflow and a greater baroreceptor reflex, however molecular mechanisms for the gender differences of AP regulation are still not well understood. Since the nucleus tractus solitarius (NTS), a pivotal region of the medulla oblongata for regulating the set-point of AP, is strongly associated with the AP level, we hypothesized that a different neuronal functions at the level of NTS between men and women could contribute to the gender difference in cardiovascular homeostasis. Since females Spontaneous Hypertensive Rats (SHRs) clearly exhibit lower AP levels than their male counterparts at similar age, we investigated whether the NTS of SHRs exhibit gender differences in gene expression by using microarray technique.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29373075" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100198" }, "primaryId" : "GEO:GSE100198", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100198" } ] }, "title" : "Gender differences of gene expression profiles in brain cardiovascular centers of SHRs [hypothalamus]", "dateAssigned" : "2017-06-19T00:00:00.000-05:00", "summary" : "Arterial pressure (AP) is lower in pre-menopausal women than in men of similar age. Pre-menopausal women exhibit a lower sympathetic outflow and a greater baroreceptor reflex, however molecular mechanisms for the gender differences of AP regulation are still not well understood. Since the hypothalmus is strongly functionnaly connected to the nucleus tractus solitarius (NTS), a pivotal region of the medulla oblongata for regulating the set-point of AP, we hypothesized that a different neuronal functions at the level of hypothalamus between men and women could contribute to the gender difference in cardiovascular homeostasis. Since females Spontaneous Hypertensive Rats (SHRs) clearly exhibit lower AP levels than their male counterparts at similar age, we investigated whether the hypothalamus of SHRs exhibit gender differences in gene expression by using microarray technique.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29373075" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100203" }, "primaryId" : "GEO:GSE100203", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100203" } ] }, "title" : "RNA sequencing analysis of the LEW versus BN rat, with or without T. gondii infection, in order to unravel molecular factors directing the robust and rapid early T. gondii-killing mechanisms in the LEW rat", "dateAssigned" : "2017-06-19T00:00:00.000-05:00", "summary" : "Compared to the uninfected BN rat, the uninfected LEW rat has inherently higher transcript levels of cytochrome enzymes [Cyp2d3, Cyp2d5 and Cybrd1 that catalyze generation of reactive oxygen species (ROS)], with concomitant higher levels of ROS.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100235" }, "primaryId" : "GEO:GSE100235", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100235" } ] }, "title" : "Circulating mRNA Profiles Differ between Qi-Deficiency and Yin deficiency in Ischemic Stroke Rats with Blood Stasis Syndrome", "dateAssigned" : "2017-06-20T00:00:00.000-05:00", "summary" : "This study was conducted to distinguish these two syndromes at transcriptomics level and explore the underlying mechanisms.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100280" }, "primaryId" : "GEO:GSE100280", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100280" } ] }, "title" : "Ras signaling inhibitors in in Adjuvant-induced Arthritis via targeting pathogenic antigen-specific Th17-type cells", "dateAssigned" : "2017-06-21T00:00:00.000-05:00", "summary" : "The Ras family of GTPases play an important role in signaling nodes downstream to T cell receptor and CD28 activation, potentially lowering the threshold for TCR activation by autoantigens. Somatic mutation in NRAS or KRAS may cause a rare autoimmune disorder coupled with abnormal expansion of lymphocytes. T cells from Rheumatoid Arthritis (RA) patients show excessive activation of Ras/MEK/ERK pathway. The small molecule farnesylthiosalicylic acid (FTS) interferes with the interaction between Ras GTPases and their prenyl-binding chaperones to inhibit proper plasma membrane localization. In the present study, we tested the therapeutic and immunomodulatory effects of FTS and its derivative 5-fluoro-FTS (F-FTS) in the rat adjuvant-induced arthritis model (AIA). We show that AIA severity was significantly reduced by oral FTS and F-FTS treatment compared to vehicle control treatment. FTS was as effective as the mainstay anti-rheumatic drug methotrexate, and combining the two drugs significantly increased efficacy compared to each drug alone. We also discovered that FTS therapy inhibited both the CFA-driven in vivo induction of Th17 and IL-17/IFN-g producing double positive as well as the upregulation of serum levels of the Th17-associated cytokines IL-17A and IL-22. By gene microarray analysis of effector CD4+ T cells from CFA-immunized rats, re-stimulated in vitro with the mycobacterium tuberculosis heat-shock protein 65 (Bhsp65), we determined that FTS abrogated the Bhsp65-induced transcription of a large list of genes (e.g. Il17a/f, Il22, Ifng, Csf2, Lta, and Il1a). The functional enrichment bioinformatics analysis showed significant overlap with predefined gene sets related to inflammation, immune system processes and autoimmunity. In Conclusions, FTS and F-FTS display broad immunomodulatory effects in AIA with inhibition of the Th17-type response to a dominant arthritogenic antigen. Hence, targeting Ras signal-transduction cascade is a potential novel therapeutic approach for RA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28736556" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100349" }, "primaryId" : "GEO:GSE100349", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100349" } ] }, "title" : "Detailing Novel Epigenetic Events Associated with Diet-Induced Obesity in the Rat", "dateAssigned" : "2017-06-22T00:00:00.000-05:00", "summary" : "We applied Whole Transcriptome Termini Site Sequencing (WTTS-seq) to detect differences in use of alternative polyadenylation sites between diet-induced obesity rats and control rats. Our finding clear showed that a nutritionally complete high fat diet would affect pre-translational alternative polyadenylation events on hypothalamic transcripts that both stimulate and counter regulate body weight.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31728018" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100355" }, "primaryId" : "GEO:GSE100355", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100355" } ] }, "title" : "Isolation and differential transcriptome of vascular smooth muscle cells and mid-capillary pericytes from the rat brain", "dateAssigned" : "2017-06-22T00:00:00.000-05:00", "summary" : "VSMC and mcPC were freshly isolated from the rat brain by magnetic-activated cell sorting and their transcriptome was analyzed by RNA-Seq", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30116021" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100366" }, "primaryId" : "GEO:GSE100366", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100366" } ] }, "title" : "Identification of candidate genes for generalized tonic–clonic seizures in Noda Epileptic Rat", "dateAssigned" : "2017-06-22T00:00:00.000-05:00", "summary" : "The Noda epileptic rat (NER) exhibits generalized tonic–clonic seizures (GTCS). A genetic linkage analysis demonstrated two GTCS-associated loci, Ner1 on Chr 1 and Ner3 on Chr 5. In single-locus congenic lines, neither wild-type Ner1 nor Ner3 allele suppressed GTCS, but both wild-type alleles suppressed GTCS when they were combined in double-locus congenic lines. Global expression analysis showed that Cckbr and St5 locating within Ner1 and Phf24 locating within Ner3 were significantly　downregulated. De novo BAC sequencing detected an insertion of an endogenous retrovirus sequence in intron 2 of the Phf24 gene in the NER genome. PHF24 protein was almost absent in the NER brain. It has been known that the Phf24 gene encodes Gαi-interacting protein which is involved in GABAB receptor signaling pathway. Together, we concluded that Cckbr, St5, and Phf24 were strong candidate genes for GTCS in NER.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28936718" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100410" }, "primaryId" : "GEO:GSE100410", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100410" } ] }, "title" : "Changes in the transcriptome, proteome and phosphoproteome in a cardiomyocyte model of nitroxidative stress", "dateAssigned" : "2017-06-23T00:00:00.000-05:00", "summary" : "We used a multi-omic approach to investigate different dynamics of transcripts, proteins and phosphoproteins during nitroxidative stress.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100454" }, "primaryId" : "GEO:GSE100454", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100454" } ] }, "title" : "Gene-Expression Based Measure of Chronic Stress Exposure", "dateAssigned" : "2017-06-26T00:00:00.000-05:00", "summary" : "Analysis of mRNA expression in the adrenal glands of rats from two different models of chronic stress: chronic shock (CS) and chronic variable stress (CVS)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30139969" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100499" }, "primaryId" : "GEO:GSE100499", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100499" } ] }, "title" : "Exploring acupuncture mechanism in preconditioning of IRI", "dateAssigned" : "2017-06-26T00:00:00.000-05:00", "summary" : "JJ group compared with the MX group, 703 differentially expressed genes were screened out, among which 542 were up-regulated and 161 genes were down-regulated; compared with DZ group, 1529 differentially expressed genes were screened, 1212 genes were up-regulated and 317 genes were down-regulated. KEGG Pathway analysis enriched the Wnt pathway, and screened 11 genes; among which 9 genes were up-regulated, including Wnt5b, Wnt9b, Wnt10b, Fzd2, Plch1, Plch2, dkkl1, Amer and Amer3, and 2 were down-regulated, including plcb1 and sapcd2.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100502" }, "primaryId" : "GEO:GSE100502", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100502" } ] }, "title" : "Hepatic transcriptomic alterations for N,N-dimethyl-p-toluidine (DMPT) and p-toluidine after 5-day exposure in rats", "dateAssigned" : "2017-06-26T00:00:00.000-05:00", "summary" : "A total of 511 gene transcripts were differentially expressed due to DMPT treatment and 354 gene transcripts were differentially expressed due to p-toluidine treatment (false discovery rate (FDR) < 0.05).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100505" }, "primaryId" : "GEO:GSE100505", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100505" } ] }, "title" : "Transcriptional Profiling Reveals Extraordinary Diversity Among Skeletal Muscle Tissues", "dateAssigned" : "2017-06-26T00:00:00.000-05:00", "summary" : "Skeletal muscles are a diverse family of highly specialized tissues that perform a wide array of physiological activities and maintain whole-body glucose metabolism and energy homeostasis. Functional diversity is a distinctive feature of muscle tissues, which demonstrate remarkable variability in their speed of contraction, metabolic profile, resistance to fatigue, and regenerative capacity. Unsurprisingly, many disorders of skeletal muscle afflict a remarkably specific subset of tissues, including muscular dystrophies, cancer cachexia, aging sarcopenia, and amyotrophic lateral sclerosis. Taken as a whole, these observations indicate that specific genetic programs establish and maintain physiological specialization of muscle tissues. Elucidating these genetic programs is essential to understanding muscle specialization and propensity for disease. Nevertheless, most global profiling studies performed to-date have not directly addressed intrinsic variability between different muscle tissues. This gap in the literature is particularly glaring for more sophisticated mechanisms of gene expression regulation such as circadian control, post-transcriptional regulation and non-coding RNA expression, despite their well-established roles in many disease mechanisms. In an effort to understand the variability present within specific skeletal muscles with respect to gene expression, our lab has performed RNA-Seq on a variety of skeletal muscle tissues.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29809149" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100540" }, "primaryId" : "GEO:GSE100540", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100540" } ] }, "title" : "The transcriptional response to unilateral nephrectomy with and without ischemia-reperfusion injury", "dateAssigned" : "2017-06-27T00:00:00.000-05:00", "summary" : "Array data was processed in the Affymetrix Console Software.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29267404" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100631" }, "primaryId" : "GEO:GSE100631", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100631" } ] }, "title" : "Transcriptome sequencing identified RNAs associated with renal fibrosis in UUO rat model (kidney)", "dateAssigned" : "2017-06-28T00:00:00.000-05:00", "summary" : "Renal fibrosis as the final outcome of many renal diseases, has always been paid more attention to by the researchers. To better understand whether lncRNAs could be a player in this process or be a biomarker for renal fibrosis diagnosis, we compared transcriptome sequencing data on renal tissues and urine respectively between UUO and shamed (Sham) rat model. Numerous genes including lncRNAs with significant changes in their expression were identified. 24 lncRNAs were up-regulated and 79 lncRNAs were down-regulated in the renal tissues of the UUO rats. 625 lncRNAs were up-regulated and 177 lncRNAs were down-regulated in urines of the UUO rats. Among the lncRNAs upregulated in renal tissue of UUO rats, 19 lncRNAs were predicted containing several conserved Smad3 binding motifs in the promoter. Among them, lncRNAs with putative promoter containing more than 4 conserved Smad3 binding motifs were demonstrated to be induced by TGF-β significantly in NRK-52E cells. We further confirmed that lncRNA TCONS_00088786 and TCONS_01496394 were regulated by TGF-β stimulation and also can influence the expression of some fibrosis-related genes through a feedback loop. Based on transcriptome sequencing data, bioinformatics analysis and qRT-PCR detection, we also demonstrated lncRNA in Urine are detectable and might be a novel biomarker of renal fibrosis. These data provide new information about the involvement of lncRNAs in renal fibrosis, indicating that they may serve as candidate biomarkers or therapeutic targets in the future.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28912732" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100632" }, "primaryId" : "GEO:GSE100632", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100632" } ] }, "title" : "Transcriptome sequencing identified RNAs associated with renal fibrosis in UUO rat model (urine)", "dateAssigned" : "2017-06-28T00:00:00.000-05:00", "summary" : "Renal fibrosis as the final outcome of many renal diseases, has always been paid more attention to by the researchers. To better understand whether lncRNAs could be a player in this process or be a biomarker for renal fibrosis diagnosis, we compared transcriptome sequencing data on renal tissues and urine respectively between UUO and shamed (Sham) rat model. Numerous genes including lncRNAs with significant changes in their expression were identified. 24 lncRNAs were up-regulated and 79 lncRNAs were down-regulated in the renal tissues of the UUO rats. 625 lncRNAs were up-regulated and 177 lncRNAs were down-regulated in urines of the UUO rats. Among the lncRNAs upregulated in renal tissue of UUO rats, 19 lncRNAs were predicted containing several conserved Smad3 binding motifs in the promoter. Among them, lncRNAs with putative promoter containing more than 4 conserved Smad3 binding motifs were demonstrated to be induced by TGF-β significantly in NRK-52E cells. We further confirmed that lncRNA TCONS_00088786 and TCONS_01496394 were regulated by TGF-β stimulation and also can influence the expression of some fibrosis-related genes through a feedback loop. Based on transcriptome sequencing data, bioinformatics analysis and qRT-PCR detection, we also demonstrated lncRNA in Urine are detectable and might be a novel biomarker of renal fibrosis. These data provide new information about the involvement of lncRNAs in renal fibrosis, indicating that they may serve as candidate biomarkers or therapeutic targets in the future.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28912732" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100641" }, "primaryId" : "GEO:GSE100641", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100641" } ] }, "title" : "DNA methylation reprogramming after spinal nerve injury", "dateAssigned" : "2017-06-29T00:00:00.000-05:00", "summary" : "Purpose: Nerve injury-induced hyperactivity of primary sensory neurons in the dorsal root ganglion (DRG) contributes critically to chronic pain development, but its underlying mechanisms remain incompletely understood. Chronic neuropathic pain has a clear epigenetic component, however, most studies so far have focused on histone modifications. We determined changes of DNA methylation in the rat DRG, spinal cord, and prefrontal cortex after spinal nerve ligation (SNL).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29875269" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100696" }, "primaryId" : "GEO:GSE100696", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE100696" } ] }, "title" : "Expression data from Csf1r deficient rats", "dateAssigned" : "2017-06-30T00:00:00.000-05:00", "summary" : "Spleen gene expression was compared to BMDM to identify splenic-specific genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30249809" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101012" }, "primaryId" : "GEO:GSE101012", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101012" } ] }, "title" : "Expression data from rat pituitary adenoma cells", "dateAssigned" : "2017-07-09T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying in treatment of CAB and BRC, and identified distinct classes of up-regulated genes during this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101112" }, "primaryId" : "GEO:GSE101112", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101112" } ] }, "title" : "Whole transcriptome analysis of brain hippocampal tissue from SAMP8 mice and rat primary neurons treated with the Alzheimer's disease drug candidates CMS121 and J147", "dateAssigned" : "2017-07-10T00:00:00.000-05:00", "summary" : "Alzheimer's disease (AD) drug discovery has rarely been addressed in the context of aging even though sporadic AD accounts for 99% of the cases. Phenotypic screens based upon old age-associated brain toxicities were used to develop the potent AD drug candidates CMS121 and J147. The aim of this project was to investigate whether these two different AD drug candidates prevented the progression of dementia in SAMP8 mice when administered at advanced stages of disease, and whether they shared common modes of action. These transcriptomic data are part of an integrative multi-omics approach that also investigated protein expression, metabolite levels as well as cognition. In addition, in order to further investigate the effect of the drugs in in vitro neuronal cultures, rat primary neurons were treated with the compounds and the transcriptome sequenced.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31742554" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101127" }, "primaryId" : "GEO:GSE101127", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101127" } ] }, "title" : "Seasoning ingredients in a medium fat diet regulate lipid metabolism [hypothalamus]", "dateAssigned" : "2017-07-11T00:00:00.000-05:00", "summary" : "Our results suggest that these ingredients may affect lipid homeostasis via the HP axis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101128" }, "primaryId" : "GEO:GSE101128", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101128" } ] }, "title" : "Seasoning ingredients in a medium fat diet regulate lipid metabolism [Liver]", "dateAssigned" : "2017-07-11T00:00:00.000-05:00", "summary" : "Our results suggest that these ingredients may affect lipid homeostasis via the HP axis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101129" }, "primaryId" : "GEO:GSE101129", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101129" } ] }, "title" : "Seasoning ingredients in a medium fat diet regulate lipid metabolism [WAT]", "dateAssigned" : "2017-07-11T00:00:00.000-05:00", "summary" : "Our results suggest that these ingredients may affect lipid homeostasis via the HP axis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101153" }, "primaryId" : "GEO:GSE101153", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101153" } ] }, "title" : "cAMP Signaling Regulates DNA Demethylation by Augmenting the Intracellular Labile Ferrous Iron Pool", "dateAssigned" : "2017-07-11T00:00:00.000-05:00", "summary" : "In this study we show that cAMP helps regulate cytosine demethylation through augmenting the intracellular labile ferrous iron pool.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29239726" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101337" }, "primaryId" : "GEO:GSE101337", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101337" } ] }, "title" : "Expression data of two single colony (No.4 and No.8) derived from C6 glioma", "dateAssigned" : "2017-07-12T00:00:00.000-05:00", "summary" : "The top 10 most-expressed genes in colony No. 8 were prkcb, postn, mpz, cd55, ct55, plxdc2, antxr1, fmr1nb, igfbp5", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101338" }, "primaryId" : "GEO:GSE101338", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101338" } ] }, "title" : "Expression data from C6 glioma and small molecule induced glial cells (SMiG)", "dateAssigned" : "2017-07-12T00:00:00.000-05:00", "summary" : "Gene ontology related to myelination and glial differentiation were significantly up-regulated in SMiG.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101634" }, "primaryId" : "GEO:GSE101634", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101634" } ] }, "title" : "Short-term in vitro culture of rat fetal testes with all-trans retinoic acid", "dateAssigned" : "2017-07-19T00:00:00.000-05:00", "summary" : "Retinoic acid exposure in cultured fetal testis has previously been demonstrated to have significant effects on the histology of the fetal testis in multiple species, as well as to alter the meiotic states of germ cells. However, previous experiments have not analyzed the mechanisms by which retinoic acid exposure leads to altered tubulogenesis and loss of seminiferous cord structure. This experiment demonstrated that retinoic acid exposure activated signaling pathways that promote the ovary development program and oppose normal testis development in mid-gestational rat fetal testes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101798" }, "primaryId" : "GEO:GSE101798", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101798" } ] }, "title" : "Next-Generation sequencing of the hippocampus transcriptome in aged and cognitive impaired rats", "dateAssigned" : "2017-07-24T00:00:00.000-05:00", "summary" : "The current study employed next generation RNA sequencing using two different platforms (Illumina and Ion Proton) to examine gene expression differences related to brain aging, cognitive decline, and hippocampus subregions (CA1, CA3, DG). Young and aged rats were trained on a spatial episodic memory task. The results describe regional differences in gene expression and point to regional differences in vulnerability to aging. Aging was associated with increased expression of immune response related genes, particularly in the dentate gyrus. For the memory task, impaired performance of aged animals was linked to the regulation of Ca2+ and synaptic function in region CA1. Finally, we provided a transcriptomic characterization of the three subregions regardless of age or cognitive status, highlighting and confirming a correspondence between cytoarchitectural boundaries and molecular profiling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29276487" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101844" }, "primaryId" : "GEO:GSE101844", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101844" } ] }, "title" : "Integrated metabolic models for xenobiotic induced mitochondrial toxicity in skeletal muscle (compound 177 experiments)", "dateAssigned" : "2017-07-25T00:00:00.000-05:00", "summary" : "There is a need for robust in vitro models to sensitively capture skeletal muscle adverse toxicities early in the research and development of novel xenobiotics. To this end, an in vitro rat skeletal muscle model (L6) was used to study the translation of transcriptomics data generated from an in vivo rat model. Novel sulfonyl isoxazoline herbicides were associated with skeletal muscle toxicity in an in vivo rat model. Gene expression pathway analysis on skeletal muscle tissues taken from in vivo repeat dose studies identified enriched pathways associated with mitochondrial dysfunction, oxidative stress, energy metabolism, protein regulation and cell cycle. Mitochondrial dysfunction and oxidative stress were further explored in an in vitro L6 model. This model demonstrated that the sulfonyl isoxazoline compounds induced mitochondrial dysfunction, mitochondrial superoxide production and apoptosis. These in vitro findings accurately concurred with the in vivo transcriptomics data, thereby confirming the ability of the L6 skeletal muscle model to identify relevant in vivo mechanisms of xenobiotic-induced toxicity. Moreover, these results highlight the sensitivity of the L6 galactose media model to study mitochondrial perturbation associated with skeletal muscle toxicity; this model may be utilised to rank the potency of novel xenobiotics upon further validation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101845" }, "primaryId" : "GEO:GSE101845", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101845" } ] }, "title" : "Integrated metabolic models for xenobiotic induced mitochondrial toxicity in skeletal muscle (compound 197 experiments)", "dateAssigned" : "2017-07-25T00:00:00.000-05:00", "summary" : "There is a need for robust in vitro models to sensitively capture skeletal muscle adverse toxicities early in the research and development of novel xenobiotics. To this end, an in vitro rat skeletal muscle model (L6) was used to study the translation of transcriptomics data generated from an in vivo rat model. Novel sulfonyl isoxazoline herbicides were associated with skeletal muscle toxicity in an in vivo rat model. Gene expression pathway analysis on skeletal muscle tissues taken from in vivo repeat dose studies identified enriched pathways associated with mitochondrial dysfunction, oxidative stress, energy metabolism, protein regulation and cell cycle. Mitochondrial dysfunction and oxidative stress were further explored in an in vitro L6 model. This model demonstrated that the sulfonyl isoxazoline compounds induced mitochondrial dysfunction, mitochondrial superoxide production and apoptosis. These in vitro findings accurately concurred with the in vivo transcriptomics data, thereby confirming the ability of the L6 skeletal muscle model to identify relevant in vivo mechanisms of xenobiotic-induced toxicity. Moreover, these results highlight the sensitivity of the L6 galactose media model to study mitochondrial perturbation associated with skeletal muscle toxicity; this model may be utilised to rank the potency of novel xenobiotics upon further validation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101916" }, "primaryId" : "GEO:GSE101916", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101916" } ] }, "title" : "Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia [Rat ATAC-Seq]", "dateAssigned" : "2017-07-26T00:00:00.000-05:00", "summary" : "Determination of the molecular properties of genetically targeted cell types has led to fundamental insights into mouse brain function and dysfunction. Here, we report an efficient strategy for precise exploration of gene expression events in specific cell types in a broad range of species. We demonstrate that classically defined, homologous neuronal and glial cell types differ between rodent and human by the expression of hundreds of orthologous, cell specific genes. Confirmation that these genes are differentially active was obtained using epigenetic mapping, quantitative PCR, and immunofluorescence localization. Studies of sixteen human postmortem brains revealed cell-specific molecular responses to aging, and the induction of a shared, robust response to an unknown external event experienced by three donors. Our data establish a comprehensive approach for analysis of unique molecular events associated with specific circuits and cell types in a wide variety of human conditions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30320555" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101917" }, "primaryId" : "GEO:GSE101917", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101917" } ] }, "title" : "Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia [RAT RNA-Seq]", "dateAssigned" : "2017-07-26T00:00:00.000-05:00", "summary" : "Determination of the molecular properties of genetically targeted cell types has led to fundamental insights into mouse brain function and dysfunction. Here, we report an efficient strategy for precise exploration of gene expression events in specific cell types in a broad range of species. We demonstrate that classically defined, homologous neuronal and glial cell types differ between rodent and human by the expression of hundreds of orthologous, cell specific genes. Confirmation that these genes are differentially active was obtained using epigenetic mapping, quantitative PCR, and immunofluorescence localization. Studies of sixteen human postmortem brains revealed cell-specific molecular responses to aging, and the induction of a shared, robust response to an unknown external event experienced by three donors. Our data establish a comprehensive approach for analysis of unique molecular events associated with specific circuits and cell types in a wide variety of human conditions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30320555" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101933" }, "primaryId" : "GEO:GSE101933", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE101933" } ] }, "title" : "Evolution of an X-linked miRNA family predominately expressed in mammalian male germ cells", "dateAssigned" : "2017-07-26T00:00:00.000-05:00", "summary" : "microRNAs (miRNAs) are important post-transcriptional regulators of gene expression. However, comprehensive expression profiles of miRNAs during spermatogenesis in mammals is lacking. In the present study, we sequenced small RNAs in highly purified spermatogonial stem cells (SSCs), spermatocytes in the pre-leptotene, leptotene, zygotene and pachytene stages, haploid round spermatids and spermatozoa. We found that a family of X-linked miRNAs, named spermiRs, is predominantly expressed in spermatogonia and early meiotic phases. Profiling of small RNAs in different mammalian tissues revealed a conserved high expression pattern of spermiRs in testes. spermiR appears to originate from THER1 in marsupial, a retrotransposon that is extinct in current mammals. It has expanded rapidly and has diversified into two clusters, spermiR-L and spermiR-R, by tandem duplication, which was partially mediated by flanking retrotransposable elements. Notably, despite the highly frequent lineage-specific duplication events, all spermiR family members are strictly located between two conserved protein coding genes, Slitrk2 and Fmr1. Intriguingly, spermiR-Ls and spermiR-Rs have evolved different expression preferences during spermatogenesis in different mammals. Moreover, the sequences of spermiRs and their precursors, including the seed regions, are highly divergent within and among mammals. However, their target genes are largely overlapping in male reproduction-related pathways. When miR-741, the most highly expressed spermiRs during mouse spermatogenesis, was knocked out in SSCs, another spermiR, miR-465, was dramatically up-regulated and became the most abundant one, indicating functional compensation between spermiR family members. All these observations indicate a strong co-evolution between spermiRs and their targets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30649414" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102003" }, "primaryId" : "GEO:GSE102003", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102003" } ] }, "title" : "GLP-1 induced transcriptomic profile in INS-1 cells", "dateAssigned" : "2017-07-28T00:00:00.000-05:00", "summary" : "Conclusion: GLP-1 has a varied effect on the transcriptomic profile of INS-1 cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102015" }, "primaryId" : "GEO:GSE102015", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102015" } ] }, "title" : "Ozone-Induced Vascular Contractility and Pulmonary Injury are Differentially Impacted by Diets Enriched with Coconut Oil, Fish Oil, and Olive Oil", "dateAssigned" : "2017-07-28T00:00:00.000-05:00", "summary" : "Fish oil, olive oil, and coconut oil dietary supplementation have several cardioprotective benefits, but it is not established if they can protect against air pollution-induced adverse effects. We hypothesized that these dietary supplements would attenuate ozone-induced systemic and pulmonary effects. Male Wistar Kyoto rats were fed either a normal diet, or a diet enriched with fish, olive, or coconut oil starting at 4 weeks of age for 8 weeks. Animals were then exposed to air or ozone (0.8 ppm), 4h/day for 2 consecutive days. The fish oil diet completely abolished phenylephrine-induced vasoconstriction that was increased following ozone exposure in the animals fed all other diets. Only the fish oil diet increased baseline levels of bronchoalveolar lavage fluid (BALF) markers of lung injury and inflammation. Ozone-induced pulmonary injury/inflammation were comparable in rats on normal, coconut oil, and olive oil diets with altered expression of markers in animals fed the fish oil diet. Fish oil, regardless of exposure, led to enlarged, foamy macrophages in the BALF that coincided with decreased mRNA expression of cholesterol transporters, cholesterol receptors, and nuclear receptors in the lung. Serum miRNA profile was assessed using small RNA-sequencing in normal and fish oil groups and demonstrated marked depletion of a variety of miRNAs, several of which were of splenic origin. No ozone-specific changes were noted. Collectively, these data indicate that while fish oil offered protection from ozone-induced aortic vasoconstriction, it increased pulmonary injury/inflammation and impaired lipid transport mechanisms resulting in foamy macrophage accumulation, demonstrating the need to be cognizant of potential off-target pulmonary effects that might offset the overall benefit of this vasoprotective dietary supplement.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29329427" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102054" }, "primaryId" : "GEO:GSE102054", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102054" } ] }, "title" : "FFK506-Binding Protein 12.6/1b, a negative regulator of [Ca2+], rescues memory and restores genomic regulation in the hippocampus of aging rats", "dateAssigned" : "2017-07-31T00:00:00.000-05:00", "summary" : "Hippocampal overexpression of FK506-binding protein 12.6/1b (FKBP1b), a negative regulator of ryanodine receptor Ca2+ release, reverses aging-induced memory impairment and neuronal Ca2+ dysregulation. Here, we test the hypothesis that FKBP1b also can protect downstream transcriptional networks from aging-induced dysregulation. We gave hippocampal microinjections of FKBP1b-expressing viral vector to male rats at either 13-months-of-age (long-term) or 19-months-of-age (short-term) and tested memory performance in the Morris water maze at 21-months-of-age. Aged rats treated short- or long-term with FKBP1b substantially outperformed age-matched vector controls and performed similarly to each other and young controls. Transcriptional profiling in the same animals identified 2342 genes whose hippocampal expression was up-/down-regulated in aged controls vs. young controls (the aging effect). Of these aging-dependent genes, 876 (37%) also showed altered expression in aged FKBP1b-treated rats compared to aged controls, with FKBP1b restoring expression of essentially all such genes (872/876, 99.5%) in the direction opposite the aging effect and closer to levels in young controls. This inverse relationship between the aging and FKBP1b effects suggests that the aging effects arise from FKBP1b deficiency. Functional category analysis revealed that genes downregulated with aging and restored by FKBP1b associated predominantly with diverse brain structure categories, including cytoskeleton, membrane channels and extracellular region. Conversely, genes upregulated with aging but not restored by FKBP1b associated primarily with glial-neuroinflammatory, ribosomal and lysosomal categories. Immunohistochemistry confirmed aging-induced rarefaction, and FKBP1b-mediated restoration, of neuronal microtubular structure. Thus, a previously-unrecognized genomic network modulating diverse brain structural processes is dysregulated by aging and restored by FKBP1b overexpression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29255009" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102071" }, "primaryId" : "GEO:GSE102071", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102071" } ] }, "title" : "A diet enriched with low or high molecular weight oat beta-glucans on blood inflammatory and oxidative stress status in rats with LPS-induced enteritis", "dateAssigned" : "2017-07-31T00:00:00.000-05:00", "summary" : "The aim of this study was to evaluate the ability of a diet enriched with two types of oat beta-glucans on inflammatory and oxidative stress status in blood cells in rats with LPS-induced enteritis", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102082" }, "primaryId" : "GEO:GSE102082", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102082" } ] }, "title" : "Evaluating the relative potency and mechanism of action of azoles in the rat Whole Embryo Culture", "dateAssigned" : "2017-07-31T00:00:00.000-05:00", "summary" : "We evaluated the effect of azoles on embryonic development in the rat whole embryo culture (WEC). Using the total morphological scoring system (TMS), we calculated the effective dose for 10% decrease in TMS. We collected transcriptomics data for rat WEC exposed to azoles at their ID10 for 4 hours. Results revealed shared expressions responses in genes involved in the retinoic acid (RA) and sterol biosynthesis pathways, which are respectively representatives of developmental toxicity and desired fungicidal action of the azoles. Azoles with more pronounced effects on the regulation of RA-associated genes were generally characterized as more potent embryotoxicants.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28970091" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102194" }, "primaryId" : "GEO:GSE102194", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102194" } ] }, "title" : "Gene expression alternations in liraglutide treated rats cardiac muscle", "dateAssigned" : "2017-08-03T00:00:00.000-05:00", "summary" : "Diabetic rats changes gene exprssion in liraglutide treated rats cardiac muscle", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29440457" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102195" }, "primaryId" : "GEO:GSE102195", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102195" } ] }, "title" : "miRNA expression alterations in vildagliptin treated rats arota", "dateAssigned" : "2017-08-03T00:00:00.000-05:00", "summary" : "vildagliptin may distrub miRNA expression in diabetic rats arota", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102196" }, "primaryId" : "GEO:GSE102196", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102196" } ] }, "title" : "Gene expression alternations in vildagliptin treated rats arota", "dateAssigned" : "2017-08-03T00:00:00.000-05:00", "summary" : "Diabetic rats changes gene exprssion in vildagliptin treated rats arota", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102198" }, "primaryId" : "GEO:GSE102198", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102198" } ] }, "title" : "miRNA expression alterations in liraglutide treated rats arota", "dateAssigned" : "2017-08-03T00:00:00.000-05:00", "summary" : "liraglutide may distrub miRNA expression in diabetic rats arota", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102217" }, "primaryId" : "GEO:GSE102217", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102217" } ] }, "title" : "The effect of obestatin contained in the breast milk on the structural and functional development of the offspring in the early postnatal period", "dateAssigned" : "2017-08-03T00:00:00.000-05:00", "summary" : "Recent studies indicated that obestatin may play a regulatory role in the development of gastrointestinal track in the early postnatal period. The project aimed to understand the effect of obestatin in the development of structure and function ot he small intestine in the early postnatal period. Results shown that enteral administration of obestatin to suckling rats significanlty effects on activity of brush border enzymes, morphometry of intestinal wall as well as small intestinal epithelial renewal. The effect of observed changes was dependent on the segment of intestine studied. Significant changes in the transcriptomic gene profile were founded both in the middle part of intestine and stomach", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102350" }, "primaryId" : "GEO:GSE102350", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102350" } ] }, "title" : "Substrate stiffness-dependent gene expression profile for cortical neurons", "dateAssigned" : "2017-08-08T00:00:00.000-05:00", "summary" : "We undertook mRNA microarray and gene ontology analyses to screen out substrate stiffness-dependent genes. Total mRNA were extracted from E17 cortical neurons grown on soft or stiff substrates at 5 or 16 hr time points. We identified 114 differentially-expressed mRNA transcripts in cells grown on 0.1 kPa and 20 kPa gels at the 5 hr time-point. Among them, 66 were upregulated in 0.1 kPa gel cultures and the remainder were downregulated (compared to cells grown on stiffer substrates). The expressions of three endocytic genes (Cltc, Dab2, and Myo6) and four adhesion genes(Vcl, Robo2, Nrcam, and Cad11) were confirmed by QGP and smRNA FISH.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29271742" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102458" }, "primaryId" : "GEO:GSE102458", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102458" } ] }, "title" : "MicroRNA-19a-PTEN axis is involved in the developmental decline of axon regenerative capacity in retinal ganglion cells", "dateAssigned" : "2017-08-09T00:00:00.000-05:00", "summary" : "Irreversible blindness from glaucoma and optic neuropathies is attributed to retinal ganglion cells (RGCs) losing the ability to regenerate axons. While several transcription factors and proteins have demonstrated enhancement of axon regeneration after optic nerve injury, mechanisms contributing to the age-related decline in axon regenerative capacity remains elusive. Here, we show that microRNAs are differentially expressed during RGC development, and identify microRNA-19a (miR-19a) as a heterochronic marker; developmental decline of miR-19a relieves suppression of PTEN, a key regulator of axon regeneration, and serves as a temporal indicator of decreasing axon regenerative capacity. Intravitreal injection of miR-19a promotes axon regeneration after optic nerve crush in adult mice, and increases axon extension in RGCs isolated from aged human donors. This uncovers a previously unrecognized involvement of the miR-19a-PTEN axis in RGC axon regeneration, and demonstrates therapeutic potential of microRNA-mediated restoration of axon regenerative capacity via intravitreal injection in patients with optic neuropathies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32599451" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102471" }, "primaryId" : "GEO:GSE102471", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102471" } ] }, "title" : "Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression", "dateAssigned" : "2017-08-09T00:00:00.000-05:00", "summary" : "We report gene expression profiles in the medial basal hypothalami of 28-day-old female rats infected with a lentivirus construct that overexpresses EED and matched controls infected with a GFP-expression construct.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102523" }, "primaryId" : "GEO:GSE102523", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102523" } ] }, "title" : "Microarray expression profile of circular RNAs in lung tissues from rats with lipopolysaccharide-induced acute respiratory distress syndrome", "dateAssigned" : "2017-08-11T00:00:00.000-05:00", "summary" : "Acute respiratory distress syndrome (ARDS) remains a common and devastating syndrome. CircRNAs are crucial in a variety of diseases and can provide new potential diagnostic and therapeutic targets for disease. The development of circular RNA (circRNA) microarray has facilitated the study of the role of circRNAs in regulating gene expression. This research was designed to explore the expression profile of circRNAs in lung tissues from rats with lipopolysaccharide-induced ARDS. Our findings indicate that the expression profiles of circRNAs has changed in ARDS as compared with normal rat lung tissue, and may provide novel insight into the molecular mechanism underlying the disease and potential novel diagnostic or therapeutic targets for ARDS.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29085873" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102529" }, "primaryId" : "GEO:GSE102529", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102529" } ] }, "title" : "Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families [ATAC-Seq]", "dateAssigned" : "2017-08-11T00:00:00.000-05:00", "summary" : "We used a differential open chromatin approach, coupled with active enhancer mark ,transcriptomic and computational TFs binding analysis to map cell-type-specific active enhancers in cardiac fibroblasts and cardiomyocytes, and outline the TFs that control them. We identified Tead, Sox9, Smad, Tcf, Meis, Rbpj, and Runx1 as the main cardiac fibroblasts TF groups. Our analysis shows that in cardiomyocytes and cardiac fibroblasts, distal enhancers, containing concentrated combinatorial clusters of multiple tissue expressed TFs recognition motifs, are combinatorically clustered around tissue specific genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102530" }, "primaryId" : "GEO:GSE102530", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102530" } ] }, "title" : "Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families [ChIP-Seq]", "dateAssigned" : "2017-08-11T00:00:00.000-05:00", "summary" : "We used a differential open chromatin approach, coupled with active enhancer mark ,transcriptomic and computational TFs binding analysis to map cell-type-specific active enhancers in cardiac fibroblasts and cardiomyocytes, and outline the TFs that control them. We identified Tead, Sox9, Smad, Tcf, Meis, Rbpj, and Runx1 as the main cardiac fibroblasts TF groups. Our analysis shows that in cardiomyocytes and cardiac fibroblasts, distal enhancers, containing concentrated combinatorial clusters of multiple tissue expressed TFs recognition motifs, are combinatorically clustered around tissue specific genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102531" }, "primaryId" : "GEO:GSE102531", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102531" } ] }, "title" : "Enhancer analysis of rat cardiac myocytes and fibroblasts reveals a collaborative control by transcription factor families [RNA-Seq]", "dateAssigned" : "2017-08-11T00:00:00.000-05:00", "summary" : "We used a differential open chromatin approach, coupled with active enhancer mark ,transcriptomic and computational TFs binding analysis to map cell-type-specific active enhancers in cardiac fibroblasts and cardiomyocytes, and outline the TFs that control them. We identified Tead, Sox9, Smad, Tcf, Meis, Rbpj, and Runx1 as the main cardiac fibroblasts TF groups. Our analysis shows that in cardiomyocytes and cardiac fibroblasts, distal enhancers, containing concentrated combinatorial clusters of multiple tissue expressed TFs recognition motifs, are combinatorically clustered around tissue specific genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102546" }, "primaryId" : "GEO:GSE102546", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102546" } ] }, "title" : "Integrative analysis of the genomic architecture of a complex kidney damage QTL in inbred hypertensive rats implies Tmem63c for translational research", "dateAssigned" : "2017-08-11T00:00:00.000-05:00", "summary" : "Despite recent advances in genomics, the identification of genes underlying complex diseases remains challenging. Inbred rat strains offer well-established experimental models to support the identification of susceptibility genes for diseases such as kidney damage associated with elevated blood pressure or hypertension. Here, we combined quantitative trait locus (QTL) mapping in two contrasting inbred rat strains with targeted next generation sequencing (NGS), compartment-specific transcriptome sequencing (RNA-Seq), and phenotype directed follow-up translational analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30900988" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102609" }, "primaryId" : "GEO:GSE102609", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102609" } ] }, "title" : "JIP1 knockout in PE and TSA treated NRVMS", "dateAssigned" : "2017-08-14T00:00:00.000-05:00", "summary" : "Jip1 was knocked out in neonatal rat ventricular myocytes in the presence of phenylephrine and trichostatin a", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28886967" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102770" }, "primaryId" : "GEO:GSE102770", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102770" } ] }, "title" : "Sequencing facilitates quantitative analysis of transcriptomes in wild type and Lrp6-knockdown cells", "dateAssigned" : "2017-08-17T00:00:00.000-05:00", "summary" : "Results and conclusions: We detected a substantial number of Lrp6 loss-induced AS events, and up to nearly 50 of them were exon-skipped. A gene ontology analysis of the conserved LRP6-driven network showed enrichment for ninety-four genes encoding proteins mainly involved in cellular and metabolic processes . Among them, a decade of genes with LRP6-dependent isoform expression showed identical splicing patterns on the exon level across species. The RNA sequencing results were further verified by Semiquantitative PCR. We conclude that LRP6 could regulate mRNA splicing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30070011" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102811" }, "primaryId" : "GEO:GSE102811", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102811" } ] }, "title" : "Leptin and fractalkine: Novel subcutaneous cytokines in burn injury.", "dateAssigned" : "2017-08-18T00:00:00.000-05:00", "summary" : "Burn injury remains a major clinical challenge to both survival and to quality of life. Its progressive, aberrant inflammation underlies the lethal dysfunction of various organs and the pain it induces is excruciating and notoriously difficult to manage. While it is known that burn injury’s complex local and disseminating pathology is orchestrated from the burned tissue, few studies have sought to characterise the local signalling environment. An enhanced understanding of the local and acutely temporally-dynamic processes defining burn injury and its progression is required for the development of novel therapeutic interventions. Microdialysis was used as an interstitial sampling technique, conducted over three hours post-burn. Samples were analysed by metabolomics and a multiplex cytokine immunoassay. Next-Generation sequencing libraries of the burn and control microdialysis sites were prepared to measure transcriptional changes potentially underlying the interstitial profile characterising burn injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102868" }, "primaryId" : "GEO:GSE102868", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102868" } ] }, "title" : "Gene expression profiling in rat liver after H2 administration with or without dietary stress", "dateAssigned" : "2017-08-21T00:00:00.000-05:00", "summary" : "Molecular hydrogen (H2) is a biologically active gas that is used medically to ameliorate various systemic pathological conditions. H2 also regulates gene expression involved in intracellular signaling and metabolic pathways. Therefore, we attempted to identify genes that exhibit similar changes in expression in response to H2 by employing DNA microarrays and gene set enrichment analysis. We found that H2 activated the expression of sets of genes regulated by histone H3K27 methylation status. H2 also modified the expression of many genes regulated by a wide variety of signaling pathways.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28890349" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102946" }, "primaryId" : "GEO:GSE102946", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102946" } ] }, "title" : "Cannabinoid Modulation of Eukaryotic Initiation Factors (eIF2α and eIF2B1) and Behavioral Cross-Sensitization to Cocaine in Adolescent Rats", "dateAssigned" : "2017-08-22T00:00:00.000-05:00", "summary" : "Reduced eukaryotic Initiation Factor 2 (eIF2)α phosphorylation (p-eIF2α) enhances protein synthesis, memory formation, and addiction-like behaviors. However, p-eIF2α has not been examined with regard to psychoactive cannabinoids and cross-sensitization. Here, we find that a cannabinoid receptor agonist (WIN 55,212-2 mesylate [WIN]) reduced p-eIF2α in vitro by upregulating GADD34 (PPP1R15A), the recruiter of protein phosphatase 1 (PP1). The induction of GADD34 was linked to ERK/CREB signaling and to CREB-binding protein (CBP)-mediated histone hyperacetylation at the Gadd34 locus. In vitro, WIN also upregulated eIF2B1, an eIF2 activator subunit. We next found that WIN administration in vivo reduced p-eIF2α in the nucleus accumbens of adolescent, but not adult, rats. By contrast, WIN increased dorsal striatal levels of eIF2B1 and ΔFosB among both adolescents and adults. In addition, we found cross-sensitization between WIN and cocaine only among adolescents. These findings show that cannabinoids can modulate eukaryotic initiation factors, and they suggest a possible link between p-eIF2α and the gateway drug properties of psychoactive cannabinoids.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29539420" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102964" }, "primaryId" : "GEO:GSE102964", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE102964" } ] }, "title" : "Novel targets in injured cord in an obese SCI rat model", "dateAssigned" : "2017-08-23T00:00:00.000-05:00", "summary" : "In the present study, we sought to understand the impact of obesity/metabolic disease (high-fat induced) on spinal cord injury (SCI) by examining transcriptome. Adult, male Long Evans rats received either thoracic level contusion of the spinal cord or sham laminectomy and then were allowed to recover on normal rat chow for 4 weeks and further on HFD for an additional 8 weeks. Spinal cord tissues harvested from the rats were processed for Affymetrix microarray and further transcriptomic analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28821567" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103011" }, "primaryId" : "GEO:GSE103011", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103011" } ] }, "title" : "Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics", "dateAssigned" : "2017-08-23T00:00:00.000-05:00", "summary" : "Prostate organogenesis involves epithelial growth in response to inductive signalling from specialised subsets of mesenchyme. To identify regulators and morphogens active in mesenchyme, we performed transcriptomic analysis using Tag-seq, RNA-seq, and single cell RNA-seq and defined new mesenchymal subsets and markers. We documented transcript expression using Tag-seq and RNA-seq in female rat Ventral Mesenchymal Pad (VMP) as well as adjacent urethra comprised of smooth muscle and peri-urethral mesenchyme. Transcripts enriched in VMP were identified in Tag-seq data from microdissected tissue, and RNA-seq data derived from cell populations and single cells. We identified 400 transcripts as enriched or specific to the VMP using bio-informatic comparisons of Tag-seq and RNA-seq data. Comparison with single cell RNA-seq identified transcripts yielded 45 transcriptscommon to both approaches. Cell subset analysis showed that VMP and adjacent mesenchyme were composed of distinct cell types and that each tissue was comprised of two subgroups. Markers for these subgroups were highly subset specific. Thirteen transcripts were validated by qPCR to confirm cell specific expression in microdissected tissues, as well as expression in neonatal prostate. Immunohistochemical staining demonstrated that Ebf3 and Meis2 showed a restricted expression pattern in VMP condensed mesenchyme. Taken together, we demonstrate that the VMP shows limited cellular heterogeneity and that our high-resolution transcriptomic analysis identified new mesenchymal subset markers associated with prostate organogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29180763" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103020" }, "primaryId" : "GEO:GSE103020", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103020" } ] }, "title" : "Progressive kidney disease is suppressed by a small molecule inhibitor of TRPC5", "dateAssigned" : "2017-08-23T00:00:00.000-05:00", "summary" : "Conclusions: In short, the in vivo gene expression profiles support a Rac1-TRPC5 disease-promoting pathway in proteinuric kidney disease that is reversed by treatment with AC1903.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29217578" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103039" }, "primaryId" : "GEO:GSE103039", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103039" } ] }, "title" : "RNA-seq analysis of in vivo differentiated and dedifferentiated mouse Schwann cells", "dateAssigned" : "2017-08-24T00:00:00.000-05:00", "summary" : "Schwann cells were acultely purified from intact nerves and the bridge and distal regions of transected nerves at different time-points following transection and sequenced to determine gene expression profiles of the differentiated and dedifferentiated state and its regulation by the wound microenvironment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28957681" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103065" }, "primaryId" : "GEO:GSE103065", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103065" } ] }, "title" : "RNA-seq of Wistar-rat skin from young and old animals", "dateAssigned" : "2017-08-24T00:00:00.000-05:00", "summary" : "Comparison of gene expression level by Illumina sequencing of rat skin from young and old animals. We identified differentially expressed genes and provide functional profiles, which give insights into the aging process of short-lived rodents.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28916632" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103109" }, "primaryId" : "GEO:GSE103109", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103109" } ] }, "title" : "Expression data from renal cortexes of diabetic rats", "dateAssigned" : "2017-08-25T00:00:00.000-05:00", "summary" : "We used microarray data to study the effect of transgenic renal AT2R overexpression on the renal expression profile at early stages of diabetes", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103110" }, "primaryId" : "GEO:GSE103110", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103110" } ] }, "title" : "Effect of 20% fructose feeding and dietary salt on RNA expression in the renal cortex of rats", "dateAssigned" : "2017-08-25T00:00:00.000-05:00", "summary" : "Elevated fructose consumption has been associated with metabolic and renal diseases. It is controversial whether kidney problems are a result of systemic metabolic disease or stem, at least in part, from changes due to local fructose metabolism. To study the short-term effect of fructose on genetic programs in renal proximal tubules, the diet for rats in experimental groups was supplemented for 7 days with 20% fructose in the drinking water. Two sets of 8 rats each on different baseline rodent diets were used in this study. 4 animals of each set received fructose in the drinking water while the other 4 served as controls. Animals were sacrificed after the experimental period of 7 days and slices of superficial kidney cortex were used for total RNA extraction. The RNA was analyzed with Affymetrix RaGene-2_0-st.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30067804" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103151" }, "primaryId" : "GEO:GSE103151", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103151" } ] }, "title" : "Temporal expression profiling of Arterial Remodeling in Rats", "dateAssigned" : "2017-08-28T00:00:00.000-05:00", "summary" : "We explored the global expression profile of the arterialized rat jugular vein to identify candidate genes and cellular pathways underlying the arterialization remodeling process.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30717394" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103167" }, "primaryId" : "GEO:GSE103167", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103167" } ] }, "title" : "The renoprotective effects of soy protein in the aging kidney.", "dateAssigned" : "2017-08-28T00:00:00.000-05:00", "summary" : "Late-life intervention with a soy-enriched diet attenuated age-dependent changes in renal structure and dysfunction in male Fischer 344 rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103266" }, "primaryId" : "GEO:GSE103266", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103266" } ] }, "title" : "Rat Rotator Cuff Tear RNASeq", "dateAssigned" : "2017-08-30T00:00:00.000-05:00", "summary" : "Myosteatosis is the pathological accumulation of lipid that occurs in conjunction with atrophy and fibrosis following skeletal muscle injury or disease. Little is known about the mechanisms by which lipid accumulates in myosteatosis, but many studies have demonstrated the degree of lipid infiltration negatively correlates with muscle function and regeneration. Our goal was to identify biochemical pathways that lead to muscle dysfunction and lipid accumulation in injured rotator cuff muscles, a model that demonstrates severe myosteatosis. Adult rats were subjected to a massive tear to the rotator cuff musculature. After a period of either 0 (healthy control), 10, 30, or 60 days, muscles were prepared for RNA sequencing, shotgun lipidomics, metabolomics, biochemical measures, electron microscopy, and muscle fiber contractility. Following rotator cuff injury, there was a decrease in muscle fiber specific force production that was lowest at 30d. There was a dramatic time dependent increase in triacylglyceride content. Interestingly, genes related to not only triacylglyceride synthesis, but also lipid oxidation were largely downregulated over time. Using bioinformatics techniques, we identified that biochemical pathways related to mitochondrial dysfunction and reactive oxygen species were considerably increased in muscles with myosteatosis. Long chain acyl-carnitines and L-carnitine, precursors to beta-oxidation, were depleted following rotator cuff tear. Electron micrographs showed injured muscles displayed large lipid droplets within mitochondria at early time points, and an accumulation of peripheral segment mitochondria at all time points. Several markers of oxidative stress were elevated following rotator cuff tear. The results from this study suggest that the accumulation of lipid in myosteatosis is not a result of canonical lipid synthesis, but occurs due to decreased lipid oxidation in mitochondria. A failure in lipid utilization by mitochondria would ultimately cause an accumulation of lipid even in the absence of increased synthesis. Further study will identify whether this process is required for the onset of myosteatosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30939247" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103416" }, "primaryId" : "GEO:GSE103416", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103416" } ] }, "title" : "Gene expression profiling in knee cartilage in a rat model of osteoarthritis", "dateAssigned" : "2017-09-01T00:00:00.000-05:00", "summary" : "Osteoarthritis (OA) is a chronic degenerative disease that leads to joint failure with pain and disability. Gene regulations are implicated in driving an imbalance between the expression of catabolic and anabolic factors, leading eventually to osteoarthritic cartilage degeneration. The different stages of disease progression are described by the complex pattern of transcriptional regulations. The dynamics in pattern alterations were monitored in each individual animal during the time-course of OA progression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103444" }, "primaryId" : "GEO:GSE103444", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103444" } ] }, "title" : "Identification of mRNA subsets interacting to RNA binding proteins in regenerating axons", "dateAssigned" : "2017-09-05T00:00:00.000-05:00", "summary" : "The goal of this study is to compare the mRNA interactome of different RBPs in regenerating axons utilizing RNA-immunoprecipitation (RIP). Interacting mRNAs to each target RBPs were co-immunoprecipitated from axoplasm of sciatic nerve, injured 7 days ago. Interactome of each RBPs were identified by Next-generation sequencing (NGS).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30038033" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103572" }, "primaryId" : "GEO:GSE103572", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103572" } ] }, "title" : "Discovering the process of bladder healing as the milestone for its regeneration", "dateAssigned" : "2017-09-06T00:00:00.000-05:00", "summary" : "Molecular mechanism underlying regeneration process, triggered by stem cells in tissue engineered urinary bladder, is still poorly explained. The study aimed to explore underlining pathways associated with regeneration process in urinary bladder reconstructed with stem cell seeded graft. The study was performed on 110 Wistar rats. Urinary bladders were augmented with bladder acellular matrix (BAM)(n=52) or BAM seeded with adipose derived stem cells (ADSCs)(n=52). The process of bladder healing was analyzed at 7, 30, 90 and 180 days postoperatively. Gene expression was evaluated using microarrays and analyzed in GeneSpring Software. Gene ontology (GO) and pathway enrichment analyses of differentially expressed genes (DEGs) were performed. A total of 4023, 4674, 7997 and 1120 of DEGs between the bladders augmented with ADSCs seeded BAM and BAM only were identified at 7, 30, 90 and 180 days postoperatively, respectively. The DEGs were enriched in GO terms associated with cellular and intercellular events, morphogenesis, epithelium, smooth muscles and nerves regeneration, angiogenesis, inflammatory response and wound healing. Numerous differentially expressed pathways between the bladders augmented with ADSCs seeded BAM and BAM only were identified. In conclusion, this study provided the unequivocal evidence that stem cells changed healing milieu in tissue engineered urinary bladder and indicated underlying pathways that can be associated with regeneration process triggered by stem cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31196214" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103646" }, "primaryId" : "GEO:GSE103646", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103646" } ] }, "title" : "Differential gene regulation and tumor inhibitory activities of alpha-, delta- and gamma-tocopherols in estrogen-mediated mammary carcinogenesis", "dateAssigned" : "2017-09-08T00:00:00.000-05:00", "summary" : "Conclusions: Our study represents the first detailed analysis of mammary tumor transcriptomes with different tocopherol treatment generated by RNA-seq technology. The optimized data analysis reported here should provide a framework for comparative investigations of expression profiles with tocopherols.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:28972008" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103661" }, "primaryId" : "GEO:GSE103661", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103661" } ] }, "title" : "Expression data from rodents following ischemic injury, permanent middle cerebral artery occlusion (MCAO) Neuregulin-1 treatment.", "dateAssigned" : "2017-09-08T00:00:00.000-05:00", "summary" : "We used gene expression profiling to understand the cellular and molecular mechanisms of NRG1’s effects 3 hours after the induction of ischemia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29856744" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103731" }, "primaryId" : "GEO:GSE103731", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103731" } ] }, "title" : "Arraystar lncRNA and mRNA array data for H9c2 myocytes from Hypoxia/reoxygenation model", "dateAssigned" : "2017-09-12T00:00:00.000-05:00", "summary" : "Ischemia reperfusion (I/R) promotes the severity of cardiomyocyte injur. Our study provides a potential new therapeutic strategy to alleviate ischemia reperfusion injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103995" }, "primaryId" : "GEO:GSE103995", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE103995" } ] }, "title" : "PARP1 regulates VSMC phenotypic switch and neointima via Myocardin", "dateAssigned" : "2017-09-19T00:00:00.000-05:00", "summary" : "We applied the transcriptome profiling (RNA-seq) for high-throughput profiling of genes changes in VSMC dedifferentiation. Rat primary VSMCs were divided into 3 groups, control, PDGF-BB, PDGF-BB+PJ34,and mRNA sequence were performed. We found that PDGF-BB could upregualted the genes involved in cell proliferation and migration, and downregulated the VSMC contractile genes, all of which could be reversed by PARP inhibitor PJ34. Then we knockdowned the co-factor Myocardin in VSMCs, and found the above effects of PJ34 were nearly abolished.Our study first provided the transcription changes by RNA-seq in VSMC dedifferentiation, and demonstrated the key roles of PARP1 and the PARylation process in VSMC phenotypic switch.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104017" }, "primaryId" : "GEO:GSE104017", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104017" } ] }, "title" : "Rat IUGR islet transcriptome sequencing at 2 time points", "dateAssigned" : "2017-09-19T00:00:00.000-05:00", "summary" : "Intrauterine growth restriction (IUGR) increases the risk of developing type 2 diabetes during adulthood. At day 18 of gestation, we used bilatual uterine artery ligation (BUAL) to restrict nutrient supply to developing rat fetuses to produce IUGR pups. At 2 and 10 weeks of age pancreatic islets were isolated and total RNA extracted using Trizol. Samples with RNA integrity numbers greater than 7 were used to generate libraries", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29309562" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104052" }, "primaryId" : "GEO:GSE104052", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104052" } ] }, "title" : "N-methyl-D-aspartate receptors mediate activity-dependent down-regulation of potassium channel genes during the expression of homeostatic intrinsic plasticity", "dateAssigned" : "2017-09-20T00:00:00.000-05:00", "summary" : "Using whole-cell patch clamp recording and unbiased gene expression profiling in rat dissociated hippocampal neurons cultured at high density, we demonstrate here that chronic activity blockade induced by the sodium channel blocker tetrodotoxin leads to a homeostatic increase in action potential firing and down-regulation of potassium channel genes. In addition, chronic activity blockade reduces total potassium current, as well as protein expression and current of voltage-gated Kv1 and Kv7 potassium channels, which are critical regulators of action potential firing. Importantly, inhibition of N-Methyl-D-Aspartate receptors alone mimics the effects of tetrodotoxin, including the elevation in firing frequency and reduction of potassium channel gene expression and current driven by activity blockade, whereas inhibition of L-type voltage-gated calcium channels has no effect.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25599691" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104164" }, "primaryId" : "GEO:GSE104164", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104164" } ] }, "title" : "Wnt-signaling pathways are dysregulated in female cerebellum following an early methyl donor deficiency in a rat nutritional model", "dateAssigned" : "2017-09-22T00:00:00.000-05:00", "summary" : "Early methyl donor –especially B9 and B12 vitamins- deficiency (MDD) is involved in birth defects and brain development retardation. Molecular mechanisms that take place in response to MDD still remain not well understood. In this study we took advantage of a rat nutritional MDD model and performed a microarray analysis on female cerebellum, in order to identify which genes and molecular pathways are disrupted in response to MDD. We found that cerebellum development is altered, with a decrease of the granular cell layer thickness in cerebellum at P21. Furthermore, we investigated the involvement of Wnt-signaling pathway –a major molecular pathway involved in neuronal development but also later in synaptic assembly and neurotransmission. We found that Wnt canonical and Ca2+ pathways are disrupted following early MDD. Notably, we identified GSK3β as a pivotal player affected by MDD, affecting synaptic assembly and signaling. These results could explain the structural brain defects previously observed in response to early MDD and identify new genes and a new molecular pathway that is affected following nutritional methyl donor deprivation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29804229" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104191" }, "primaryId" : "GEO:GSE104191", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104191" } ] }, "title" : "A senescent liver is rejuvenated in a young systemic environment: A study based on comparison of chronological and biological ages", "dateAssigned" : "2017-09-25T00:00:00.000-05:00", "summary" : "Though the liver plays central roles in metabolism, the pivotal biological events throughout its aging are still unknown, resulting in ambiguity as to whether liver senescence could be reversed. To establish a criterion for liver-aging evaluation, dynamic hepatic biological features, including liver function, histology, transcriptional profile and protein expression, were screened in a cohort of Lewis rats at sequential chronological ages from 3 months to 24 months.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104317" }, "primaryId" : "GEO:GSE104317", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104317" } ] }, "title" : "Treatment with Albumin (A)-Hydroxyoleic acid (HOA) complex restores sensorimotor function in rats with spinal cord injury: Efficacy and gene expression regulation", "dateAssigned" : "2017-09-27T00:00:00.000-05:00", "summary" : "Sensorimotor dysfunction following incomplete spinal cord injury (SCI) is often characterized by paralysis, spasticity and pain. Previously, we showed that intrathecal (i.t.) administration of the albumin-oleic acid (A-OA) complex in rats with SCI produced partial improvement of these symptoms and that oral 2-hydroxyoleic acid (HOA), a non-hydrolyzable OA analogue), was efficacious in the modulation and treatment of nociception and pain-related anxiety, respectively. Here we observed that intrathecal treatment with the complex albumin-HOA (A-HOA) every 3 days following T9 spinal contusion injury promoted significant recovery in locomotor function and marked an inhibition of TA noxious reflex activity (i.e., nociception) in Wistar rats. To investigate the mechanism of action of A-HOA, microarray analysis was carried out in the spinal cord lesion area. Representative genes involved in pain and neuroregeneration were selected to validate the changes observed in the microarray analysis by quantitative real-time RT-PCR. Comparison of the expression between healthy rats, SCI rats, and SCI treated with A-HOA rats revealed relevant changes in the expression of genes associated with neuronal morphogenesis and growth, neuronal survival, pain and inflammation. Thus, treatment with A-HOA not only induced a significant overexpression of growth and differentiation factor 10 (GDF10), tenascin C (TNC), aspirin (ASPN) and sushi-repeat-containing X-linked 2 (SRPX2), but also a significant reduction in the expression of prostaglandin E synthase (PTGES) and phospholipases A1 and A2 (PLA1/2). Currently, SCI has very important unmet clinical needs. A-HOA proved to downregulate genes involved in inflammation and upregulate genes involved in neuron growth, which balanced the important body response to medular lesion and allowed recovery from paralysis and pain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29244816" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104324" }, "primaryId" : "GEO:GSE104324", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104324" } ] }, "title" : "Soluble Neuregulin1 is a negative regulator of myelination", "dateAssigned" : "2017-09-27T00:00:00.000-05:00", "summary" : "Peripheral nerves are characterized by the ability to regenerate after injury. The activity of Schwann cells is fundamental for all steps of peripheral nerve regeneration: immediately after injury they de-differentiate, remove myelin debris, proliferate and repopulate the injured nerve. Neuregulin1 (NRG1) is a factor strongly up-regulated and released by Schwann cells immediately after nerve injury, known to play an important role for their de-differentiation, proliferation and survival. Nevertheless, up to now, the global analysis of the genes regulated by NRG1 was not performed. For this reason, we planned a deep RNA sequencing to generate a transcriptome database and identify all the genes regulated following stimulation of primary adult rat Schwann cells with soluble recombinant NRG1. Interestingly, the gene ontology analysis of the transcriptome shows that NRG1 regulates genes belonging to categories strongly regulated in the peripheral nerve immediately following injury. In particular, NRG1 strongly inhibits the expression of genes involved in myelination and in glial cell differentiation, suggesting that NRG1 plays a fundamental role in the de-differentiation (or “trans-differentiation”) process of Schwann cells from a myelinating to a repair phenotype. Moreover, NRG1 inhibits genes involved in the apoptotic process, therefore promoting cell survival, and up-regulates genes positively regulating the ribosomal RNA processing, thus suggesting that NRG1 actively stimulates new protein expression. This transcriptome analysis demonstrates that NRG1, which is strongly up-regulated immediately after injury, drives the expression of many important genes, thus playing a major role in the regeneration process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104338" }, "primaryId" : "GEO:GSE104338", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104338" } ] }, "title" : "Expression data from hypothalamus of rats fed omega-3 or omega-6 essential fats", "dateAssigned" : "2017-09-27T00:00:00.000-05:00", "summary" : "To differentiate the roles of essential dietary PUFA on hypothalamic function, we fed male rats high-fat diets (35% kcal/d) containing either safflower (linoleic acid) or flaxseed (alpha-linolenic acid) oil for 2 months. Control rats were fed a low-fat (16% kcal/d) diet containing soybean oil. Hypothalmic gene expression was investigated by microrray.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29413363" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104387" }, "primaryId" : "GEO:GSE104387", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104387" } ] }, "title" : "Purification of replicating pancreatic β-cells for gene expression studies", "dateAssigned" : "2017-09-28T00:00:00.000-05:00", "summary" : "The global transcriptome of replicating and quiescent pancreatic β-cells was analysed using gene expression arrays.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29235543" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104448" }, "primaryId" : "GEO:GSE104448", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104448" } ] }, "title" : "Fibrinogen activates BMP signaling in oligodendrocyte progenitor cells (OPCs) and inhibits remyelination after vascular damage [Rat_OPC_12h_Fibrinogen]", "dateAssigned" : "2017-09-29T00:00:00.000-05:00", "summary" : "We used microarrays to determine the genes involved in OPC responses to fibrinogen, which is deposited in the CNS after blood-brain barrier disruption.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29103804" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104449" }, "primaryId" : "GEO:GSE104449", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104449" } ] }, "title" : "Fibrinogen activates BMP signaling in oligodendrocyte progenitor cells (OPCs) and inhibits remyelination after vascular damage [Rat_OPC_48h_Fibrinogen]", "dateAssigned" : "2017-09-29T00:00:00.000-05:00", "summary" : "We used microarrays to determine the genes involved in OPC responses to fibrinogen, which is deposited in the CNS after blood-brain barrier disruption.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29103804" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104497" }, "primaryId" : "GEO:GSE104497", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104497" } ] }, "title" : "Derivation of hypoblast stem cells from rat embryonic stem cells.[RNA-seq]", "dateAssigned" : "2017-10-02T00:00:00.000-05:00", "summary" : "We report the mRNA profiles of single cells with high-throughput sequencing (RNA-seq) of hypoblast stem cells derived from rat embryonic stem cells. The single-cell data was combined with the previously published dataset: transcriptomes of mouse embryo cells (inner cell mass or trophectoderm). The clustering revealed that rat embryonic stem cell-derived hypoblast stem cells were similar to the mouse inner cell mass cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104538" }, "primaryId" : "GEO:GSE104538", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104538" } ] }, "title" : "Gene activity induced by denervation in the rat urinary bladder [mRNA]", "dateAssigned" : "2017-10-03T00:00:00.000-05:00", "summary" : "Bilateral freezing of the pelvic ganglia in female rats were performed to denervate the urinary bladder. Sham operated rats were used as controls. The rats were sacrificed 10 days after surgery. The urinary bladders (including the urothelium) were frozen and used for RNA extraction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29357417" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104539" }, "primaryId" : "GEO:GSE104539", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104539" } ] }, "title" : "Gene activity induced by denervation in the rat urinary bladder [miRNA]", "dateAssigned" : "2017-10-03T00:00:00.000-05:00", "summary" : "Bilateral freezing of the pelvic ganglia in female rats were performed to denervate the urinary bladder. Sham operated rats were used as controls. The rats were sacrificed 10 days after surgery. The urinary bladders (including the urothelium) were frozen and used for RNA extraction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29357417" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104548" }, "primaryId" : "GEO:GSE104548", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104548" } ] }, "title" : "Transcriptomic RNA sequence analysis of bone marrow mesenchymal stem cells derived neural progenitor-like cells under the influence of different growth factor combinations", "dateAssigned" : "2017-10-03T00:00:00.000-05:00", "summary" : "Conclusion: Our study represents the first detailed analysis of mesenchymal stem cells derived neural progenitor-like cell transcriptomes, generated by RNA-seq technology. Our data has explored crucial and novel genes involved during the early differentiation of mesenchymal stem cells into neural progenitor-like cells under the influence of different growth factor combinations.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33133516" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104561" }, "primaryId" : "GEO:GSE104561", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104561" } ] }, "title" : "Systematic evaluation of RNA quality and microarray data reliability in rat formalin-fixed paraffin-embedded and fresh frozen tissue samples", "dateAssigned" : "2017-10-03T00:00:00.000-05:00", "summary" : "We assessed the feasibility and reliability of microarray studies using formalin-fixed paraffin-embedded (FFPE) tissue-derived RNA compared with transcriptome data from paired fresh-frozen (FF) material. We established a robust workflow to generate highly reproducible microarray datasets from only 2 ng RNA input. For prior quality assessment, inspection of Agilent Bioanalyzer electropherograms, calculation of RNA fragment size distribution (DV200) and routine qPCR for selected references genes were done.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29679021" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104567" }, "primaryId" : "GEO:GSE104567", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104567" } ] }, "title" : "Expression data from tibialis anterior muscle of rats fed different fatty acid enriched diets", "dateAssigned" : "2017-10-03T00:00:00.000-05:00", "summary" : "To differentiate the roles of essential dietary PUFA on skeletal muscle function, we fed male rats a control diet (AIN-93G) or diets containing 10% safflower oil or flaxseed oil. Skeletal muscle gene expression was investigated by microrray.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29727591" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104584" }, "primaryId" : "GEO:GSE104584", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104584" } ] }, "title" : "Liver from CSF1-Fc- or PBS-treated neonatal rats and rat bone marrow derived macrophages", "dateAssigned" : "2017-10-04T00:00:00.000-05:00", "summary" : "Livers were harvested from neonatal rats on Day 6, following 5 days treatment with 1 ug/g porcine CSF1-Fc or PBS by subcutaneous injection. Bone marrow derived macrophages were generated in vitro by culture in CSF1.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29351395" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104588" }, "primaryId" : "GEO:GSE104588", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104588" } ] }, "title" : "Understanding the role of miRNA-143 (miR-143) in ischemia-induced retinopathy via RNA transcriptome profiling ", "dateAssigned" : "2017-10-04T00:00:00.000-05:00", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104593" }, "primaryId" : "GEO:GSE104593", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104593" } ] }, "title" : "Profiling the retinal microRNA (miRNA) expression in rodents by Next-Generation Sequencing", "dateAssigned" : "2017-10-04T00:00:00.000-05:00", "summary" : "Conclusion: Our study represents the first detailed analysis of retinal miRNA profile in adult rat and mouse. Our results also suggested that both species have a similar expression patterns of retinal miRNAs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104620" }, "primaryId" : "GEO:GSE104620", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104620" } ] }, "title" : "Profiling the retinal microRNA (miRNA) transcriptomes in a rat model of oxygen-induced retinopathy (OIR) by next-generation sequencing", "dateAssigned" : "2017-10-05T00:00:00.000-05:00", "summary" : "Conclusion: Our study represents the first detailed analysis of retinal miRNA expression profile in rat model of OIR by miRNA-NGS technology.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104697" }, "primaryId" : "GEO:GSE104697", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104697" } ] }, "title" : "Derivation of hypoblast stem cells from rat embryonic stem cells. [Affymetrix]", "dateAssigned" : "2017-10-06T00:00:00.000-05:00", "summary" : "Global transcriptome of rESC-derived hypoblast stem cells (cHypoSCs) was similar to that of rat embryo-derived hypoblast stem cells and rat multipotent adult progenitor cells. In addition, the transcriptome of these cells were compared with the previously published datasets including transcriptome of mouse embryonic stem cells, extraembryonic endoderm cells, single cells of mouse embryos (E3.25, E3.5, and E4.5). The comparison revealed that cHypoSCs have the transcriptome similar to that of extraembryonic endoderm cells and E3.5 primitive endoderm cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104740" }, "primaryId" : "GEO:GSE104740", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE104740" } ] }, "title" : "c-Met activation leads to the establishment of a TGFb regulatory network required for bladder cancer invasion", "dateAssigned" : "2017-10-09T00:00:00.000-05:00", "summary" : "Aberrant c-Met activation and upregulation of its cognate ligand HGF are frequently observed in bladder cancer and have been shown to regulate downstream pathways involved in proliferation, motility, and invasion. The precise mechanism underlying HGF/c-MET mediated invasion in bladder cancer is partly addressed by this microarray dataset. HGF activates the canonical TGFb signaling pathway to enhance epithelial mesenchymal transition and bladder carcinoma invasion.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31554791" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE105453" }, "primaryId" : "GEO:GSE105453", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE105453" } ] }, "title" : "Impact of cognitive performance and normal aging on transcriptomic changes in the prefrontal cortex of rats", "dateAssigned" : "2017-10-20T00:00:00.000-05:00", "summary" : "We investigated how cognitive stimulation impacts gene expression in the prefrontal cortex (PFC), a brain region known to regulate higher cognitive functions including the control of attention, in young and aged rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31185277" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106125" }, "primaryId" : "GEO:GSE106125", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106125" } ] }, "title" : "Epigenetic Transgenerational Inheritance of Altered Sperm Histone Retention Sites", "dateAssigned" : "2017-10-24T00:00:00.000-05:00", "summary" : "Female and male rats of an outbred female Sprague Dawley rats were administered daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day), or DDT (25 mg/kg BW/day) or dimethyl sulfoxide (DMSO) in oil (1 µl/kg BW/day vehicle). Treatment lineages are designated “control” or “vinclozolin” or “DDT” lineages. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1. Non-littermate females and males aged 70-90 days from F1 generation of control, vinclozolin or DDT were bred to obtain F2 generation offspring. The F2 generation rats were similarly bred to obtain the F3 generation offspring. Individuals were maintained for 120 days and euthanized for sperm collection. Sperm from multiple individual rats was pooled into single samples. For the control samples, 2 pools were made using 6 animals and 1 pool with 5 animals. For the DDT samples, 3 pools were mady using 4 animals. For the Vinclozolin samples, 3 pools were made using 4 animals. Genomic DNA was isolated and histone chromatin immunoprecipitation with genomic DNA was performed. Each pooled sample received a separate index primer. NGS was performed at the WSU Spokane Genomics Core using Ilumina HiSeq 2500 with a PE50 application, with a read size of approximately 50 bp and approximately 35 million reads per pool.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29482626" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106158" }, "primaryId" : "GEO:GSE106158", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106158" } ] }, "title" : "Comparative gene expression profiling of mouse pXEN, XEN, ES, and rat XENP cells", "dateAssigned" : "2017-10-25T00:00:00.000-05:00", "summary" : "We derived and describe a novel mouse cell type that we name primitive XEN (pXEN) cells, and compare their gene expression profiles with other stem cell types previously derived from rodent blastocysts.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29843002" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106314" }, "primaryId" : "GEO:GSE106314", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106314" } ] }, "title" : "microRNA expression data from medial prefrontal cortex (mPFC) of Rat", "dateAssigned" : "2017-10-30T00:00:00.000-05:00", "summary" : "We found that 97 miRNAs (59 upregulated and 38 downregulated) were altered more than 2-fold in the mPFC from chronic morphine-treated rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29282124" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106323" }, "primaryId" : "GEO:GSE106323", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106323" } ] }, "title" : "Hippocampal methylome of rats exposed to lead at different developmental stages", "dateAssigned" : "2017-10-30T00:00:00.000-05:00", "summary" : "NimbleGen Rat CpG Island plus RefSeq Promoter 720k array", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29571894" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106326" }, "primaryId" : "GEO:GSE106326", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106326" } ] }, "title" : "Altered microRNA expression in sciatic nerve following injury in rat model (0d-14d)", "dateAssigned" : "2017-10-30T00:00:00.000-05:00", "summary" : "We used microarrays to distinguish the miRNA expression differences among different time points in sciatic nerve after injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106333" }, "primaryId" : "GEO:GSE106333", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106333" } ] }, "title" : "miRNA Profiling of Exosomes from Spontaneous Hypertensive Rats by Next-Generation Sequencing", "dateAssigned" : "2017-10-30T00:00:00.000-05:00", "summary" : "The role and miRNA expression profile of exosomes in hypertension remain largely unknown, therefore, next generation sequencing was used to define the miRNA expression profile of plasma exosomes in spontaneously hypertensive rats (SHRs), the most widely used animal model of human essential hypertension, and their controls, normotensive Wistar-Kyoto rats (WKYs). Results revealed that percentages of miRNA in the total small RNA isolated from WKYs and SHRs were not significantly different. Twenty-seven miRNAs were significantly differentially expressed (DE) between WKY and SHR exosomes, among which 23 were upregulated and 4 were downregulated in SHR exosomes compared with WKY exosomes. Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis of top 10 DE miRNAs identified hypertension-specific target genes/signaling pathways. In conclusion, our findings indicate the selective packing of miRNA cargoes into exosomes under hypertensive status, while facilitating the development of potential targets for the diagnosis, prevention and treatment of hypertension.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106348" }, "primaryId" : "GEO:GSE106348", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106348" } ] }, "title" : "MicroRNA Contents in Matrix Vesicles Produced by Growth Plate Chondrocytes Are Cell Maturation Dependent", "dateAssigned" : "2017-10-30T00:00:00.000-05:00", "summary" : "Chondrocytes at different maturation states in the growth plate produce matrix vesicles (MVs), membrane organelles found in the extracellular matrix, with a wide range of contents, such as matrix processing enzymes and receptors for hormones. We have shown that MVs harvested from growth zone (GC) chondrocyte cultures contain abundant small RNAs, including miRNAs. Here, we determined whether RNA also exists in MVs produced by less mature resting zone (RC) chondrocytes and, if so, whether it differs from the RNA in MVs produced by GC cells. Our results showed that RNA, small RNA specifically, was present in RC-MVs, and it was well-protected from RNase by the phospholipid membrane. A group of miRNAs was enriched in RC-MVs compared RC-cells, suggesting that miRNAs are selectively packaged into MVs. High throughput array and RNA sequencing showed that ~39% miRNAs were differentially expressed between RC-MVs and GC-MVs. Individual RT-qPCR also confirmed that miR-122-5p and miR-150-5p were expressed at significantly higher levels in RC-MVs compared to GC-MVs. This study showed that growth plate chondrocytes at different differentiation stages produce different MVs with different miRNA contents, further supporting extracellular vesicle miRNAs play a role as “matrisomes” that mediate the cell–cell communication in cartilage and bone development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29483516" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106377" }, "primaryId" : "GEO:GSE106377", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106377" } ] }, "title" : "Relaxin reverses inflammatory and immune signals in aged hearts", "dateAssigned" : "2017-10-31T00:00:00.000-05:00", "summary" : "Conclusion: These data support the hypothesis that relaxin alters gene transcription and suppresses inflammatory pathways and genes associated with HF and aging. Relaxin’s suppression of inflammation and fibrosis supports its potential as a therapy for cardiovascular and inflammation-related diseases, such as HF, AF and diabetes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29346407" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106495" }, "primaryId" : "GEO:GSE106495", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106495" } ] }, "title" : "Glutamine 5 serotonylation on histone H3 is a permissive modification that functions combinatorialy with H3K4me3 to potentiate TFIID interactions", "dateAssigned" : "2017-11-03T00:00:00.000-05:00", "summary" : "Chemical modifications of histone proteins, along with the ?writers,? ?erasers? and ?readers? of these modifications, are capable of mediating a diverse set of DNA-templated processes including gene transcription1-7. Here, we provide evidence for a new class of histone posttranslational modification (PTM), serotonylation of glutamine, which occurs at position 5 (Q5ser) on histone H3 in serotonin (5-hydroxytryptamine, 5-HT) producing organisms. We demonstrate that the tissue Transglutaminase 2 (TGM2) enzyme, a transamidase that is both necessary and sufficient to deposit the mark, can serotonylate H3 on lysine 4 tri-methylated (H3K4me3) nucleosomes resulting in the presence of combinatorial H3K4me3Q5ser in vivo. H3K4me3Q5ser displays a ubiquitous pattern of tissue expression in mammals, with predicted enrichment observed in brain and gut, two organ systems responsible for the bulk of 5-HT production. Genome-wide analyses of its enrichment in human serotonergic neurons, developing mouse brain and cultured serotonergic cells, using an H3K4me3Q5ser specific antibody, indicate that the mark is enriched in euchromatin, is sensitive to cellular differentiation and correlates with permissive gene expression, phenomena that are linked to the mark?s potentiation of TFIID8-10 interactions with H3K4me3. Cells ectopically expressing an H3 mutant that cannot be serotonylated display significantly altered expression of H3K4me3Q5ser target loci leading to deficits in differentiation. Taken together, these data identify a direct role for 5-HT, independent from its contributions to neurotransmission and cellular signaling, in the mediation of permissive gene expression in mammalian cells, and further define its biophysical activities as a putative co-regulator of TFIID recruitment to H3K4me3 marked chromatin.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30867594" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106501" }, "primaryId" : "GEO:GSE106501", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106501" } ] }, "title" : "The effect of estrogen on microRNA expression in primary cultured rat neonatal cardiomyocytes", "dateAssigned" : "2017-11-03T00:00:00.000-05:00", "summary" : "We used a microRNA microarray screening approach to address the miRs expression profiling in estrogen-treated cardiomyocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29867756" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106511" }, "primaryId" : "GEO:GSE106511", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106511" } ] }, "title" : "A novel class of tRNA-derived small non-coding RNAs in response to myocardial hypertrophy and contribute to intergenerational inheritance", "dateAssigned" : "2017-11-03T00:00:00.000-05:00", "summary" : "tRNA-derived fragments (tRFs) have served as new class of non-coding RNA and played important role in regulating cellular RNA processing and protein translation, which was also proved have function on the intergenerational effects of paternal disease. However, there was no study reported the influence of tRFs on myocardial hypertrophy. In the current study, we explore the hypothesis that tRFs in response to myocardial hypertrophy and contribute to intergenerational inheritance.We used isoproterenol induced myocardial hypertrophy rat model. Small RNA (< 40 nt) tanscriptome sequencing was used to select differential expressed tRFs. We over-expressed the highest foldchange tRFs on H9c2 cell to check its function in enlarging cardiocytes surface area. We also compared the tRFs expression pattern in F0 sperm and F1 offspring heart between myocardial hypertrophy (Hyp) and control group (Con), as well as evaluated the phynotype of myocardial hypertrophy in F1 offspring. ISO successfully induced a typical cardiac hypertrophy model in our study. Small RNA-seq revealed tRFs were extremely enriched (84%) in Hyp heart. Overexpression tRFs1 and tRFs2 would both enlarge the surface area of cardiac cell and increase hypertrophic markers (ANF, BNP, and β-MHC) expression. tRFs1, tRFs2, tRFs3 and tRFs4 were also significantly high expressed in Hyp F0 sperm and in Hyp F1 offspring heart, but no function of tRFs7, tRFs9 and tRFs10. Compared to Con F1 offspring, Hyp F1 offspring had high expression levels of β-MHC and ANP genes, and increased fibrosis levles and apoptotic cell in heart.We demonstrate that tRFs are involved in regulating the response of myocardial hypertrophy, it might serve as novel epigenetic factor and contribute to intergenerational inheritance of cardiac hypertrophy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30012983" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106515" }, "primaryId" : "GEO:GSE106515", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106515" } ] }, "title" : "Optogenetic neural stem cells microarray", "dateAssigned" : "2017-11-03T00:00:00.000-05:00", "summary" : "The application of optogenetics in neural stem cell (NSC), allow photo-modulation of NSC in an activity-dependent manner. This provided spatio-temporal tool for studying activity dependent neurogenesis, including the potential of regulating the differentiation and maturation process of transplanted NSC. Currently, this is mainly driven by virally transfected of Channelrhodopsin-2 (ChR2) gene, which also requires high irradiance and complex in vitro stimulation systems. Additionally, despite the extensive application of optogenetics in neuroscience, the question of what transcriptome changes does optogenetic stimulation induced in developing NSCs have not been elucidated yet. To address these questions, we established a NSC line, expressing high light-sensitivity step-function opsin (SFO) variant of the chimeric channelrhodopsin, ChRFR(C167A) (~40x higher than ChR2), via the non-viral piggyBac transposon system. We set up a simple low-irradiance optogenetics stimulation-incubation system, which sufficiently induced depolarization in differentiating NSCs. We significantly enhance neurogenesis with low power optogenetic stimulation by 3 folds. Through microarray analysis, we have identified the genes and signaling pathways in axonal remodeling, synaptic plasticity and microenvironment modulation from optogenetic stimulation. Our results elucidate the transcriptome effects of optogenetics and the ability to drive neurogenesis with low irradiance optogenetics.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106518" }, "primaryId" : "GEO:GSE106518", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106518" } ] }, "title" : "The dynamic recruitment of TRBP to neuronal membranes mediates dendritogenesis during development", "dateAssigned" : "2017-11-03T00:00:00.000-05:00", "summary" : "MicroRNAs are important regulators of local protein synthesis during neuronal development. We investigated the dynamic regulation of microRNA production and found that the majority of the microRNA-generating complex, consisting of Dicer, TRBP and PACT, specifically associates with intra-cellular membranes in developing neurons. Stimulation with brain-derived neurotrophic factor (BDNF), which promotes dendritogenesis, caused the re-distribution of TRBP from the endoplasmic reticulum into the cytoplasm, and its dissociation from Dicer, in a Ca2+-dependent manner. As a result, the processing of a subset of neuronal precursor microRNAs, among them the dendrite-enriched pre-miR16, was impaired. Decreased production of miR-16-5p, which targeted the BDNF mRNA itself, was rescued by expression of a membrane-targeted TRBP. Moreover, miR-16-5p or membrane-targeted TRBP expression blocked BDNF-induced dendritogenesis, demonstrating the importance of neuronal TRBP dynamics for activity-dependent neuronal development. We propose that neurons employ specialized mechanisms to modulate local gene expression in dendrites, via the dynamic regulation of microRNA biogenesis factors at intracellular membranes of the endoplasmic reticulum, which in turn is crucial for neuronal dendrite complexity and therefore neuronal circuit formation and function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29263199" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106547" }, "primaryId" : "GEO:GSE106547", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106547" } ] }, "title" : "Analysis of microRNA expression profiles induced by Yiqifumai Powder Injection in rats with chronic heart failure", "dateAssigned" : "2017-11-06T00:00:00.000-06:00", "summary" : "To investigate the mechanism of Yiqifumai Powder Injectionthe on treating chronic heart diseases. We have employed a microRNAs microarray to identify the pivotal miRNAs altered by Yiqifumai compared to chronic heart injury and control group samples. 7 miRNAs accord with a 4-fold change (or more) or 1/4 (or less) and reverse rate between 1 and 2 were picked out as the reversible miRNAs for their expression after Yiqifumai treatment reversed significantly compared to model group. Among them, miR-21-3p and miR-542-3p were reported to associate with cardiac hypertrophy and tumer poliferation,respectively and they were validated by RT-PCR, which showed the consistent results as the microarray ones.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29467665" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106653" }, "primaryId" : "GEO:GSE106653", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106653" } ] }, "title" : "GLP-1 signaling suppresses menin's transcriptional block by phosphorylation in beta cells", "dateAssigned" : "2017-11-07T00:00:00.000-06:00", "summary" : "We find that GLP-1 signaling-activated PKA directly phosphorylates menin at serine 487 residue, relieving menin mediated suppression of insulin expression in beta cells and islets of diabetic GK rat. Mechanistically, GLP-1-induced PKA activation leads to menin Ser487 phosphorylation, and phosphorylated menin gains increased binding affinity to cytoskeleton proteins such as beta actin and myosin. Sequestration of Ser487 phosphorylated menin from the Ins1 gene promoter leads to reduced binding of menin-associating repressive epigenetic regulators such as SUV39H1 and HDAC1 at the locus, resulting in increased Ins1 transcription. Our results have linked GLP-1 signaling to physiologically suppression of menin function in repressing insulin expression, and uncovered a potential step to modulate menin phosphorylation to improve T2D therapy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106655" }, "primaryId" : "GEO:GSE106655", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106655" } ] }, "title" : "Developmental Exposure to Endocrine-Disrupting Chemicals Alters Gene Expression in Myometrium of Exposed Animals", "dateAssigned" : "2017-11-08T00:00:00.000-06:00", "summary" : "The goal of this study was to compare NGS-derived murine myometrial progenitor cell transcriptome profiling (RNA-seq) of an animal model of uterine fibroid tumorigenesis in rats exposed during uterine development to an endocrine-disrupting chemical, diethylstilbestrol (DES) versus vehicle (VEH) control, unexposed animals, to determine the pathways and biological processes, whose gene expression may be altered as a result of the exposure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106680" }, "primaryId" : "GEO:GSE106680", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106680" } ] }, "title" : "Transcriptomic study on protective effects of Danhong Injection against cerebral ischemia/reperfusion-induced damage", "dateAssigned" : "2017-11-08T00:00:00.000-06:00", "summary" : "This study compared the gene expression change of rat brain (cerebral ischemia reperfusion model) before and after Danhong injection treatment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29632486" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106682" }, "primaryId" : "GEO:GSE106682", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106682" } ] }, "title" : "Cellular and molecular basis of increased renal ammonia excretion in hyperammonemic conditions", "dateAssigned" : "2017-11-08T00:00:00.000-06:00", "summary" : "First, to characterize experimentally the changes in metabolic processes and gene expression associated with systemic hyperammonemia, in order to better understand the mechanisms responsible for this pathology; second, to construct a predictive a metabolic model of the pathways involved in order to investigate how the development of hyperammonemia can be explained by fundamental shifts in cellular metabolic objectives and gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36539425" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106766" }, "primaryId" : "GEO:GSE106766", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106766" } ] }, "title" : "Short-term mastication after weaning upregulates GABAergic signalling and reduces dendritic spine in thalamus", "dateAssigned" : "2017-11-10T00:00:00.000-06:00", "summary" : "These results suggest that mastication in the early developing period upregulates GABAergic signaling genes, with a decrease of spine pruning in thalamus", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29524403" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106862" }, "primaryId" : "GEO:GSE106862", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106862" } ] }, "title" : "The oligodendrocyte \"protrusiosome\": Identification of compartmentalized enrichment of transcripts in newly-formed protrusions of oligodendrocyte precursor cells (OPC) by RNAseq", "dateAssigned" : "2017-11-14T00:00:00.000-06:00", "summary" : "Like neurons, oligodendrocytes (OL) are cells with elaborate morphology that probably require asymmetrical spatial regulation of biological processes. Formation of membrane protrusions is critical for OL development and interaction with axons. We hypothesized that the enrichment of specific mRNAs in protrusions of oligodendrocyte precursor cells (OPC) is important for morphological differentiation, thus having an impact in myelination. To explore this hypothesis, we established a modified Boyden chamber system to physically separate soma from membrane protrusions of rat primary OPC cultured in vitro for 24h. We performed a whole transcriptome analysis (RNAseq) of primary rat OPC soma and membrane protrusion fractions and found a subcellular enrichment of mRNAs in these structures during initial protrusion formation. At the very initial stage of OPC protrusion extension, there is a significant subcellular enrichment of transcripts encoding proteins related to cellular component assembly and cytoskeleton organization, particularly of actin-related molecules. This suggests that the regulation of the cytoskeleton dynamics may be locally controlled in OPCs and probably relevant for their differentiation program.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29732611" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106883" }, "primaryId" : "GEO:GSE106883", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106883" } ] }, "title" : "Impact of bariatric surgery on placental transcriptome", "dateAssigned" : "2017-11-14T00:00:00.000-06:00", "summary" : "In the present study, we sought to understand the impact of bariatric surgery [using vertical sleeve gastrectomy (VSG)] on transcriptome changes in the placenta . Female Adult, Long Evans were fed high fat diet (HFD, #D03082706, Research Diets) for 4 weeks, divided into sham-VSG or VSG groups, and following surgeries one group of sham-VSG and VSG were switched to normal diet (lean), while one sham-VSG group (obese) continued HFD. At gestdational day 18, placenta tissues harvested from pregnant female rats were processed for Affymetrix microarray and transcriptomic analysis performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29167317" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106919" }, "primaryId" : "GEO:GSE106919", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106919" } ] }, "title" : "LncRNA and mRNA changes during postnatal islet maturation", "dateAssigned" : "2017-11-15T00:00:00.000-06:00", "summary" : "To elucidate the mechanisms involved in the acquisition of a fully differentiated beta-cell phenotype, we compared by microarray the mRNAs and the long non-coding RNAs expressed in newborn and adult rat islets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30115652" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106924" }, "primaryId" : "GEO:GSE106924", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106924" } ] }, "title" : "High-throughput sequencing and analysis of gene modification regulated by epigenetics modification in adult and old intracerebral hemorrhage rats. [RNA-Seq]", "dateAssigned" : "2017-11-15T00:00:00.000-06:00", "summary" : "Here we performed in depth epigenome sequencing and analysis to study the mechanism of high mortality rate of ICH in rat brain. It reveals a systematical transcription activation of mRNA genes enriched in inflammation and immune responses. These genes are clustered to specific genomic loci and regulated by repressive and activation chromatin markers. We show that epigenetic reprogramming responding to ICH in old rat brains differs greatly from that in the adult.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106931" }, "primaryId" : "GEO:GSE106931", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106931" } ] }, "title" : "Expression data from cerebral CD163+ perivascular and meningeal macrophages (PV) obtained from controls (C) and ischemic (I) rats", "dateAssigned" : "2017-11-15T00:00:00.000-06:00", "summary" : "The goal was to identify the changes in the gene expression profile of PV after brain ischemia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30092836" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106951" }, "primaryId" : "GEO:GSE106951", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106951" } ] }, "title" : "High-throughput sequencing and analysis of gene modification regulated by epigenetics modification in adult and old intracerebral hemorrhage rats. [ChIP-Seq]", "dateAssigned" : "2017-11-15T00:00:00.000-06:00", "summary" : "Here we performed in depth epigenome sequencing and analysis to study the mechanism of high mortality rate of ICH in rat brain. It reveals a systematical transcription activation of mRNA genes enriched in inflammation and immune responses. These genes are clustered to specific genomic loci and regulated by repressive and activation chromatin markers. We show that epigenetic reprogramming responding to ICH in old rat brains differs greatly from that in the adult.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106990" }, "primaryId" : "GEO:GSE106990", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE106990" } ] }, "title" : "Histone methylation in rat peripheral nerve", "dateAssigned" : "2017-11-16T00:00:00.000-06:00", "summary" : "The goal of this study was to determine the distribution of H3K27me3 in rat peripheral nerve, which is formed by PRC2, polycomb repressive complex 2.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30306639" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107020" }, "primaryId" : "GEO:GSE107020", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107020" } ] }, "title" : "Algesic MBP peptide induce pain-specific signaling in rodent Schwann Cells", "dateAssigned" : "2017-11-16T00:00:00.000-06:00", "summary" : "We demonstrated the pain-specific response to the algesic peptide fragment MBP84-104 of myelin basic protein that induces pain if injected into sciatic nerve of rats and mice. We used the wild-type peptide MBP 84-104, H89G mutant peptide (MBP84-104-H89G), scramble peptide (MBP84-104-SCR) and phosphomimetic peptide MBP84-104-mimTT to stimulate the primary rat Schwann cell cultures. After 24h we isolated total RNA and conducted genome wide RNA-seq. In addition, we performed RNA-seq using Schwann cells constitutively expressing an MBP84-104-mCherry construct. The gene expression data was analyzed using Ingenuity Pathway Analysis software. We conclude that the Schwann cells expressing MBP84-104 constructs stimulate pain-specific signaling pathways thus representing a relevant model to study neuropathic pain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30079618" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107066" }, "primaryId" : "GEO:GSE107066", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107066" } ] }, "title" : "mRNA expression in liver of adult F2 female rats born to F0-fathers fed a chow or high-fat diet", "dateAssigned" : "2017-11-17T00:00:00.000-06:00", "summary" : "Liver mRNA expression profiling of F2-female from F0-founders fed either a chow or a chronic HFD challenged. Adult females were challenge or not a high-fat diet for 12 weeks. Liver was dissected at an endpoint experiment. Rats were subjected to 4 hours fasting prior to anesthesia with pentobarbital and tissue collection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30768368" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107180" }, "primaryId" : "GEO:GSE107180", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107180" } ] }, "title" : "Comprehensive analysis of Long non-coding RNA expression in dorsal root ganglion reveals cell type specificity and dysregulation following nerve injury [rodent DRG]", "dateAssigned" : "2017-11-20T00:00:00.000-06:00", "summary" : "Dorsal root ganglion (DRG) neurons provide connectivity between peripheral tissues and spinal cord. Transcriptional plasticity within DRG sensory neurons after peripheral nerve injury contributes to nerve repair but also leads to maladaptive plasticity, including the development of neuropathic pain. This study presents tissue and neuron specific expression profiling of both known and novel Long Non-Coding RNAs (LncRNAs) in rodent DRG following nerve injury. We have identified a large number of novel LncRNAs expressed within rodent DRG, a minority of which were syntenically conserved between mouse and rat and which including both- intergenic and antisense LncRNAs. We have also identified neuron type-specific LncRNAs in mouse DRG, and LncRNAs that are expressed in human IPS cell-derived sensory neurons. We show significant plasticity in LncRNA expression following nerve injury, which in mouse is strain dependant. This resource is publicly available and will aid future studies of DRG neuron identity and the transcriptional landscape in both naïve and injured DRG.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30335683" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107259" }, "primaryId" : "GEO:GSE107259", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107259" } ] }, "title" : "Environment-dependent striatal gene expression in the BACHD rat model for Huntington disease", "dateAssigned" : "2017-11-22T00:00:00.000-06:00", "summary" : "We examined effects of early life stress (ELS) and environmental enrichment (EE) during development on BACHD rat striatal gene expression using RNA sequencing", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29643462" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107274" }, "primaryId" : "GEO:GSE107274", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107274" } ] }, "title" : "The gene expression profile of rat hepatocytes grown on decelllularized liver", "dateAssigned" : "2017-11-22T00:00:00.000-06:00", "summary" : "The objective of this study was to determine the gene expression profile of rat hepatocytes grown on decellularized rat liver matrices as a function of time.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29377912" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107324" }, "primaryId" : "GEO:GSE107324", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107324" } ] }, "title" : "Hypothalamic transcriptome of Spraque Dawley rat at postnatal day 10 exposed to maternal high fat diet or control diet", "dateAssigned" : "2017-11-24T00:00:00.000-06:00", "summary" : "We have compared hypothalamic transcriptome of rat offspring exposed to maternal high fat diet or control diet", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29240779" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107378" }, "primaryId" : "GEO:GSE107378", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107378" } ] }, "title" : "Mechanical stretch induced transcriptomic profiles in cardiac myocytes [1-12 hours]", "dateAssigned" : "2017-11-27T00:00:00.000-06:00", "summary" : "The effect of cyclic mecanical stretch on cardiac microRNA expression was studied in neonatal rat ventricular myocytes (NRVMs).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29549296" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107379" }, "primaryId" : "GEO:GSE107379", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107379" } ] }, "title" : "Mechanical stretch induced transcriptomic profiles in cardiac myocytes [24-48 hours]", "dateAssigned" : "2017-11-27T00:00:00.000-06:00", "summary" : "The effect of cyclic mecanical stretch on cardiac microRNA expression was studied in neonatal rat ventricular myocytes (NRVMs).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29549296" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107551" }, "primaryId" : "GEO:GSE107551", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107551" } ] }, "title" : "Mechanical stretch induced transcriptomic profiles in cardiac myocytes II", "dateAssigned" : "2017-11-30T00:00:00.000-06:00", "summary" : "The effect of cyclic mecanical stretch on cardiac gene expression was studied in neonatal rat ventricular myocytes (NRVMs).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29549296" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107582" }, "primaryId" : "GEO:GSE107582", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107582" } ] }, "title" : "RNA-seq analysis for mRNA expression change in alpha-synclein fibril-treated cultured oligodendrocyte precursor cells", "dateAssigned" : "2017-12-01T00:00:00.000-06:00", "summary" : "Glial cytoplasmic inclusion is the pathological hallmark of multiple system atrophy commonly observed as alpha-synulcien-positive aggregates within oligodendrocytes. We elucidated that preformed alpha-synulcien fibrils triggers multimerization and upsurge of endogenous alpha-synulcien in oligodendrocyte precursor cells which is attributable to insufficient autophagic proteolysis. To assess the functional influence of alpha-synuclein fibrils application on oligodendrocyte precursor cells, RNA-seq analysis was performed. The data revealed that alpha-synulcien fibrils interfered with numerous protein expressions associated with neuronal support and myelination.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29337114" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107587" }, "primaryId" : "GEO:GSE107587", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107587" } ] }, "title" : "RNA expression profiling in cardiomyocytes", "dateAssigned" : "2017-12-01T00:00:00.000-06:00", "summary" : "Using the highly sensitive RNA array, we assessed the effect of 11β-HSD1 and BVT.2733 on modulating RNAs expression in the neonatal rat ventricular cardiomyocytes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107658" }, "primaryId" : "GEO:GSE107658", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107658" } ] }, "title" : "Gender differences of gene expression profiles in brain cardiovascular centers of WKY rats [nucleus of solitarii tract]", "dateAssigned" : "2017-12-04T00:00:00.000-06:00", "summary" : "Arterial pressure (AP) is lower in pre-menopausal women than in men of similar age. Pre-menopausal women exhibit a lower sympathetic outflow and a greater baroreceptor reflex, however molecular mechanisms for the gender differences of AP regulation are still not well understood. Since the nucleus tractus solitarius (NTS), a pivotal region of the medulla oblongata for regulating the set-point of AP is strongly associated with the AP level, we hypothesized that a different neuronal functions at the level of the NTS between men and women could contribute to the gender difference in cardiovascular homeostasis. Females Spontaneous Hypertensive Rats (SHRs) clearly exhibit lower AP levels than their male counterparts at similar age and their NTS is characterized by a specific gene expression profile. This gender dependence of AP level is less marked in the normotensive strain, Wistar Kyoto rats (WKY). In this study, we investigated the gender-dependent gene expression profile of the NTS of WKY by using microarray technique.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29373075" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107659" }, "primaryId" : "GEO:GSE107659", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107659" } ] }, "title" : "Gender differences of gene expression profiles in brain cardiovascular centers of WKY rats [hypothalamus]", "dateAssigned" : "2017-12-04T00:00:00.000-06:00", "summary" : "Arterial pressure (AP) is lower in pre-menopausal women than in men of similar age. Pre-menopausal women exhibit a lower sympathetic outflow and a greater baroreceptor reflex, however molecular mechanisms for the gender differences of AP regulation are still not well understood. Since the hypothalmus is strongly functionnaly connected to the nucleus tractus solitarius (NTS), a pivotal region of the medulla oblongata for regulating the set-point of AP, we hypothesized that a different neuronal functions at the level of hypothalamus between men and women could contribute to the gender difference in cardiovascular homeostasis. Females Spontaneous Hypertensive Rats (SHRs) clearly exhibit lower AP levels than their male counterparts at similar age and their hypothalamus is characterized by a specific gene expression profile. This gender dependence of AP level is less marked in the normotensive strain, Wistar Kyoto rats (WKY). In this study, we investigated the gender-dependent gene expression profile of the hypothalamus of WKY rats by using microarray technique.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29373075" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107725" }, "primaryId" : "GEO:GSE107725", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107725" } ] }, "title" : "Estrogen protects neurotransmission transcriptome during status epilepticus", "dateAssigned" : "2017-12-05T00:00:00.000-06:00", "summary" : "Epilepsy in women is often accompanied by hormonal disturbances including irregular cycles and premature onset of menopause. Decline in estrogen levels results in increased risk for neurodegenerative diseases, with strong participation of chronic inflammation. We have shown that estradiol (EB) has neuroprotective effects against seizure-induced damage in the sensitive hilar region of hippocampal dentate gyrus associated with neuropeptide Y (NPY) upregulation. Here, we quantify the alterations caused by kainic acid-induced status epilepticus in the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic synapse transcriptomes of dentate gyrus of ovariectomized female rats and the recovery effects of the EB replacement. Our data indicate that the EB replacement reduces the number of significantly regulated genes in seizured ovariectomized female rats by about 45%. The new measure Pathway Restoration Efficiency (PRE) indicates the dopaminergic synapse to be the most protected (65%) and the GABAergic synapse the least protected (37%) by the EB replacement.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29973860" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107837" }, "primaryId" : "GEO:GSE107837", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107837" } ] }, "title" : "Transcriptomics but not DNA methylomics find Tp73, Cebpd, Pax6 and Spi1 transcription factors as treatment targets for traumatic brain injury", "dateAssigned" : "2017-12-07T00:00:00.000-06:00", "summary" : "TBI was induced with lateral fluid-percussion injury in adult male rats. MBD-seq of the perilesional cortex, ipsilateral thalamus and ipsilateral hippocampus was performed at 3 months post-TBI. The data was used to identify differential methylation of gene promoter, gene body, and exons in the perilesional cortex , thalamus and hippocampus.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29482641" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107847" }, "primaryId" : "GEO:GSE107847", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107847" } ] }, "title" : "Altered molecular signatures during kidney development after intrauterine growth restriction of different origins", "dateAssigned" : "2017-12-08T00:00:00.000-06:00", "summary" : "Intrauterine growth restriction (IUGR) has been linked to predisposition towards an unfavorable course of glomerulopathies and early loss of kidney function. This study was performed to identify transcriptional alterations in male IUGR rats during and at the end of nephrogenesis in order to generate hypotheses which molecular mechanisms contribute to adverse kidney programming. IUGR was induced by low protein (LP) diet throughout pregnancy, bilateral uterine vessel ligation (LIG), or intrauterine stress (IUS) by sham operation. Offspring of unimpaired dams served as controls. Significant acute kidney damage was ruled out by negative results for proteins indicative of ER-stress, autophagy, apoptosis or infiltration with macrophages. Renal gene expression was examined by transcriptome microarrays, demonstrating 53 (LP, n=12; LIG, n=32; IUS, n=9) and 134 (LP, n=10; LIG, n=41; IUS, n=83) differentially expressed transcripts on postnatal days (PND) 1 and 7, respectively. Reduced Pilra (all IUGR groups, PND 7), Nupr1 (LP and LIG, PND 7) and Kap (LIG, PND 1) as well as increased Ccl20, S100a8/a9 (LIG, PND 1), Ifna4 and Ltb4r2 (IUS, PND 7) indicated that inflammation-related molecular dysregulation could be a “common” feature after IUGR of different origins. Network analyses of transcripts and predicted upstream regulators hinted at proinflammatory adaptions mainly in LIG (arachidonic acid-binding, neutrophil aggregation, toll-like-receptor, NF-kappa B and TNF signaling) and dysregulation of AMPK and PPAR signaling in LP pups. The latter may increase susceptibility towards obesity-associated kidney damage. Western blots of the most prominent predicted upstream regulators confirmed significant dysregulation of RICTOR in LP (PND 7) and LIG pups (PND 1), suggesting that mTOR-related processes could further modulate kidney programming in these groups of IUGR pups. ", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107919" }, "primaryId" : "GEO:GSE107919", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE107919" } ] }, "title" : "Chromatin remodeler CHD8 in CNS myelination and remyelination", "dateAssigned" : "2017-12-11T00:00:00.000-06:00", "summary" : "Mutations in CHD8, an ATP-dependent chromodomain-helicase-DNA-binding protein 8, are known to cause a set of Autism Spectrum Disorders (ASD). We found that CHD8 is highly expressed in myelinating oligodendrocytes (OL) and their progenitors in the developing central nervous system (CNS).We performed CHD8 chIP-seq analysis in cultured oligodendrocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29920279" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108168" }, "primaryId" : "GEO:GSE108168", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108168" } ] }, "title" : "Gene Expression profile of brain in SCI rat by MSC intravenous transplantation.", "dateAssigned" : "2017-12-17T00:00:00.000-06:00", "summary" : "We used Clariom D / Gene Chip® Rat Transcriptome Array (RTA 1.0., Affymetrix, Santa Clara, CA, USA).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29901416" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108182" }, "primaryId" : "GEO:GSE108182", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108182" } ] }, "title" : "Localization of dimethylated histone three lysine four in the Rattus norvegicus sperm genome", "dateAssigned" : "2017-12-18T00:00:00.000-06:00", "summary" : "We examined the precise localization of dimethylated histone three lysine four (H3K4me2) in mature rat sperm.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108342" }, "primaryId" : "GEO:GSE108342", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108342" } ] }, "title" : "Expression Profiles of Long Noncoding RNAs and mRNAs in Post-Cardiac Arrest Rat Brains", "dateAssigned" : "2017-12-20T00:00:00.000-06:00", "summary" : "To investigate lncRNA and mRNA expression profiles in post-cardiac arrest (CA) brains, an external transthoracic electrical current was applied for eight minutes to induce CA (the CA group). Four rats received sham-operations and served as the blank control (BC) group. Upon return of spontaneous circulation (ROSC), lncRNA and mRNA expression in the rat cerebral cortex was assayed with high-throughput Agilent lncRNA and mRNA microarrays. Thirty-seven lncRNAs were upregulated and 21 lncRNAs were downregulated in the CA group, and 258 mRNA transcripts were differentially expressed with 177 mRNAs upregulated and 81 mRNAs downregulated in the CA group.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108348" }, "primaryId" : "GEO:GSE108348", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108348" } ] }, "title" : "Transcriptome variations across species, organs and developmental stages", "dateAssigned" : "2017-12-20T00:00:00.000-06:00", "summary" : "We sequenced polyA-selected transcriptomes from three species (mouse, rat and chicken), four organs (brain, kidney, liver and testis) and five developmental stages (two embryonic stages, newborn, young adult and aged adult individuals). We analyzed gene expression pattern variations across species, organs and developmental stages for protein-coding and long non-coding RNA genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31539080" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108484" }, "primaryId" : "GEO:GSE108484", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108484" } ] }, "title" : "Transcriptome analysis of Chrdl1-treated RGCs", "dateAssigned" : "2017-12-23T00:00:00.000-06:00", "summary" : "Chrdl1 treatment promotes formation of synapses and GluA2-AMPAR recruitment in Retinal ganglion cell (RGC) cultures. Analysis of the transcriptome of RGCs with or without Chrdl1 treatment let us determine potential alterations in the expression of genes related to BMP signaling, or genes involved in excitatory synaptogenesis and AMPAR trafficking.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30344043" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108499" }, "primaryId" : "GEO:GSE108499", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108499" } ] }, "title" : "Gene expression-based, individualized outcome prediction for exposure of rat ovarian tissue", "dateAssigned" : "2017-12-24T00:00:00.000-06:00", "summary" : "Using the selection criteria (FC ≥ 2, p ≤ 0.05), 86 up-regulated genes and 71 down-regulated genes were identified in the TBT100 group. In the BPA50 group, 45 up-regulated genes and 95 down-regulated genes were identified using the same criteria. The TBT+BPA group had 258 up-regulated genes and 234 down-regulated genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108752" }, "primaryId" : "GEO:GSE108752", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108752" } ] }, "title" : "Expression data from rat NSCs co-cultured with green fluorescence protein (GFP)-ectodermal mesenchymal stem cells (EMSCs) versus mono-cultured rat NSCs", "dateAssigned" : "2018-01-04T00:00:00.000-06:00", "summary" : "In order to reveal the gene expression profiles of NSCs under these two diffferent culture conditions, we used microassrays to examine the global programme of gene expression of NSCs under these two diffferent culture conditions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30633831" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108776" }, "primaryId" : "GEO:GSE108776", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108776" } ] }, "title" : "Whole transcriptome analysis of brain hippocampal tissue from SAMP8 mice and rat primary neurons treated with the Alzheimer’s disease drug candidate CAD031", "dateAssigned" : "2018-01-04T00:00:00.000-06:00", "summary" : "Alzheimer’s disease (AD) drug discovery has rarely been addressed in the context of aging even though sporadic AD accounts for 99% of the cases. Phenotypic screens based upon old age-associated brain toxicities were used to develop the potent AD drug candidate CAD031. The aim of this project was to investigate whether CAD031 prevented the progression of dementia in SAMP8 mice when administered at advanced stages of disease, and the possible mechanism of this prevention effect. These transcriptomic data are part of an integrative multi-omics approach that also investigated protein expression, metabolite levels as well as cognition. In addition, in order to further investigate the effect of the drugs in in vitro neuronal cultures, rat primary neurons were treated with the compound and the transcriptome sequenced.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32705410" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108823" }, "primaryId" : "GEO:GSE108823", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108823" } ] }, "title" : "Selection of well-tolerated GalNAc-conjugated siRNAs by screening for RNAi-mediated off-target effects in rodent toxicity studies", "dateAssigned" : "2018-01-05T00:00:00.000-06:00", "summary" : "Small interfering RNAs (siRNAs) conjugated to a trivalent N-acetylgalactosamine (GalNAc) ligand are being evaluated in investigational clinical studies for a variety of indications. The typical development candidate selection process includes evaluation of the most active compounds for toxicity in rats at pharmacologically-exaggerated doses. The subset of GalNAc-siRNAs that show rat hepatotoxicity is not advanced to clinical development. Potential mechanisms of hepatotoxicity include toxicities associated with the intracellular accumulation of oligonucleotides and their metabolites, RNA interference (RNAi)-mediated hybridization-based off-target effects, and/or perturbation of endogenous RNAi pathways. Here we show that rodent hepatotoxicity observed at supratherapeutic exposures can be largely attributed to RNAi-mediated off-target effects, but not chemical modifications or the perturbation of RNAi pathways. Furthermore, these off-target effects can be mitigated by modulating seed-pairing using a thermally destabilizing chemical modification, which significantly improves the safety profile of a GalNAc-siRNA in rat and may minimize the occurrence of hepatotoxic siRNAs across species.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29459660" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108904" }, "primaryId" : "GEO:GSE108904", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108904" } ] }, "title" : "Heart tissue expression data from dTGR rats treated with or without BAY 41-8543 and Sprague Dawley control rats", "dateAssigned" : "2018-01-08T00:00:00.000-06:00", "summary" : "We used microarrays to detail the effect of NOsGC-stimulation on cardiac gene expression in heart failure with preserved ejection fraction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29467337" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108965" }, "primaryId" : "GEO:GSE108965", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108965" } ] }, "title" : "Molecular Effects of Developmental FM 550 Exposure in Wistar Rat Fetal Forebrain", "dateAssigned" : "2018-01-09T00:00:00.000-06:00", "summary" : "Firemaster® 550 (FM 550) is a flame retardant (FR) mixture that has become one of the most commonly used FRs in foam-based furniture and baby products. Human exposure to this commercial mixture, comprised of brominated and organophosphate components, is widespread. We have repeatedly shown that developmental exposure can lead to sex-specific behavioral effects in rats. Accruing evidence of endocrine disruption and potential neurotoxicity have raised concerns regarding the neurodevelopmental effects of FM 550 exposure, but the specific mechanisms of action remains unclear. Additionally, we observed significant, and in some cases sex-specific, accumulation of FM 550 in placental tissue following gestational exposure. Because the placenta is an important source of hormones and neurotransmitters for the developing brain, it may be a critical target of toxicity to consider in the context of developmental neurotoxicity. Using a mixture of targeted and exploratory approaches, the goal of the present study was to identify possible mechanisms of action in the developing forebrain and placenta. Wistar rat dams were orally exposed to FM 550 (0, 300, or 1,000 µg/day;) for 10 days during gestation and placenta and fetal forebrain tissue collected for analysis. In placenta, evidence of endocrine, inflammatory, and neurotransmitter signaling pathway disruption was identified. Notably, 5-HT turnover was reduced in placental tissue and fetal forebrains indicating that 5-HT signaling between the placenta and the embryonic brain may be disrupted. These findings demonstrate that environmental contaminants, like FM 550, have the potential to impact the developing brain by disrupting normal placental functions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29351906" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108978" }, "primaryId" : "GEO:GSE108978", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE108978" } ] }, "title" : "Short-term low-dose mTORC1 inhibition in aged rats counter-regulates age-related gene changes and blocks age-related kidney pathology", "dateAssigned" : "2018-01-09T00:00:00.000-06:00", "summary" : "Rapalogs, inhibitors of mTORC1 (mammalian target of rapamycin complex 1), increase life span and delay age-related phenotypes in many species. However, the molecular mechanisms have not been fully elucidated. We determined gene expression changes comparing 6- and 24-month-old rats in the kidney, liver, and skeletal muscle, and asked which of these changes were counter-regulated by a clinically-translatable (short-term and low-concentration) treatment, with a rapalog (RAD001). Surprisingly, RAD001 had a more pronounced effect on the kidney under this regimen in comparison to the liver or skeletal muscle. Histologic evaluation of kidneys revealed that the severity of chronic progressive nephropathy lesions was lower in kidneys from 24-month-old rats treated with RAD001 compared with vehicle. In addition to other gene expression changes, c-Myc, which has been shown to regulate aging, was induced by aging in the kidney and counter-regulated by RAD001. RAD001 caused a decrease in c-Myc protein, which could be rescued by a proteasome inhibitor. These findings point to settings for use of mTORC1 inhibitors to treat age-related disorders, and highlight c-Myc regulation as one of the potential mechanisms by which mTORC1 inhibition is perturbing age-related phenotypes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29304191" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109013" }, "primaryId" : "GEO:GSE109013", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109013" } ] }, "title" : "Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats I", "dateAssigned" : "2018-01-10T00:00:00.000-06:00", "summary" : "The notion that adverse health effects produced by exposure to environmental contaminants (EC) may be modulated by the presence of non-chemical stressors is gaining attention. Previously, our lab demonstrated that cross-fostering (adoption of a litter at birth) acted as a non-chemical stressor that amplified the influence of developmental exposure to EC on the glucocorticoid stress-response in adult rats. Using liver from the same rats, the aim of the current study was to investigate whether cross-fostering might also modulate EC-induced alterations in hepatic gene expression profiles. During pregnancy and nursing, Sprague-Dawley dams were fed cookies laced with corn oil (control, C) or a chemical mixture (M) composed of polychlorinated biphenyls (PCB), organochlorine pesticides (OCP), and methylmercury (MeHg), at 1 mg/kg/day. This mixture simulated the contaminant profile reported in maternal human blood. At birth, some control and M treated litters were crossfostered to form two additional groups with different biological/nursing mothers (CC and MM). The hepatic transcriptome was analyzed by DNA microarray in male offspring at postnatal days 21 and 78–86. Mixture exposure altered the expression of detoxification and energy metabolism genes in both age groups, but with different sets of genes affected at day 21 and 78–86. Cross-fostering modulated the effects of M on gene expression pattern (MM vs M), as well as expression of energy metabolism genes between control groups (CC vs C). In conclusion, while describing short- and long-term effects of developmental exposure to EC on hepatic transcriptomes, these cross-fostering results further support the consideration of non-chemical stressors in EC risk assessments.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30744511" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109014" }, "primaryId" : "GEO:GSE109014", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109014" } ] }, "title" : "Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats II.", "dateAssigned" : "2018-01-10T00:00:00.000-06:00", "summary" : "The notion that adverse health effects produced by exposure to environmental contaminants (EC) may be modulated by the presence of non-chemical stressors is gaining attention. Previously, our lab demonstrated that cross-fostering (adoption of a litter at birth) acted as a non-chemical stressor that amplified the influence of developmental exposure to EC on the glucocorticoid stress-response in adult rats. Using liver from the same rats, the aim of the current study was to investigate whether cross-fostering might also modulate EC-induced alterations in hepatic gene expression profiles. During pregnancy and nursing, Sprague-Dawley dams were fed cookies laced with corn oil (control, C) or a chemical mixture (M) composed of polychlorinated biphenyls (PCB), organochlorine pesticides (OCP), and methylmercury (MeHg), at 1 mg/kg/day. This mixture simulated the contaminant profile reported in maternal human blood. At birth, some control and M treated litters were crossfostered to form two additional groups with different biological/nursing mothers (CC and MM). The hepatic transcriptome was analyzed by DNA microarray in male offspring at postnatal days 21 and 78–86. Mixture exposure altered the expression of detoxification and energy metabolism genes in both age groups, but with different sets of genes affected at day 21 and 78–86. Cross-fostering modulated the effects of M on gene expression pattern (MM vs M), as well as expression of energy metabolism genes between control groups (CC vs C). In conclusion, while describing short- and long-term effects of developmental exposure to EC on hepatic transcriptomes, these cross-fostering results further support the consideration of non-chemical stressors in EC risk assessments.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30744511" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109015" }, "primaryId" : "GEO:GSE109015", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109015" } ] }, "title" : "Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats III.", "dateAssigned" : "2018-01-10T00:00:00.000-06:00", "summary" : "The notion that adverse health effects produced by exposure to environmental contaminants (EC) may be modulated by the presence of non-chemical stressors is gaining attention. Previously, our lab demonstrated that cross-fostering (adoption of a litter at birth) acted as a non-chemical stressor that amplified the influence of developmental exposure to EC on the glucocorticoid stress-response in adult rats. Using liver from the same rats, the aim of the current study was to investigate whether cross-fostering might also modulate EC-induced alterations in hepatic gene expression profiles. During pregnancy and nursing, Sprague-Dawley dams were fed cookies laced with corn oil (control, C) or a chemical mixture (M) composed of polychlorinated biphenyls (PCB), organochlorine pesticides (OCP), and methylmercury (MeHg), at 1 mg/kg/day. This mixture simulated the contaminant profile reported in maternal human blood. At birth, some control and M treated litters were crossfostered to form two additional groups with different biological/nursing mothers (CC and MM). The hepatic transcriptome was analyzed by DNA microarray in male offspring at postnatal days 21 and 78–86. Mixture exposure altered the expression of detoxification and energy metabolism genes in both age groups, but with different sets of genes affected at day 21 and 78–86. Cross-fostering modulated the effects of M on gene expression pattern (MM vs M), as well as expression of energy metabolism genes between control groups (CC vs C). In conclusion, while describing short- and long-term effects of developmental exposure to EC on hepatic transcriptomes, these cross-fostering results further support the consideration of non-chemical stressors in EC risk assessments.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30744511" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109016" }, "primaryId" : "GEO:GSE109016", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109016" } ] }, "title" : "Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats IV.", "dateAssigned" : "2018-01-10T00:00:00.000-06:00", "summary" : "The notion that adverse health effects produced by exposure to environmental contaminants (EC) may be modulated by the presence of non-chemical stressors is gaining attention. Previously, our lab demonstrated that cross-fostering (adoption of a litter at birth) acted as a non-chemical stressor that amplified the influence of developmental exposure to EC on the glucocorticoid stress-response in adult rats. Using liver from the same rats, the aim of the current study was to investigate whether cross-fostering might also modulate EC-induced alterations in hepatic gene expression profiles. During pregnancy and nursing, Sprague-Dawley dams were fed cookies laced with corn oil (control, C) or a chemical mixture (M) composed of polychlorinated biphenyls (PCB), organochlorine pesticides (OCP), and methylmercury (MeHg), at 1 mg/kg/day. This mixture simulated the contaminant profile reported in maternal human blood. At birth, some control and M treated litters were crossfostered to form two additional groups with different biological/nursing mothers (CC and MM). The hepatic transcriptome was analyzed by DNA microarray in male offspring at postnatal days 21 and 78–86. Mixture exposure altered the expression of detoxification and energy metabolism genes in both age groups, but with different sets of genes affected at day 21 and 78–86. Cross-fostering modulated the effects of M on gene expression pattern (MM vs M), as well as expression of energy metabolism genes between control groups (CC vs C). In conclusion, while describing short- and long-term effects of developmental exposure to EC on hepatic transcriptomes, these cross-fostering results further support the consideration of non-chemical stressors in EC risk assessments.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30744511" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109017" }, "primaryId" : "GEO:GSE109017", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109017" } ] }, "title" : "Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats V.", "dateAssigned" : "2018-01-10T00:00:00.000-06:00", "summary" : "The notion that adverse health effects produced by exposure to environmental contaminants (EC) may be modulated by the presence of non-chemical stressors is gaining attention. Previously, our lab demonstrated that cross-fostering (adoption of a litter at birth) acted as a non-chemical stressor that amplified the influence of developmental exposure to EC on the glucocorticoid stress-response in adult rats. Using liver from the same rats, the aim of the current study was to investigate whether cross-fostering might also modulate EC-induced alterations in hepatic gene expression profiles. During pregnancy and nursing, Sprague-Dawley dams were fed cookies laced with corn oil (control, C) or a chemical mixture (M) composed of polychlorinated biphenyls (PCB), organochlorine pesticides (OCP), and methylmercury (MeHg), at 1 mg/kg/day. This mixture simulated the contaminant profile reported in maternal human blood. At birth, some control and M treated litters were crossfostered to form two additional groups with different biological/nursing mothers (CC and MM). The hepatic transcriptome was analyzed by DNA microarray in male offspring at postnatal days 21 and 78–86. Mixture exposure altered the expression of detoxification and energy metabolism genes in both age groups, but with different sets of genes affected at day 21 and 78–86. Cross-fostering modulated the effects of M on gene expression pattern (MM vs M), as well as expression of energy metabolism genes between control groups (CC vs C). In conclusion, while describing short- and long-term effects of developmental exposure to EC on hepatic transcriptomes, these cross-fostering results further support the consideration of non-chemical stressors in EC risk assessments.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30744511" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109018" }, "primaryId" : "GEO:GSE109018", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109018" } ] }, "title" : "Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats VI.", "dateAssigned" : "2018-01-10T00:00:00.000-06:00", "summary" : "The notion that adverse health effects produced by exposure to environmental contaminants (EC) may be modulated by the presence of non-chemical stressors is gaining attention. Previously, our lab demonstrated that cross-fostering (adoption of a litter at birth) acted as a non-chemical stressor that amplified the influence of developmental exposure to EC on the glucocorticoid stress-response in adult rats. Using liver from the same rats, the aim of the current study was to investigate whether cross-fostering might also modulate EC-induced alterations in hepatic gene expression profiles. During pregnancy and nursing, Sprague-Dawley dams were fed cookies laced with corn oil (control, C) or a chemical mixture (M) composed of polychlorinated biphenyls (PCB), organochlorine pesticides (OCP), and methylmercury (MeHg), at 1 mg/kg/day. This mixture simulated the contaminant profile reported in maternal human blood. At birth, some control and M treated litters were crossfostered to form two additional groups with different biological/nursing mothers (CC and MM). The hepatic transcriptome was analyzed by DNA microarray in male offspring at postnatal days 21 and 78–86. Mixture exposure altered the expression of detoxification and energy metabolism genes in both age groups, but with different sets of genes affected at day 21 and 78–86. Cross-fostering modulated the effects of M on gene expression pattern (MM vs M), as well as expression of energy metabolism genes between control groups (CC vs C). In conclusion, while describing short- and long-term effects of developmental exposure to EC on hepatic transcriptomes, these cross-fostering results further support the consideration of non-chemical stressors in EC risk assessments.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30744511" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109041" }, "primaryId" : "GEO:GSE109041", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109041" } ] }, "title" : "Analysis of pathways elicited by empty SV40 capsids (VLPs) in septic rats 6 hours post 2CLP operation", "dateAssigned" : "2018-01-10T00:00:00.000-06:00", "summary" : "During the first hours after infection, before SV40 DNA enters the nucleus, empty capsids (VLPs) and the wild-type virus have the same effect on cellular signaling. VLPs were previously found to ameliorate toxic acute kidney injury (AKI) in a mouse model, counteracting apoptosis by inducing the Akt-1 survival pathway. Here we tested their effect on severe sepsis in rats. VLP pre-treatment increased survival and recovery from zero to 75%. RNAseq studies demonstrated that unlike AKI, here the VLPs did not induce survival pathways. Instead they affected thousands of genes and many cellular functions, eliminating deleterious pathways and inducing beneficial ones: immune response, resolution of inflammation, regeneration and cell and system homeostasis. In contrast, only four genes were affected following VLP administration to healthy rats. We propose that SV40 VLPs respond specifically to perturbation in cellular activities. The study suggests that diseases with complex pathophysiology may require treatments affecting wide-spectrum functions. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32110278" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109056" }, "primaryId" : "GEO:GSE109056", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109056" } ] }, "title" : "Paternal exposure to Arctic contaminants alters the sperm epigenome and induces negative pregnancy outcomes transgenerationally", "dateAssigned" : "2018-01-10T00:00:00.000-06:00", "summary" : "Paternal exposure to environmentally-relevant Arctic contaminants induces adverse health outcomes and alters the sperm methylome over three generations.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34968297" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109145" }, "primaryId" : "GEO:GSE109145", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109145" } ] }, "title" : "Histone 3 (k14) acetilation in hyperbilirubinmia", "dateAssigned" : "2018-01-12T00:00:00.000-06:00", "summary" : "Bilirubin toxicity to the CNS has been widely studied for decades, and shown impacting potential toxic/adaptation mechanisms by a significant modulation of gene expression, suggesting that mechanisms having crucial role on the regulation of gene expression, such as epigenetic mechanisms, should have a strong impact in unconjugated bilirubin toxicity. In this work, we followed the levels of histone 3 acetylation (H3K14Ac) in the cerebellum (Cll) of the developing (2, 9, 17 days after the birth and in adult age) Gunn rat (the natural model for neonatal hyperbilirubinemia and kernicterus) by Western blot, discovering an age specific alteration of the H3K14Ac in the hyperbilirubinemic animals. Then, the H3K14Ac linked chromatin was immune-precipitated and submitted to sequencing (ChIP-Seq). The GeneOntology analysis revealed that almost the 45% of H3K14Ac ChiP-Seq TSS-promoter genes were involved in the CNS development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30209300" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109148" }, "primaryId" : "GEO:GSE109148", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109148" } ] }, "title" : "Identification of novel diagnostic markers for fatal hypothermia by body temperature-dependent gene expression analysis in rats", "dateAssigned" : "2018-01-12T00:00:00.000-06:00", "summary" : "Diagnosis of fatal hypothermia is considered to be difficult in forensic practice. In this study, in order to identify novel molecular markers of fatal hypothermia, we made rat models of mild, moderate and severe hypothermia, and performed body temperature-dependent gene expression analysis in illiopsoas muscle using next-generation sequencing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29959558" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109412" }, "primaryId" : "GEO:GSE109412", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109412" } ] }, "title" : "Pharmacokinetic, antihypertension and deep sequencing MiRNomes analysis of aorta from SHR fed with EGCG", "dateAssigned" : "2018-01-19T00:00:00.000-06:00", "summary" : "Mechanism (s) of the epigallocatechin-3-gallate (EGCG) as major effective components in green tea regarding the reduction of hypertensive risk might associate with microRNAs (miRNAs). The plasma distribution of EGCG and epigallocatechin (EGC) in Sprague-Dawley rats were analyzed pharmacokinetically and found that they did not distribute well in plasma but widely in tissues, and their plasma deposition best fitted a mono-compartmental model with Cmax (6.65 vs 4.45 μg/mL) and Tmax (15 vs 10 min). Blood pressure monitoring of spontaneously hypertensive rats (SHR) intragastrically administrated with 300 mg/kg BW showed that systolic blood pressure (SBP) decreased to the lowest point by 34.04 mmHg and recovered by 23.39 mmHg after 15 and 30 min of administration, respectively, and it decreased again at 60 min and recovered at time 2 h. Total 150 upregulated and 18 downregulated miRNAs were identified via the deep sequencing and were 1.0 or 0.5 fold to the control group (P<0.01) after EGCG administration. And, hypertension-associated miRNA-126-3p and miRNA-150 were further validated by qRT-PCR. It might help explore novel pathways involving antihypertensive effect of EGCG.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109441" }, "primaryId" : "GEO:GSE109441", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109441" } ] }, "title" : "RNA-seq of a high glucose induced oxidative stress and apoptosis model on primary rat cardiomyocytes", "dateAssigned" : "2018-01-19T00:00:00.000-06:00", "summary" : "Diabetic hyperglycemia promotes reactive oxygen species (ROS) production to lead to oxidative stress and apoptosis responsible for progressive deterioration of the structure and function of organs. It has been indicated that factors and pathways regulating ROS production and the cellular redox state play a key role in the progression of diabetes and diabetes complications including cardiomyopathy. Recent studies had demonstrated that long non-coding RNAs (lncRNAs) played crucial roles on modulation of oxidative stress and apoptosis activity. In this study, we first established a high glucose induced oxidative stress and apoptosis model on primary rat cardiomyocytes. ROS formation and apoptosis activity were significantly increased at 24h/48h after high glucose stimulation. RNA sequencing analysis was applied to detect differentially expressed lncRNAs during cardiomyocytes oxidative stress and apoptosis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109445" }, "primaryId" : "GEO:GSE109445", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109445" } ] }, "title" : "RNA sequencing analysis of gene expression in rat hippocampus exposed to chronic stress and albiforin treatment", "dateAssigned" : "2018-01-19T00:00:00.000-06:00", "summary" : "We performed high-throughput profiling of gene expression in rat hippocampus in response to chronic unpredictable mild stress (CUMS) and albiflorin treatment. Total 415 differentially expressed genes (DEGs) were identified in rat hippocampus in response to albiflorin treatment compared with CUMS rats treated with saline (CUMS-Sal). We conducted the integrated metabolomics and transcriptomics analysis and found the correction of 16 biochemical pathways by albiflorin such as sphingolipids, phospholipids, tryptophan metabolism, fatty acid oxidation, and purine and pyrimidine metabolism. Our study provided deep insights into the understanding of the molecular mechanisms underlying the rapid antidepressant actions of albiflorin.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109568" }, "primaryId" : "GEO:GSE109568", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109568" } ] }, "title" : "Systemic hormonal modulation induces sperm nucleosomal imbalance in rat spermatozoa", "dateAssigned" : "2018-01-24T00:00:00.000-06:00", "summary" : "The male gamete has an immense role in reproduction. Besides contributing one half of the genomic DNA, it contributes important epigenetic information that controls and orchestrates its expression during the early stages of embryo development. Although, DNA methylation is a widely studied epigenetic modification, other epigenetic changes like histone modifications, nucleosome landscape and chromatin compaction are also gaining significant consideration. Sperm chromatin despite being majorly compacted with protamines; strategically retains 2-4% of the genome in nucleosomes. While DNA bases are resilient, epigenetic marks are highly susceptible to reprogramming. Environmental pollutants have been known to affect epigenetic marks and many of those pollutants are known to be xeno-estrogenic. Previous studies using tamoxifen, a Selective Estrogen Receptor Modulator – SERM, has been shown to be associated with post implantation loss and DNA methylation aberration in rats. Also, Cyperoterone acetate (CPA), an antiandrogen, has been shown to induce retention of histone modifications in testis. In this study, we show by MNase-sequencing that systemic hormonal disruption leads to deviation in the nucleosomal localization in spermatozoa at many genes of significance during early embryo development. Thus, environmental pollutants, which are mainly estrogenic or antiandrogenic in nature, may exert epigenetic aberrations in the spermatozoa through hormonal disruption which may lead to severe complications during embryo development or in adult life.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29920734" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109622" }, "primaryId" : "GEO:GSE109622", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109622" } ] }, "title" : "Comparison of the transcriptomes of immortalized Hertwig’s epithelial root sheath (HERS) cell line HERS-H1 and HERS-C2", "dateAssigned" : "2018-01-25T00:00:00.000-06:00", "summary" : "We compared the transcriptome of the immortalized HERS cell line HERS-H1 and HERS-C2, using the Agilent Rat 4x44K Gene Expression Microarrays. We used primary Hertwig’s epithelial root sheath (HERS) cells as naïve cell reference.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30606270" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109656" }, "primaryId" : "GEO:GSE109656", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109656" } ] }, "title" : "Change expression of genes in iron chelation and deficient conditions", "dateAssigned" : "2018-01-25T00:00:00.000-06:00", "summary" : "Firstly, cell senescence and anti-oxidant genes were down-regulated by iron deficient mice and iron-specific chelator deferoxamine (DFO) using a DNA microarray. Our data suggested that down-regulation of anti-oxidant genes and cell senescence gene induced oxidative stress in iron-deficient and -specific chelated condition.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109685" }, "primaryId" : "GEO:GSE109685", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109685" } ] }, "title" : "Transcriptomic profile in the liver of rats treated with the chemopreventive butyrate-containing structured lipids.", "dateAssigned" : "2018-01-25T00:00:00.000-06:00", "summary" : "It is widely believed that the prevention of cancer is the most promising strategy for reducing both cancer incidence and cancer-related mortality. Dietary bioactive components have been found to modulate many dysregulated molecular pathways associated with the development of cancer. Epidemiological and pre-clinical data suggest that sodium butyrate and its derivatives possess chemopreventive properties. Specifically, the butyrate-containing structured lipid (STL) presented strong chemopreventive proprieties in experimental hepatocarcinogenesis. To determine the mechanistic basis, the hepatic transcriptomic profiles in rats submitted to a classic “resistant hepatocyte” model of hepatocarcinogenesis and treated with butyrate-containing STL were evaluated. A total of 1583 genes were found to be differentially expressed in the livers of rats treated with butyrate-containing STL. Pathways analysis of the differentially expressed genes demonstrated a strong enrichment in genes involved in epithelial mesenchymal transition, vasculogenesis, and cell proliferation. In conclusion, tumor-suppressing activity of butyrate containing STLs is associated with its ability to regulated major hepatocarcinogenesis-related pathways at early stages of rat liver carcinogenesis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109697" }, "primaryId" : "GEO:GSE109697", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109697" } ] }, "title" : "Altered Expression Profiles of Transfer-RNA-Derived Small RNAs Reveal the Regulating Functions in Rat Brain After Intracerebral Hemorrhage (ICH) and the Potential Therapeutic Targets of Buyang Huanwu Decoction in ICH", "dateAssigned" : "2018-01-26T00:00:00.000-06:00", "summary" : "Transfer-RNA-Derived Small RNA (tsRNA) is s a novel class of short non-coding RNA including stress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF). Using RNA sequencing, we evaluated the tsRNA expression profiles in the brain of intracerebral hemorrhage (ICH) and sham rats at days 21. Meanwhile, tsRNA levels in ICH treated with the Traditional Chinese Medicine named Buyang Huanwu Decoction (BYHWD) were detected. Bioinformatics analyses indicated that tsRNAs were the important regulators in ICH and potential new therapeutic targets of BYHWD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33203799" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109775" }, "primaryId" : "GEO:GSE109775", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109775" } ] }, "title" : "Alterations in Sperm DNA Methylation, Non-coding RNA and Histone Retention Associate with DDT Induced Epigenetic Transgenerational Inheritance of Disease", "dateAssigned" : "2018-01-29T00:00:00.000-06:00", "summary" : "Environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease through the germline. This study was designed to investigate DDT induced concurrent alterations of a number of different epigenetic processes including DNA methylation and histone retention in sperm. Gestating female rats were exposed transiently to DDT during fetal gonadal development and then F1, F2 and F3 generation sperm were analyzed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33436057" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109849" }, "primaryId" : "GEO:GSE109849", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109849" } ] }, "title" : "Expression data of mRNA from kidney of SD rats with chronic exposure to cadmium", "dateAssigned" : "2018-01-30T00:00:00.000-06:00", "summary" : "We used Affymetrix RTA arrays to detail the global gene expression profile of kidney tissues of SD rats with chronic exposure to Cadmium, and identified distinct classes of cadmium exposure related mRNA and pathways.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109902" }, "primaryId" : "GEO:GSE109902", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109902" } ] }, "title" : "Transcriptional screen in the target region of sprouting hindlimb corticospinal fibers after thoracic spinal cord injury in rats", "dateAssigned" : "2018-01-30T00:00:00.000-06:00", "summary" : "We hypothesize that sectreted factors and guidance and adhesion molecules are specifically expressed in the intermediate laminae of the cervical spinal cord to direct and target the ingrowth of the sprouting hindlimb CST fibers. To test our hypothesis the transcription profile of the target region of sprouts was investigated with RNA sequencing of total RNA extracted from the intermediate laminae (IV-VII) of the spinal gray matter at cervical level C3. Four major comparisons were performed, which were then again compared to each other. The first comparison was between samples of animals with an SCI sacrificed at four different time points after injury (1, 3, 6, 12 weeks after injury). The second and third comparison was between samples of rats with a SCI compared to their sham controls sacrificed at the same time point after surgery (1 week or 12 weeks respectively). The fourth comparison was between samples from animals of the two control groups, rats with a sham surgery which were either sacrificed at one or at twelve weeks after injury. We found that most changes in gene expression ocurred at one week after SCI and least changes occured at twelve weeks after SCI, suggesting that the largest effects on a global level of gene expression occur during early time points after injury. Interestingly, also we also found changes in gene expression when comparing the samples from the two control groups, which suggests that sham surgery consisting of a laminectomy is sufficient to induce transcriptional changes in the spinal cord. This is the first study to provide insight into transcriptional changes in the target region of sprouts investigating the role of the cervical spinal cord (target region) for sprouting of hindlimb CST fibers.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109973" }, "primaryId" : "GEO:GSE109973", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE109973" } ] }, "title" : "Intergrated epigenetics, transcriptomics and metabolomics to analyze the mechanism of Benzo[a]pyrene neurotoxicity in hippocampus", "dateAssigned" : "2018-02-01T00:00:00.000-06:00", "summary" : "Conclusions: B[a]P could bring on the epigenetics changes as well as the transcriptomics changes and further affected gene expression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110115" }, "primaryId" : "GEO:GSE110115", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110115" } ] }, "title" : "Identifiation of lncRNA expression profiles and ceRNA analysis in the spinal cord of morphine tolerance rats", "dateAssigned" : "2018-02-05T00:00:00.000-06:00", "summary" : "The mechanism of morphine tolerance remains unclear, and lncRNA have been promising molecule in many pathophysiological processes. However, the role of lncRNA on morphine tolerance hasn’t been explored yet. So we explore this issue, and our results indicated that the expression profiles of lncRNAs have changed in morphine tolerance rats as compared with normal rats, and among those, some differentially expressed lncRNAs might be new therapeutic targets for morphine tolerance.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29636075" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110197" }, "primaryId" : "GEO:GSE110197", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110197" } ] }, "title" : "Differential gene expression in the stellate ganglia of 16 week wistar and spontaneously hypertensive rat samples", "dateAssigned" : "2018-02-06T00:00:00.000-06:00", "summary" : "Hypertension remains a poorly understood condition, and the understanding of the sympathetic nervous systems role in this disease remains even more limited. In this study, RNA-sequencing is used to identify transcriptomal differences in the sympathetic stellate ganglia between the 16-week-old normotensive wistar strain and the spontaneously hypertensive rat strain.This dataset should allow for further molecular characterisation of hypertensive changes in a cardiac-innervating sympathetic ganglion.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29686017" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110231" }, "primaryId" : "GEO:GSE110231", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110231" } ] }, "title" : "Analysis of altered miRNA expression profiles in the streptozotocin-induced diabetic rats compared to normal SD rats", "dateAssigned" : "2018-02-06T00:00:00.000-06:00", "summary" : "Diabetes mellitus (DM) is one of the most common chronic diseases around the world, and diabetic peripheral neuropathy (DPN) is one of the most common complications of DM. We used microarrays to identify the differentially expressed miRNAs in dorsal root ganglia (DRG) tissues from streptozotocin (STZ)-induced diabetic rats, taking normal SD rats as controls, and tried to find out the related genes which may be involved in the development of DPN.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110233" }, "primaryId" : "GEO:GSE110233", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110233" } ] }, "title" : "Analysis of altered lncRNA and mRNA expression profiles in the streptozotocin-induced diabetic rats compared to normal SD rats", "dateAssigned" : "2018-02-06T00:00:00.000-06:00", "summary" : "Diabetes mellitus (DM) is one of the most common chronic diseases around the world, and diabetic peripheral neuropathy (DPN) is one of the most common complications of DM. We used microarrays to identify the differentially expressed lncRNAs and mRNAs in dorsal root ganglia (DRG) tissues from streptozotocin (STZ)-induced diabetic rats, taking normal SD rats as controls, and tried to find out the related genes which may be involved in the development of DPN.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110282" }, "primaryId" : "GEO:GSE110282", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110282" } ] }, "title" : "2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) Alters Hepatic Polyunsaturated Fatty Acid Metabolism and Eicosanoid Biosynthesis in Female Sprague-Dawley Rats [ChIP-Seq]", "dateAssigned" : "2018-02-07T00:00:00.000-06:00", "summary" : "2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a potent aryl hydrocarbon receptor (AhR) agonist that elicits a broad spectrum of dose-dependent effects in the liver, including hepatic lipid accumulation coupled with inflammation. To determine the role of inflammatory lipid mediators in TCDD-mediated hepatotoxicity, eicosanoid metabolism was investigated in female Sprague-Dawley (SD) rats. Rats were gavaged with sesame oil vehicle or 0.01-10 µg/kg TCDD every 4 days for 28 days. Hepatic RNA-Seq data from female SD rats was compared with data from female C57BL/6 mice and functionally annotated to determine key toxicogenomic differences between the two species regarding TCDD exposure. Hepatic RNA-Seq data from female SD rats integrated with untargeted metabolomics of liver, serum, and urine identified dose-dependent changes in linoleic acid (LA) and arachidonic acid (AA) metabolism. TCDD also elicited dose-dependent differential gene expression associated with cyclooxygenase, lipoxygenase, and cytochrome P450 epoxidation/ hydroxylation pathways with corresponding changes in omega-6 (e.g. AA and LA) and omega-3 polyunsaturated fatty acids (PUFAs) as well as their eicosanoid metabolites. Overall, total omega-6 PUFAs increased, while total omega-3 PUFAs decreased. Phospholipase A2 (Pla2g12a) was induced 6-fold consistent with increased AA metabolism, while AA utilization by lipoxygenases Alox5 (2-fold) and Alox15 (10-fold) increased leukotrienes (LTs), important mediators signaling an inflammatory response. More specifically, TCDD increased pro-inflammatory eicosanoids, including leukotriene (LT) B4 (3-fold), and LTB3 (5-fold), known signals for the recruitment of neutrophils to areas of tissue damage. Dose-response modeling of metabolite and gene expression changes suggests the cytochrome P450 hydroxylase/epoxygenase and the lipoxygenase pathways are the most sensitive to TCDD. While several differentially expressed genes (DEGs) associated with eicosanoid biosynthesis contained putative dioxin response elements (pDRE) within their regulatory region, ChIP-Seq analysis showed little AhR enrichment, suggesting TCDD-elicited induction of eicosanoid biosynthesis is not a direct effect of AhR activation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110293" }, "primaryId" : "GEO:GSE110293", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110293" } ] }, "title" : "2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) Alters Hepatic Polyunsaturated Fatty Acid Metabolism and Eicosanoid Biosynthesis in Female Sprague-Dawley Rats [RNA-Seq]", "dateAssigned" : "2018-02-07T00:00:00.000-06:00", "summary" : "2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a potent aryl hydrocarbon receptor (AhR) agonist that elicits a broad spectrum of dose-dependent effects in the liver, including hepatic lipid accumulation coupled with inflammation. To determine the role of inflammatory lipid mediators in TCDD-mediated hepatotoxicity, eicosanoid metabolism was investigated in female Sprague-Dawley (SD) rats. Rats were gavaged with sesame oil vehicle or 0.01-10 µg/kg TCDD every 4 days for 28 days. Hepatic RNA-Seq data from female SD rats was compared with data from female C57BL/6 mice and functionally annotated to determine key toxicogenomic differences between the two species regarding TCDD exposure. Hepatic RNA-Seq data from female SD rats integrated with untargeted metabolomics of liver, serum, and urine identified dose-dependent changes in linoleic acid (LA) and arachidonic acid (AA) metabolism. TCDD also elicited dose-dependent differential gene expression associated with cyclooxygenase, lipoxygenase, and cytochrome P450 epoxidation/ hydroxylation pathways with corresponding changes in omega-6 (e.g. AA and LA) and omega-3 polyunsaturated fatty acids (PUFAs) as well as their eicosanoid metabolites. Overall, total omega-6 PUFAs increased, while total omega-3 PUFAs decreased. Phospholipase A2 (Pla2g12a) was induced 6-fold consistent with increased AA metabolism, while AA utilization by lipoxygenases Alox5 (2-fold) and Alox15 (10-fold) increased leukotrienes (LTs), important mediators signaling an inflammatory response. More specifically, TCDD increased pro-inflammatory eicosanoids, including leukotriene (LT) B4 (3-fold), and LTB3 (5-fold), known signals for the recruitment of neutrophils to areas of tissue damage. Dose-response modeling of metabolite and gene expression changes suggests the cytochrome P450 hydroxylase/epoxygenase and the lipoxygenase pathways are the most sensitive to TCDD. While several differentially expressed genes (DEGs) associated with eicosanoid biosynthesis contained putative dioxin response elements (pDRE) within their regulatory region, ChIP-Seq analysis showed little AhR enrichment, suggesting TCDD-elicited induction of eicosanoid biosynthesis is not a direct effect of AhR activation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110426" }, "primaryId" : "GEO:GSE110426", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110426" } ] }, "title" : "Small Molecule PCSK9 Inhibitors: Hit to lead optimization", "dateAssigned" : "2018-02-09T00:00:00.000-06:00", "summary" : "Ribosome profiling is used to demonstrate improved selectivity of compounds that promote PCSK9 translational stalling", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29878763" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110507" }, "primaryId" : "GEO:GSE110507", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110507" } ] }, "title" : "The vitamin D receptor (VDR) autonomously regulates skeletal muscle mass", "dateAssigned" : "2018-02-12T00:00:00.000-06:00", "summary" : "Vitamin D (VitD) deficiency is estimated to affect ~40% of the world’s population. Notably, VitD deficiency has been associated with impaired muscle maintenance and insulin resistance. VitD exerts its actions through the ubiquitous Vitamin D-receptor (VDR), the expression of which was recently confirmed in fully-differentiated muscle. To seek a possible autonomous role of the VDR in skeletal muscle, we first generated stable VDR-knockdown cells, which exhibited impaired myogenesis (i.e. cell-cycling, differentiation and myotube formation). In vivo VDR-knockdown in rat hind-limbs elicited myofibre atrophy and triggered autophagy pathways. In contrast, in vivo VDR-overexpression yielded myofibre hypertrophy; enhancing translational efficiency (e.g. mTOR-signaling), ribosomal biogenesis and satellite cell content. Neither VDR-knockdown nor overexpression impacted muscle glucose uptake. Crucially, induction of VDR mRNA correlated with muscle hypertrophy in humans following long-term resistance exercise training, but not aspects of insulin sensitivity. The VDR autonomously regulates muscle mass, acting reciprocally to limit atrophy and promote hypertrophy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33258480" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110553" }, "primaryId" : "GEO:GSE110553", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110553" } ] }, "title" : "Effects of in utero and lactational exposure to new generation green plasticizers on adult male rats: a comparative study with di(2-ethylhexyl) phthalate", "dateAssigned" : "2018-02-13T00:00:00.000-06:00", "summary" : "The data deposited correspond to testicular gene expression in 90 day-old Sprague-Dawley rats after exposure to CORN OIL and 30 or 300 mg/kg/day DEHP, DINCH, BDB or DOS from gestational day 8 to post-natal day 21", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110622" }, "primaryId" : "GEO:GSE110622", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110622" } ] }, "title" : "PTEN Deficiency Promotes Pathological Vascular Remodeling of Human Coronary Arteries", "dateAssigned" : "2018-02-14T00:00:00.000-06:00", "summary" : "We used Affymetrix microarrays to detail the global program of gene expression changes between PTEN deficient and wild type smooth muscle cells. We identified distinct classes of up- and down-regulated genes during this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110652" }, "primaryId" : "GEO:GSE110652", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110652" } ] }, "title" : "Genome-wide map of proximity linkage to renin proximal promoter in rat", "dateAssigned" : "2018-02-15T00:00:00.000-06:00", "summary" : "Physical proximity mapping through sequencing can provide an unbiased view of the chromatin close to the proximal promoter of the renin gene (Ren). Our objective was to determine genomic regions that physically interact with the renin proximal promoter, using two different genetic backgrounds, the Dahl salt sensitive and normotensive SS-13BN, which have been shown to have different regulation of plasma renin in vivo. The chromatin conformation capture method with sequencing focused at the Ren proximal promoter in rat-derived cardiac endothelial cells was used. Cells were fixed, chromatin close to the Ren promoter was captured, and fragments were sequenced. The clustering of mapped reads produced a genome-wide map of chromatin in contact with the Ren promoter. The largest number of contacts was found on chromosome 13, the chromosome with Ren, and contacts were found on all other chromosomes except chromosome X. These contacts were significantly enriched with genes positively correlated with Ren expression and with mapped quantitative trait loci (QTLs) associated with blood pressure, cardiovascular and renal phenotypes. The results were reproducible in an independent biological replicate and in endothelial cells derived from a second rat stain. The findings reported here represent the first map between a critical cardiovascular gene and physical interacting loci throughout the genome, and will provide the basis for several new directions of research.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29521603" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110675" }, "primaryId" : "GEO:GSE110675", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110675" } ] }, "title" : "Gene expression profiling of the retinal microvessels and the brain microvessels", "dateAssigned" : "2018-02-15T00:00:00.000-06:00", "summary" : "Using these DEGs, we comprehensively analyzed gene expression of the microvessels and highlighted their involvement in critical functional structures in RMVs and BMVs, such as junctional complex, transporters and signaling pathways.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110804" }, "primaryId" : "GEO:GSE110804", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110804" } ] }, "title" : "RNA sequencing reveals RNA binding protein HuR/ELAVL1 regulates extracellular matrix gene expression in nucleus pulposus cells of the intervertebral disc", "dateAssigned" : "2018-02-19T00:00:00.000-06:00", "summary" : "We used RNA sequencing to identify transcripts that were controlled by the RNA binding factor HuR/ELAVL1 in nucleus pulposus cells of the intervertebral disc.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30092282" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110908" }, "primaryId" : "GEO:GSE110908", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE110908" } ] }, "title" : "RNA Sequencing quantitatively profiles chemical long-term potentiation (LTP) induced gene transcription alteration", "dateAssigned" : "2018-02-20T00:00:00.000-06:00", "summary" : "To identify proteins involved in activity dependent synaptic remodeling that are not caused by changes in mRNA levels we performed RNA-seq and TMT-based quantitative MS.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111134" }, "primaryId" : "GEO:GSE111134", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111134" } ] }, "title" : "A compendium of conserved cleavage and polyadenylation events in mammalian genes", "dateAssigned" : "2018-02-26T00:00:00.000-06:00", "summary" : "Cleavage and polyadenylation is essential for 3’ end processing of almost all eukaryotic mRNAs. Recent studies have shown widespread alternative cleavage and polyadenylation (APA) events leading to mRNA isoforms with different 3’UTRs and/or coding sequences. Here we present a compendium of conserved cleavage and polyadenylation sites (PASs) in mammalian genes, based on ~1.2 billion 3’ end sequencing reads from over 360 human, mouse and rat samples. We show that ~80% of mammalian mRNA genes contain at least one conserved PAS, and ~50% have conserved APA events. PAS conservation generally reduces promiscuous 3’ end processing, stabling gene expression levels across species. Conservation of APA correlates with gene age, gene expression features, and gene functions. Genes with certain functions, such as cell morphology, cell proliferation, and mRNA metabolism, are particularly enriched with APA events. While tissue-specific genes typically have a low APA rate, brain-specific genes tend to evolve APA. We show enrichment of mRNA destabilizing motifs in alternative 3’UTR sequences, leading to substantial differences in mRNA stability between 3’UTR APA isoforms. Using conserved PASs, we reveal sequence motifs surrounding APA sites and a preference of adenosine at the cleavage site. Mutations of the U-rich motif around the PAS often accompany APA profile changes between species. Analysis of lncRNA PASs indicates a mechanism of PAS fixation involving evolution of A-rich motifs. Taken together, our results present a comprehensive view of PAS evolution in mammals, and a phylogenic understanding of APA functions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30143597" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111160" }, "primaryId" : "GEO:GSE111160", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111160" } ] }, "title" : "Transcriptional analysis of trigeminal ganglia in a CFA-induced rat orofacial pain model", "dateAssigned" : "2018-02-26T00:00:00.000-06:00", "summary" : "Although several underlying pathophysiological processes have been explored, the origin and precise pathomechanism of migraine are still being debated. Inflammatory pathways have been suggested to play role in migraine, trigeminal nociceptor sensitisation, thereby causing hyperalgesia and allodynia. The aim of the present study was to investigate gene expression changes in trigeminal ganglia (TRG), central trigeminal nucleus caudalis (TNC) and peripheral blood mononuclear cells (PBMC) evoked by Complete Freund’s Adjuvant (CFA) induced peripheral inflammation. 512 differentially expressed genes were found between CFA-treated and contralateral TRG samples 7 days after CFA injection. The mRNA expression changes of G-protein coupled receptor 39 (Gpr39), kisspeptin-1 receptor (Kiss1r), kisspeptin (Kiss1) and Lkaaear1 were selected for validation. They were most upregulated on day 3 in TRGs of the CFA-treated side. CFA-induced significant orofacial mechanical allodynia in one day with a maximum on day 3. This correlated with patterns of neuronal (Fosb), glial (Iba1), and astrocyte (Gfap) activation markers in both TRG and TNC, and surprisingly in PBMCs. Similar transcriptional changes of Cgrp, the well-known key molecule in migraine pathophysiology, were also revealed. In TNCs, gene expression changes similar to TRGs were observed but Kiss1r transcripts were not significantly altered while Neurod2 was observed only in TNC. These results could indicate the involvement of Gpr39, Kiss1r and synaptic plasticity associated Lkaaear1, Neurod2 genes in the cascade of events resulting in the sensitization underlying migraine headache and the accompanying facial allodynia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29997476" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111207" }, "primaryId" : "GEO:GSE111207", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111207" } ] }, "title" : "Riboflavin deficiency regulates inflammation-associated genes in rat esophageal intraepithelial neoplasia", "dateAssigned" : "2018-02-27T00:00:00.000-06:00", "summary" : "Epidemiological studies suggest that dietary riboflavin deficiency and environmental exposure to N-nitrosomethylbenzylamine (NMBA) are common in China's high incidence area of esophageal cancer. Riboflavin deficiency has been documented as an important risk factor for esophageal cancer. In this study, we established a F344 rat esophageal tumor model that combines dietary riboflavin deficiency with exposure to NMBA. The results showed that riboflavin deficiency combined with NMBA (R0N+) enhanced the incidence of esophageal intraepithelial neoplasia, including in situ carcinoma, whereas normal levels of riboflavin combined with NMBA (RcN+) mainly induced the occurrence of esophageal benign hyperplasia and small amount of esophageal intraepithelial neoplasia. Oxidative DNA damage (8-OHdG) and DNA double-strand breaks (p-γH2AX) in R0N+ rats were higher than that in RcN+ rats. The aim of the present study is to analyze the mechanism of riboflavin deficiency-induced tumorigenesis. So, we used Affymetrix Clariom D(also known as Rat Transcriptome Array 1.0) to identify genes that were differentially expressed upon R0N+ esophageal intraepithelial neoplasia tissues.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111241" }, "primaryId" : "GEO:GSE111241", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111241" } ] }, "title" : "Expression data from the cells of rat bronchoalveolar lavage fluid", "dateAssigned" : "2018-02-28T00:00:00.000-06:00", "summary" : "LPS is the most important biological mediator of sepsis induce secretion of inflammatory cytokines including TNF-α, IL-1, and IL-6 from many cell types in response to bacterial toxins. Thus LPS has been commonly used to establish inflammatory ALI models of rats and mice. Clinically, hypoxia commonly coexists with sepsis; however, the role of hypoxia on the development of inflammatory ALI is unclear. The understanding of interaction of hypoxia and inflammation in ALI is of the importance for the treatment of ALI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30083155" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111243" }, "primaryId" : "GEO:GSE111243", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111243" } ] }, "title" : "Genome-wide transcriptional profiling of central amygdala and orbitofrontal cortex during incubation of methamphetamine craving", "dateAssigned" : "2018-02-28T00:00:00.000-06:00", "summary" : "Methamphetamine (Meth) seeking progressively increases after withdrawal (incubation of Meth craving), but the transcriptional mechanisms that contribute to this incubation are unknown. Here we used RNA-sequencing to analyze transcriptional profiles associated with incubation of Meth craving in central amygdala (CeA) and orbitofrontal cortex (OFC), two brain areas previously implicated in relapse to drug seeking. We trained rats to self-administer either saline (control condition) or Meth (10 days; 9 h/day, 0.1 mg/kg/infusion). Next, we collected brain tissue from CeA and OFC on withdrawal day 2 (when Meth seeking is low and non-incubated) and on day 35 (when Meth seeking is high and incubated), for subsequent RNA-sequencing. In CeA, we identified 10-fold more differentially expressed genes (DEGs) on withdrawal day 35 than day 2. These genes were enriched for several biological processes, including protein ubiquitination and histone methylation. In OFC, we identified many fewer expression changes than in CeA. Interestingly, there were more DEGs on withdrawal day 2 than on day 35. Several genes in OFC showed opposing expression changes on withdrawal day 2 (increase) when compared to withdrawal day 35 (decrease), which was further validated by qPCR. Our analyses highlight the CeA as a key region of transcriptional regulation associated with incubation of Meth seeking. In contrast, transcriptional regulation in OFC may contributes to Meth seeking during early withdrawal. Overall, these findings provide a unique resource of gene expression data for future studies examining transcriptional mechanisms in CeA that mediate Meth seeking after prolonged withdrawal.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30072726" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111261" }, "primaryId" : "GEO:GSE111261", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111261" } ] }, "title" : "Gene expression data of prostate of PND 30 Sprague-Dawley rats (SD:Hsd) dosed prenatally and lactationally with HMB", "dateAssigned" : "2018-02-28T00:00:00.000-06:00", "summary" : "2-hydroxy-4-methoxybenzophenone (HMB) has been reported to have weak estrogenic activity by in vivo and in vitro studies, making it a chemical with potential reproductive concern. To explore if perinatal HMB exposure altered the gene expression profiling in the rat prostate, we analyzed whole genome and mitochondria-related gene expression profiling on the Prostate ontained from Sprague-Dawley rat offspring exposed prenatally and lactationally to varying dose of HMB.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30316929" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111262" }, "primaryId" : "GEO:GSE111262", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111262" } ] }, "title" : "Gene expression data of testis of PND 30 Sprague-Dawley rats (SD:Hsd) dosed prenatally and lactationally with HMB", "dateAssigned" : "2018-02-28T00:00:00.000-06:00", "summary" : "2-hydroxy-4-methoxybenzophenone (HMB) has been reported to have weak estrogenic activity by in vivo and in vitro studies, making it a chemical with potential reproductive concern. To explore if perinatal HMB exposure altered the gene expression profiling in the rat testis, we analyzed whole genome and mitochondria-related gene expression profiling on the testis ontained from Sprague-Dawley rat offspring exposed prenatally and lactationally to varying dose of HMB.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30316929" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111302" }, "primaryId" : "GEO:GSE111302", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111302" } ] }, "title" : "Characterization of Transcriptomes of Apical OHCs and Basal OHCs in Cochlea", "dateAssigned" : "2018-03-01T00:00:00.000-06:00", "summary" : "We analyzed the transcriptomes of 30 isolated apical OHCs and basal OHCs from rat cochlea, and the results showed that more than 50 genes were differentially expressed and 20 genes were uniquely expressed among these populations. We analyzed these genes with a focus on their functions related to cellular structure and transmembrane channels and their vulnerability to and involvement in hereditary deafness caused by OHC defects. Our results could serve as a guideline for exploring the molecular mechanisms underlying the biological properties of OHCs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111362" }, "primaryId" : "GEO:GSE111362", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111362" } ] }, "title" : "Perinatal paroxetine exposure in Selcetively-bred Low Responder rats", "dateAssigned" : "2018-03-02T00:00:00.000-06:00", "summary" : "Selective serotonin reuptake inhibitor (SSRI) antidepressants are the mainstay treatment for the 10-20% of pregnant and postpartum women who suffer major depression, but the effects of SSRIs on their children’s developing brain and later emotional health are poorly understood. SSRI use during pregnancy can elicit antidepressant withdrawal in newborns and increase toddlers’ anxiety and social avoidance. In rodents, perinatal SSRI exposure increases adult depression- and anxiety-like behavior, although certain individuals are more vulnerable to these effects than others. Our study establishes a rodent model of individual differences in susceptibility to perinatal SSRI exposure, utilizing selectively-bred Low Responder (LR) and High Responder (HR) rats that were previously bred for high versus low behavioral response to novelty. Pregnant HR/LR females were chronically treated with the SSRI paroxetine (10 mg/kg/day p.o.) to examine its effects on offspring’s emotional behavior and gene expression in the developing brain. Paroxetine treatment had minimal effect on HR/LR dams’ pregnancy outcomes or maternal behavior. We found that LR offspring, naturally prone to an inhibited/anxious temperament, were susceptible to behavioral abnormalities associated with perinatal SSRI exposure (which exacerbated their Forced Swim Test immobility), while high risk-taking HR offspring were resistant. Microarray studies revealed robust perinatal SSRI-induced gene expression changes in the developing LR hippocampus and amygdala (postnatal days 7-21), including transcripts involved in neurogenesis, synaptic vesicle components, and energy metabolism. These results highlight the LR/HR model as a useful tool to explore the neurobiology of individual differences in susceptibility to perinatal SSRI exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:25451292" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111384" }, "primaryId" : "GEO:GSE111384", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111384" } ] }, "title" : "Synaptic scaling regulates the transcriptome in hippocampal neurons", "dateAssigned" : "2018-03-03T00:00:00.000-06:00", "summary" : "To better comprehend how synaptic scaling affects the neuronal transcriptome, we used the whole genome microarray expression profiling in hippocampal cultures treated with AMPARs and synaptic NMDARs antagonists for 9h and 26h, or under control conditions. Gene ontology enrichment analysis showed altered transcripts associated with synaptic signalling and synaptic plasticity classes, including transcripts of several proteins already associated with synaptic scaling mechanisms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30808806" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111398" }, "primaryId" : "GEO:GSE111398", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111398" } ] }, "title" : "RNA-Seq analysis, transcriptome assembly and gene expression profile analysis for vascular smooth muscle cells with up- or downregulation of CKLF1", "dateAssigned" : "2018-03-05T00:00:00.000-06:00", "summary" : "To understand the role of Cklf1 in the proliferation of vascular smooth muscle cells (VSMC), we quantified the whole genome transcriptomes of VSMC that were treated by Cklf1 adenovirus (n=3) or control (n=3) for 24 h using RNA-seq. In total, we obtained over 82 million clean reads from each library after trimming adaptor sequences, low quality reads and multiple mapped reads. The clean reads were mapped to 29330 genes annotated in the rat reference genome (Rattus_norvegicus 6.0). We then identified differentially expressed genes (DEGs) between Cklf1-associated adenovirus and controls by comparing RNA-Seq data between the two groups. A total of 238 DEGs for Ad-GFP vs. Ad-Cklf1 and 468 DEGs for shRNA Scramble vs. shRNA Cklf1 were defined using the thresholds of FDR ≤ 0.05, difference ratio of FPKM (fragments per kilobase of exon model per million mapped fragments) ≥ 2 and diverge probability ≥ 0.8. The increased CKLF1 resulted in 34 up-regulated and 204 down-regulated genes while knockdown of Cklf1 led to 358 up-regulated and 110 down-regulated genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111441" }, "primaryId" : "GEO:GSE111441", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111441" } ] }, "title" : "Alterations in sperm DNA Methylation, Non-Coding RNA expression, and histone retention mediate Vinclozolin induced epigenetic transgenerational inheritance of disease", "dateAssigned" : "2018-03-05T00:00:00.000-06:00", "summary" : "Environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease through the germline. This study was designed to investigate vinclozolin induced concurrent alterations of a number of different epigenetic processes including DNA methylation and histone retention in sperm. Gestating female rats were exposed transiently to vinclozolin during fetal gonadal development and then F1, F2 and F3 generation sperm were analyzed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29732173" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111442" }, "primaryId" : "GEO:GSE111442", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111442" } ] }, "title" : "Genome-wide epigenetic maps in the liver from male and female Wistar and Sprague-Daley rats", "dateAssigned" : "2018-03-06T00:00:00.000-06:00", "summary" : "We carry out methyl DNA immunoprecipitation (meDIP) and hydroxymethyl DNA immunoprecipitaion (hmeDIP) prior to sequencing on the Ion Proton semiconductor sequencing platform to report on the genome-wide epigenetic patterns in rat livers", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29130343" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111448" }, "primaryId" : "GEO:GSE111448", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111448" } ] }, "title" : "Real-time quantitative PCR analysis of the effects of chronic ethanol feeding and partial hepatectomy on gene expression in single rat hepatocytes", "dateAssigned" : "2018-03-06T00:00:00.000-06:00", "summary" : "Heaptocytes from four different rats were analyzed for gene expression. Two animals received alcohol containing liquid diet and two other littermates were pair-fed liquid carbohydrate diet for 6-8 weeks following the Lieber-De Carli feeding protocol. The rats were then anesthetized and subjected to 70% partial hepatectomy (PHx). The left lateral and medial (LLM) lobes were removed and quickly frozen in OCT. 24 hours post hepatectomy, the rats were anesthetized again and the remnant liver was harvested. Single hepatocytes were collected from LLM and PHx liver slices using laser capture microdissection. We used the 96.96 BioMark Dynamic Array (Fluidigm) to measure the expression of functionally relevant genes in each hepatocyte.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111452" }, "primaryId" : "GEO:GSE111452", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111452" } ] }, "title" : "Chronic Gene Expression after Traumatic Brain Injury", "dateAssigned" : "2018-03-06T00:00:00.000-06:00", "summary" : "This project continues our acute TBI studies and initiates chronic studies -- characterizing the temporal genomic profile of the injured brain up to 12 months post-TBI. Thus, the primary objective of this proposal is to determine the long-term effects of traumatic brain injury on gene expression in the hippocampus and cortex, two brain regions known to be particularly vulnerable to TBI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30943276" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111513" }, "primaryId" : "GEO:GSE111513", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111513" } ] }, "title" : "DNA methylation inhibition attenuates pressure overload-induced cardiac hypertrophy in rats", "dateAssigned" : "2018-03-07T00:00:00.000-06:00", "summary" : "Inhibitors of DNA methyl transferase (DNMT) might be useful for treating cardiac hypertrophy by preventing de novo methylation and reduced transcription of anti-hypertrophic genes. This approach had been tested, but without a detailed phenotypic and methylation analysis. Here, we subjected rats to pressure overload and treatment with the DNMT inhibitor N-phthalyl-L-tryptophan (RG108) and analysed DNA methylation by cardiomyocyte (CM)-specific reduced representation bisulphite sequencing (RRBS).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111514" }, "primaryId" : "GEO:GSE111514", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111514" } ] }, "title" : "The trophic effect of nerve growth factor in primary cultures of rat hippocampal neurons is associated to an anti-inflammatory and immunosuppressive transcriptional program", "dateAssigned" : "2018-03-07T00:00:00.000-06:00", "summary" : "Nerve growth factor, the prototype of a family of neurotrophins, elicits differentiation and survival of peripheral and central neuronal cells. Although its neural mechanisms have been studied extensively, relatively little is known about the transcriptional regulation governing its effects. We have previously observed that in primary cultures of rat hippocampal neurons treatment with nerve growth factor for 72 hours increases neurite outgrowth and cell survival. To obtain a comprehensive view of the underlying transcriptional program, we performed whole-genome expression analysis by microarray technology. We identified 541 differentially expressed genes and characterized dysregulated pathways related to innate immunity: the complement system and neuro-inflammatory signaling. The exploitation of such genes and pathways may help interfering with the intracellular mechanisms involved in neuronal survival and guide novel therapeutic strategies for neurodegenerative diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29741791" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111710" }, "primaryId" : "GEO:GSE111710", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111710" } ] }, "title" : "Dynamic rewiring of transcription factor networks during smooth muscle cell phenotypic modulation (ChIP-Rx data sets)", "dateAssigned" : "2018-03-12T00:00:00.000-05:00", "summary" : "Phenotypic modulation of smooth muscle cells (SMC) is a hallmark of vascular disease and a classic cell state transformation mediated by convergent signal-integration in the nucleus. Here, using PDGF-mediated SMC activation, we describe for the first time the dynamic active chromatin response and global transcriptional remodeling of cell state. We find that PDGF stimulation drives global transcriptional amplification and anabolism concurrent with increased proliferation and motility. Kinetic gene expression and Brd4 chromatin co-activator occupancy analysis reveals transcription factor (TF) directed enhancer re-wiring shaped by an immediate-early (Jun/Fos) response followed by increased nuclear hormone receptor transcriptional signaling that is Rev-erbdependent. Interdicting signaling between enhancers and transcription via Brd4 inhibition halts canonical cellular features of PDGF stimulation, and in vivo Brd4 inhibition potently abrogates vascular injury responses. These data provide a global map of TF-directed chromatin remodeling during SMC phenotypic modulation and elucidate key therapeutic mechanisms of transcriptional inhibition in vascular disease.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111712" }, "primaryId" : "GEO:GSE111712", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111712" } ] }, "title" : "Dynamic rewiring of transcription factor networks during smooth muscle cell phenotypic modulation (ChIP-Seq data sets)", "dateAssigned" : "2018-03-12T00:00:00.000-05:00", "summary" : "Phenotypic modulation of smooth muscle cells (SMC) is a hallmark of vascular disease and a classic cell state transformation mediated by convergent signal-integration in the nucleus. Here, using PDGF-mediated SMC activation, we describe for the first time the dynamic active chromatin response and global transcriptional remodeling of cell state. We find that PDGF stimulation drives global transcriptional amplification and anabolism concurrent with increased proliferation and motility. Kinetic gene expression and Brd4 chromatin co-activator occupancy analysis reveals transcription factor (TF) directed enhancer re-wiring shaped by an immediate-early (Jun/Fos) response followed by increased nuclear hormone receptor transcriptional signaling that is Rev-erbdependent. Interdicting signaling between enhancers and transcription via Brd4 inhibition halts canonical cellular features of PDGF stimulation, and in vivo Brd4 inhibition potently abrogates vascular injury responses. These data provide a global map of TF-directed chromatin remodeling during SMC phenotypic modulation and elucidate key therapeutic mechanisms of transcriptional inhibition in vascular disease.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111713" }, "primaryId" : "GEO:GSE111713", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111713" } ] }, "title" : "Dynamic rewiring of transcription factor networks during smooth muscle cell phenotypic modulation (ATAC-Seq data sets)", "dateAssigned" : "2018-03-12T00:00:00.000-05:00", "summary" : "Phenotypic modulation of smooth muscle cells (SMC) is a hallmark of vascular disease and a classic cell state transformation mediated by convergent signal-integration in the nucleus. Here, using PDGF-mediated SMC activation, we describe for the first time the dynamic active chromatin response and global transcriptional remodeling of cell state. We find that PDGF stimulation drives global transcriptional amplification and anabolism concurrent with increased proliferation and motility. Kinetic gene expression and Brd4 chromatin co-activator occupancy analysis reveals transcription factor (TF) directed enhancer re-wiring shaped by an immediate-early (Jun/Fos) response followed by increased nuclear hormone receptor transcriptional signaling that is Rev-erbdependent. Interdicting signaling between enhancers and transcription via Brd4 inhibition halts canonical cellular features of PDGF stimulation, and in vivo Brd4 inhibition potently abrogates vascular injury responses. These data provide a global map of TF-directed chromatin remodeling during SMC phenotypic modulation and elucidate key therapeutic mechanisms of transcriptional inhibition in vascular disease.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111714" }, "primaryId" : "GEO:GSE111714", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111714" } ] }, "title" : "Dynamic rewiring of transcription factor networks during smooth muscle cell phenotypic modulation (RNA-Seq data sets)", "dateAssigned" : "2018-03-12T00:00:00.000-05:00", "summary" : "Phenotypic modulation of smooth muscle cells (SMC) is a hallmark of vascular disease and a classic cell state transformation mediated by convergent signal-integration in the nucleus. Here, using PDGF-mediated SMC activation, we describe for the first time the dynamic active chromatin response and global transcriptional remodeling of cell state. We find that PDGF stimulation drives global transcriptional amplification and anabolism concurrent with increased proliferation and motility. Kinetic gene expression and Brd4 chromatin co-activator occupancy analysis reveals transcription factor (TF) directed enhancer re-wiring shaped by an immediate-early (Jun/Fos) response followed by increased nuclear hormone receptor transcriptional signaling that is Rev-erbdependent. Interdicting signaling between enhancers and transcription via Brd4 inhibition halts canonical cellular features of PDGF stimulation, and in vivo Brd4 inhibition potently abrogates vascular injury responses. These data provide a global map of TF-directed chromatin remodeling during SMC phenotypic modulation and elucidate key therapeutic mechanisms of transcriptional inhibition in vascular disease.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111718" }, "primaryId" : "GEO:GSE111718", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111718" } ] }, "title" : "Effects of Testosterone and GH on liver transcriptome", "dateAssigned" : "2018-03-12T00:00:00.000-05:00", "summary" : "Transcriptional profiling of the effects of testosterone and growth hormone on hypothyroid-orquidectomized rat (TXOX) liver", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:38144555" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111770" }, "primaryId" : "GEO:GSE111770", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111770" } ] }, "title" : "Transcriptomic profiling of trigeminal nucleus caudalis (TNC) and spinal cord dorsal horn (SC)", "dateAssigned" : "2018-03-13T00:00:00.000-05:00", "summary" : "RNA-Sequencing of the trigeminal nucleus caudalis and spinal cord, dorsal horn in male naive rats (Wistar Han) of 10 weeks old", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29723522" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111941" }, "primaryId" : "GEO:GSE111941", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE111941" } ] }, "title" : "Hydroxyurea protects hippocampal neurons against oxidative, metabolic and excitotoxic stress, and improves spatial memory in a mouse model of Alzheimer’s disease (Rat)", "dateAssigned" : "2018-03-16T00:00:00.000-05:00", "summary" : "Alzheimer’s disease (AD) is an age-related neurodegenerative disorder characterized by accumulation of amyloid β-peptide (Aβ) plaques in the brain and decreased cognitive function leading to dementia. We determined if hydroxyurea (HU), a ribonucleotide reductase inhibitor known to activate adaptive cellular stress responses in fibroblasts, could protect rat hippocampal neurons against oxidative-, excitatory-, mitochondrial-, and Aβ-induced stress and if HU treatment could improve learning and memory in a mouse model of AD (APP/PS1 double mutant transgenic mice). HU treatment attenuated the loss of cell viability induced by treatment of hippocampal neurons with hydrogen peroxide, glutamate, rotenone, and Aβ1-42. HU treatment also attenuated reductions of mitochondrial reserve capacity, maximal respiration, and cellular ATP content induced by hydrogen peroxide treatment. In vivo, treatment of APP/PS1 AD mice with HU (45 mg/kg/day) improved spatial memory performance in the hippocampus-dependent Morris water maze task. In summary, HU provides neuroprotection against toxic insults, improves mitochondrial bioenergetics, and improves spatial memory in a mouse model of AD. HU may offer a new therapeutic approach to delay cognitive decline in AD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30245242" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112108" }, "primaryId" : "GEO:GSE112108", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112108" } ] }, "title" : "Does early treatment of PKU patients with sapropterin dihydrochloride affect brain development?", "dateAssigned" : "2018-03-20T00:00:00.000-05:00", "summary" : "We show deleterious effects of SD on developing brain cells in a rat in vitro model. This observation raises the question whether the use of SD can be recommended in very young PKU patients as currently licensed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112309" }, "primaryId" : "GEO:GSE112309", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112309" } ] }, "title" : "Gene expresssion profiles in PPARalpha-Serine280 phosphorylation mutants", "dateAssigned" : "2018-03-25T00:00:00.000-05:00", "summary" : "PPARalpha regulates cardiac fatty acid metabolism. GSK-3alpha phosphorylates PPARalpha at Serine 280, which increases PPARalpha transcriptional activity in cardiomyocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30745182" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112332" }, "primaryId" : "GEO:GSE112332", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112332" } ] }, "title" : "Effects of mulberry (Morus alba L.) leaf ingestion on gene expression of peripheral whole blood [CvsQ]", "dateAssigned" : "2018-03-26T00:00:00.000-05:00", "summary" : "In the animal study, both a decrease of serum alanine aminotransferase level and whole blood gene expression changes were observed in rats fed a MLP-containing high-fat diet compared with rats fed a high-fat diet.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112333" }, "primaryId" : "GEO:GSE112333", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112333" } ] }, "title" : "Effects of mulberry (Morus alba L.) leaf ingestion on gene expression of peripheral whole blood [QvsM]", "dateAssigned" : "2018-03-26T00:00:00.000-05:00", "summary" : "In the animal study, both a decrease of serum alanine aminotransferase level and whole blood gene expression changes were observed in rats fed a MLP-containing high-fat diet compared with rats fed a high-fat diet.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112399" }, "primaryId" : "GEO:GSE112399", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112399" } ] }, "title" : "Estrogen-dependent up-regulation of Adcyap1r1 expression in nucleus accumbens is associated with genetic predisposition of sex-specific QTL for alcohol consumption on rat chromosome 4", "dateAssigned" : "2018-03-27T00:00:00.000-05:00", "summary" : "RNA-seq was performed on the nucleus accumbens of female (F) interval-specific congenic strain-B (P.NP-ISCS-B) and inbred alcohol preferring (iP) control rat", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30564267" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112464" }, "primaryId" : "GEO:GSE112464", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112464" } ] }, "title" : "siRNA knockdown of neonatal rat cardiac myocytes and fibroblasts", "dateAssigned" : "2018-03-28T00:00:00.000-05:00", "summary" : "Primary neonatal rat cardiac myocytes or fibroblasts were isolated and subjected to siRNA mediated Yap knockdown", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30295714" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112510" }, "primaryId" : "GEO:GSE112510", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112510" } ] }, "title" : "Nitrated meat products are associated with mania in humans and altered behavior and brain gene expression in rats", "dateAssigned" : "2018-03-29T00:00:00.000-05:00", "summary" : "Mania is a serious neuropsychiatric condition associated with significant morbidity and mortality. Previous studies have suggested that environmental exposures can contribute to mania pathogenesis. We measured dietary exposures in a cohort of individuals with mania and other psychiatric disorders as well as in control individual without a psychiatric disorder. We found that a history of eating nitrated dry cured meat, but not other meat or fish products, was strongly and independently associated with current mania (adjusted odds ratio 3.49, 95% confidence interval (CI) 2.24-5.45, p<8.97x 10-8). Lower odds of association were found between eating nitrated dry cured meat and other psychiatric disorders. We further found that the feeding of meat preparations with added nitrate to rats resulted in alterations in behavior and changes in intestinal microbiota. Rats fed diets with added nitrate also showed alterations of brain pathways dysregulated in mania. These findings may lead to new methods for preventing mania and for developing novel therapeutic interventions", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30022042" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112622" }, "primaryId" : "GEO:GSE112622", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112622" } ] }, "title" : "LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation", "dateAssigned" : "2018-04-03T00:00:00.000-05:00", "summary" : "De novoDNA methylation (DNAme) occurs coincident with transcription during mouse oogenesis. As many oocyte transcripts originate in Long Terminal Repeats (LTRs), which are divergent across species, we examined whether polymorphic LTR-initiated transcription units (LITs) shape the oocyte methylome. We identified thousands of syntenic regions in mouse, rat and human, including CpG islands (CGIs), that show divergent DNAmeassociated withpolymorphic LITs. Notably, many CGIpromoters methylated exclusively in mouse and/or rat are embedded within rodent-specific LITs, and show persistent maternal methylation in the blastocyst. Polymorphic LITs are also responsible for divergent methylation of CGI promoters in distantly related mouse strains, revealing that LITs also promote intra-species diversification of promoter DNAme.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30127397" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112624" }, "primaryId" : "GEO:GSE112624", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112624" } ] }, "title" : "Zonisamide facilitates survival of human iPS cell-derived dopaminergic neurons in the rat striatum", "dateAssigned" : "2018-04-03T00:00:00.000-05:00", "summary" : "ZNS promotes the survival of DA neurons after the transplantation of human iPS cell-derived DA progenitors in the rat striatum. SLITRK6 is suggested to be involved in this supportive effect of ZNS by modulating the environment of the host brain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112637" }, "primaryId" : "GEO:GSE112637", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112637" } ] }, "title" : "Gene expression profiles of rat hypertrophic zone after treatment of CNP53 or U0126 [CNP53]", "dateAssigned" : "2018-04-03T00:00:00.000-05:00", "summary" : "To investigate the similarity of gene expression profile of CNP53 and U0126 treatment in growth plate.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30235256" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112638" }, "primaryId" : "GEO:GSE112638", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112638" } ] }, "title" : "Gene expression profiles of rat hypertrophic zone after treatment of CNP53 or U0126 [U0126]", "dateAssigned" : "2018-04-03T00:00:00.000-05:00", "summary" : "To investigate the similarity of gene expression profile of CNP53 and U0126 treatment in growth plate.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30235256" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112930" }, "primaryId" : "GEO:GSE112930", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112930" } ] }, "title" : "Persistent accumulation of unrepaired DNA damage in rat cortical neurons: nuclear organization and ChIP-seq analysis of damaged DNA", "dateAssigned" : "2018-04-10T00:00:00.000-05:00", "summary" : "We investigated the nuclear topography, organization and genome-wide gH2AX distribution of unrepaired DNA in rat cortical neurons 15 dyas upon X-Ray ionizing adiation (4Gy). Unrepaired DNA is confined in persistent DNA damage foci which would help preserving genome integrity. ChIp-seq analysis revealed a number of genomic regions enriched in gH2AX. Some of these regions are in close proximity to genes encoding essential proteins for neuronal function and human neurodegenerative disorders.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112934" }, "primaryId" : "GEO:GSE112934", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE112934" } ] }, "title" : "Identification of Specific MicroRNA Biomarkers in Early Stage of Hepatocellular injury, Cholestasis, and Steatosis in Rat", "dateAssigned" : "2018-04-10T00:00:00.000-05:00", "summary" : "Recently, study on circulating microRNAs (miRNAs) as potential biomarkers of drug-induced liver injury (DILI), has received increasing attention. It has been demonstrated that miR-122 and miR-192, which are liver enriched, could be potential biomarkers of DILI, however, these miRNAs cannot discern types of injuries. In the present study, we comprehensively analyzed time-dependent plasma miRNA profiles in rats with drug- or chemical-induced hepatocellular injury, cholestasis, and steatosis with high-throughput miRNA sequencing. To enable comparison of miRNA expression levels between DILI models with different severity and peaks of injuries, stages of injury were defined as early, middle and late, according to cluster patterns of miRNA expression profiles. Through differential analysis, we characterized miRNAs that were specifically up- or down-regulated in each DILI model. Interestingly, several miRNAs were dramatically changed earlier than traditional biomarkers such as ALT and AST. For example, in APAP-induced hepatocellular injury model, let-7b-5p was up-regulated as early as 3 h after dosing, while significant change in ALT level was observed at 24 h. Thereafter, we focused on the DILI type-specific miRNAs which were up-regulated at early stage of injury. RT-qPCR study validated that let-7b-5p and miR-1-3p for hepatocellular injury, miR-143-3p and miR-218a-5p for cholestasis, and miR-320-3p for steatosis models have shown significant increase in the early stage of the injuries. The present study suggests the utility of miRNAs as specific biomarkers for early detection of DILI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30125006" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113000" }, "primaryId" : "GEO:GSE113000", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113000" } ] }, "title" : "Perinatal exposure to an environmentally-relevant mixture of BFRs and ovarian gene expression in the adult rat", "dateAssigned" : "2018-04-11T00:00:00.000-05:00", "summary" : "Brominated flame retardants (BFRs), including polybrominated diphenyl ethers (PBDEs) and hexabromocyclododecane (HBCDD), leach out from consumer products into the environment. Exposure to BFRs has been associated with effects on endocrine homeostasis. To test the hypothesis that in utero and lactational exposure to BFRs may affect the reproductive system of female offspring, adult female Sprague-Dawley rats were fed nominal doses (0, 0.06, 20, or 60 mg/kg/day) of a BFR dietary mixture formulated to mimic the levels of congeners in house dust from prior to mating until weaning. Vaginal opening and the day of first estrus occurred at a significantly earlier age among offspring from the 20 mg/kg/day BFR group, indicating that the onset of puberty was advanced. Histological analysis of ovaries from post-natal day 46 offspring revealed an increase in the incidence of multi-oocyte follicles. Toxicogenomics analysis of ovarian gene expression identified upstream regulators, including HIF1A, CREB1, EGF, the β-estradiol and PPARA pathways, predicted to be downregulated in the 20 mg/kg/day or the 60 mg/kg/day group and to contribute to the gene expression patterns observed. Thus, perinatal exposure to BFRs dysregulated ovarian folliculogenesis and signaling pathways that are fundamental for ovarian function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32207525" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113327" }, "primaryId" : "GEO:GSE113327", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113327" } ] }, "title" : "The PKC-β selective inhibitor, Enzastaurin, impairs memory in middle-aged rats", "dateAssigned" : "2018-04-18T00:00:00.000-05:00", "summary" : "Enzastaurin is a Protein Kinase C-β selective inhibitor that was developed to treat cancers. Protein Kinase C-β is an important enzyme for a variety of neuronal functions; in particular, previous rodent studies have reported deficits in spatial and fear-conditioned learning and memory with lower levels of Protein Kinase C-β. Due to Enzastaurin’s mechanism of action, the present study investigated the consequences of Enzastaurin exposure on learning and memory in 12-month-old Fischer-344 male rats. Rats were treated daily with subcutaneous injections of either vehicle or Enzastaurin, and behaviorally tested using the spatial reference memory Morris Water Maze. Rats treated with Enzastaurin exhibited decreased overnight retention and poorer performance on the latter testing day, indicating a mild, but significant, memory impairment. There were no differences during the probe trial indicating that all animals were able to spatially localize the platform to the proper quadrant by the end of testing. RNA isolated from the hippocampus was analyzed using Next Generation Sequencing (Illumina). No statistically significant transcriptional differences were noted. Our findings suggest that acute Enzastaurin treatment can impair hippocampal-based learning and memory performance, with no effects on transcription in the hippocampus. We propose that care should be taken in future clinical trials that utilize Protein Kinase C-ß inhibitors, to monitor for possible cognitive effects, future research should examine if these effects are fully reversible.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29870545" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113520" }, "primaryId" : "GEO:GSE113520", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113520" } ] }, "title" : "Co-expression Networks of mRNAs and non-coding RNAs of bones around implants in hyperlipidemic rats (RNA-seq data sets)", "dateAssigned" : "2018-04-23T00:00:00.000-05:00", "summary" : "Purpose: Hyperlipidemia has been shown to contribute to reduced implant osseointegration, but the underlying mechanism remains poorly understood. Recently, non-coding RNAs (ncRNAs) have been established as key regulators of various pathophysiological processes. Therefore, the current study aims to examine the expression profiles of mRNAs and ncRNAs in femoral tissues around surgical implants in a murine hyperlipidemia model via RNA sequencing.Materials and method: Twenty adult male Wistar rats were equally divided between an experimental group and a control group, which were fed a high-fat diet and a normal diet, respectively. Titanium root-form implants was inserted into both femoral shafts of each rat in eight weeks. Bone tissues were collected at day 10 after the insertion of the implants and subsequently used for RNA extraction and sequencing. The sequenced reads were refined, assembled and annotated to obtain mRNA, microRNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA) transcripts. The levels of all types of RNA molecules in both animal groups were quantified and differentially expressed candidates were identified. The function of the identified RNAs were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. LncRNA-miRNA-mRNA and circRNA-miRNA-mRNA co-expression network of differentially expressed RNAs were constructed. Real-time polymerase chain reactions (RT-PCR) were performed to validate the expression levels of selected candidates.Results: The serum lipid levels of the experimental group were significant higher than those of the control group (p < 0.05). In total, 389 mRNAs, 73 miRNAs, 770 lncRNAs and 7 circRNAs were shown to be differentially expressed (p < 0.05, fold change > 2).GO analysis found that regulation of bone mineralization, negative regulation of chondrocyte differentiation and bone development changed significantly. The network that maybe related to osteogenesis included 6 mRNAs, 8 miRNAs, 6 circRNAs, 119 lncRNAs and 362 associations. Expression level of most RNAs detected by RT-PCR was consistent with that by RNA sequencing.Conclusion:Functional analysis predicted a panel of differentially expressed mRNAs and ncRNAs associated with osteogenesis. The results of the current study will greatly contribute to the elucidation of the mechanism for implant osseointegration under hyperlipidemia.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113521" }, "primaryId" : "GEO:GSE113521", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113521" } ] }, "title" : "Co-expression Networks of mRNAs and non-coding RNAs of bones around implants in hyperlipidemic rats (miRNA-seq data sets)", "dateAssigned" : "2018-04-23T00:00:00.000-05:00", "summary" : "Purpose: Hyperlipidemia has been shown to contribute to reduced implant osseointegration, but the underlying mechanism remains poorly understood. Recently, non-coding RNAs (ncRNAs) have been established as key regulators of various pathophysiological processes. Therefore, the current study aims to examine the expression profiles of mRNAs and ncRNAs in femoral tissues around surgical implants in a murine hyperlipidemia model via RNA sequencing.Materials and method: Twenty adult male Wistar rats were equally divided between an experimental group and a control group, which were fed a high-fat diet and a normal diet, respectively. Titanium root-form implants was inserted into both femoral shafts of each rat in eight weeks. Bone tissues were collected at day 10 after the insertion of the implants and subsequently used for RNA extraction and sequencing. The sequenced reads were refined, assembled and annotated to obtain mRNA, microRNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA) transcripts. The levels of all types of RNA molecules in both animal groups were quantified and differentially expressed candidates were identified. The function of the identified RNAs were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. LncRNA-miRNA-mRNA and circRNA-miRNA-mRNA co-expression network of differentially expressed RNAs were constructed. Real-time polymerase chain reactions (RT-PCR) were performed to validate the expression levels of selected candidates.Results: The serum lipid levels of the experimental group were significant higher than those of the control group (p < 0.05). In total, 389 mRNAs, 73 miRNAs, 770 lncRNAs and 7 circRNAs were shown to be differentially expressed (p < 0.05, fold change > 2).GO analysis found that regulation of bone mineralization, negative regulation of chondrocyte differentiation and bone development changed significantly. The network that maybe related to osteogenesis included 6 mRNAs, 8 miRNAs, 6 circRNAs, 119 lncRNAs and 362 associations. Expression level of most RNAs detected by RT-PCR was consistent with that by RNA sequencing.Conclusion:Functional analysis predicted a panel of differentially expressed mRNAs and ncRNAs associated with osteogenesis. The results of the current study will greatly contribute to the elucidation of the mechanism for implant osseointegration under hyperlipidemia.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113528" }, "primaryId" : "GEO:GSE113528", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113528" } ] }, "title" : "Inhaled multi-walled carbon nanotubes-induced gene expression profile in rat lung (NM-401)", "dateAssigned" : "2018-04-23T00:00:00.000-05:00", "summary" : "In this work we study the pulmonary toxicological properties of carbon nanotubes using molecular toxicological approache. For this, we exposed Sprague Dawley rats by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks. Lung samples have been collected up to 180 days after the end of exposure and transcriptomics analysis were performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33332178" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113531" }, "primaryId" : "GEO:GSE113531", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113531" } ] }, "title" : "Inhaled multi-walled carbon nanotubes-induced gene expression profile in rat lung (NM-403)", "dateAssigned" : "2018-04-23T00:00:00.000-05:00", "summary" : "In this work we study the pulmonary toxicological properties of carbon nanotubes using molecular toxicological approache. For this, we exposed Sprague Dawley rats by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks. Lung samples have been collected up to 180 days after the end of exposure and transcriptomics analysis were performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33332178" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113612" }, "primaryId" : "GEO:GSE113612", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113612" } ] }, "title" : "Portal Hypertension Induced Changes in Splenic microRNA Expression", "dateAssigned" : "2018-04-24T00:00:00.000-05:00", "summary" : "Splenomegaly is caused by several pathological conditions, including portal hypertension, which is most frequently caused by chronic liver disease (e.g., liver cirrhosis). The detailed mechanisms through which portal pressure induces splenomegaly and the precise pathophysiological conditions in portal hypertension-induced splenomegaly remain to be fully elucidated. We used microarrays to identify the differential microRNA expression underlying the portal hypertension-induced splenomegaly.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30573742" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113613" }, "primaryId" : "GEO:GSE113613", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113613" } ] }, "title" : "Portal Hypertension Induced Changes in Splenic Gene Expression", "dateAssigned" : "2018-04-24T00:00:00.000-05:00", "summary" : "Splenomegaly is caused by several pathological conditions, including portal hypertension, which is most frequently caused by chronic liver disease (e.g., liver cirrhosis). The detailed mechanisms through which portal pressure induces splenomegaly and the precise pathophysiological conditions in portal hypertension-induced splenomegaly remain to be fully elucidated. We used microarrays to identify the differential gene expression underlying the portal hypertension-induced splenomegaly.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30573742" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113634" }, "primaryId" : "GEO:GSE113634", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113634" } ] }, "title" : "Transcriptome profiling of osteoblasts treated with uMSC-derived exosomes", "dateAssigned" : "2018-04-25T00:00:00.000-05:00", "summary" : "To investigate the function and affected pathways of uMSC-derived exosomes on ossification, we used human and rat osteoblast cell line hFOB1.19 and ROS1728 treated with either exosomes or exosome-free supernatent (which is the supernatent of exosome pelleting after ultracentrifugation) and a non-treated group as negative control. We take advantages of high through-put sequencing technology to fully reveal the transcriptome changes of the treated cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113686" }, "primaryId" : "GEO:GSE113686", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113686" } ] }, "title" : "Responses of retinal and brain microvasculature to diabetes revealed by global expression profiling", "dateAssigned" : "2018-04-25T00:00:00.000-05:00", "summary" : "Using these DEGs, we analyzed and compared the diabetic effects on the gene expression profiles in retinal microvasculature and brain microvasculature. In the brain microvasculature multiple compensatory mechanisms exists, serving to protect brain tissue from diabetic insults, whereas these mechanisms are not activated in the retinal microvasculature.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36606460" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113726" }, "primaryId" : "GEO:GSE113726", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113726" } ] }, "title" : "Hepatic Gene Expression during the Perinatal Transition in the Rat", "dateAssigned" : "2018-04-26T00:00:00.000-05:00", "summary" : "During the immediate postnatal period, the liver, with its role in energy metabolism and macromolecule synthesis, plays a central role in the perinatal transition. Using RNA microarrays and several complementary computational analyses, we characterized changes in hepatic gene expression in the rat across a developmental period starting with the late gestation fetus (embryonic day 21), and including 30 min postnatal (PN), 4 hr PN, 12 hr PN, 1 day PN and 1 week after birth. Following subtle changes in gene expression at the earliest postnatal time point, there were marked changes that occurred between 4 hr and 12 hr after birth. These reflected changes in multiple metabolic pathways, with expression of enzymes involved in glycolysis and cholesterol synthesis showing the greatest change. Over 50% of nuclear-encoded mitochondrial genes changed in the first 7 days of postnatal life, with 25% changing within the first 24 hr. We also observed changes coinciding with a transient period of synchronous hepatocyte proliferation that we had observed previously, which occurs during the first postnatal week. Analysis for upstream regulators of gene expression indicated multiple initiating factors, including cell stress, hormones and cytokines. Also implicated were multiple canonical transcription factor networks. We conclude that changes in gene expression during the early phases of the perinatal transition involve a complex, choreographed network of signaling pathways that respond to a variety of environmental stimuli. This transcriptomic response during the immediate postnatal period reflects a complex metabolic adaptive response that incorporates a panoply of signaling pathways and transcriptional regulators.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29929573" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113785" }, "primaryId" : "GEO:GSE113785", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113785" } ] }, "title" : "Vinclozolin induced epigenetic transgenerational inheritance of pathologies and sperm epimutation biomarkers for specific diseases", "dateAssigned" : "2018-04-27T00:00:00.000-05:00", "summary" : "F0 generation rats were exposed to vinclozolin, and the subsequent F1, F2 and transgenerational F3 generations are evaluated for diseases and pathologies. F3 generation rats showed transgenerational increases in testis, prostate, and kidney disease, changes in the age of puberty onset in males, and an increased obesity rate in females. Overall there was an increase in the rate of animals with disease, and in the incidence of animals with multiple disease. The methylation of the F3 vinclozolin lineage rat samples was determined using MeDIP-seq. Unique signatures of differential DNA methylation regions (DMRs) in sperm were found that associated with testis disease, prostate disease and kidney disease, however, these signatures were not statistically significant.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30157260" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113787" }, "primaryId" : "GEO:GSE113787", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113787" } ] }, "title" : "Deep sequencing of microRNAs in transplanted corneas", "dateAssigned" : "2018-04-27T00:00:00.000-05:00", "summary" : "Conclusions: Our study identified transplanted corneas-specific miRNA in matched pairs of isograft corneas and normal corneas, allograft corneas and isograft corneas. Furthermore, bioinformatics analysis of the key miRNA regulatory network revealed the molecular mechanisms, which suggests miRNAs may as new molecular targets for treating corneal injuries and corneal transplant rejection", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113828" }, "primaryId" : "GEO:GSE113828", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113828" } ] }, "title" : "Expression data from rat insulinoma INS-1 cells under glucotoxic condition", "dateAssigned" : "2018-04-30T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying cellularization and identified distinct classes of up and down-regulated genes during this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113877" }, "primaryId" : "GEO:GSE113877", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113877" } ] }, "title" : "Genome-wide chromatin maps in the liver from male and female Wistar rats", "dateAssigned" : "2018-04-30T00:00:00.000-05:00", "summary" : "We carry out H3K27pan-acetly chromatin imminoprecipitation (ChIP) and H3K4me1 ChIP prior to sequencing on the Illumina Nextseq 500 sequencing platform to report on the genome-wide epigenetic patterns in rat livers", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29130343" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113893" }, "primaryId" : "GEO:GSE113893", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113893" } ] }, "title" : "DDX1 regulates alternative splicing and insulin secretion in pancreatic β cells", "dateAssigned" : "2018-05-01T00:00:00.000-05:00", "summary" : "DEAD-box helicase 1 (DDX1) is a multifunction protein involved in diverse cellular processes including transcription, viral replication, mRNA/miRNA processing, and tRNA splicing. Here, we report a novel function of DDX1 in mRNA alternative splicing in pancreatic β cells. By performing integrated data analysis of high-throughput RNA sequencing (RNA-Seq), and cross-linking and immunoprecipitation coupled with deep sequencing (CLIP-Seq), we identify hundreds of alternative splicing genes that are targeted by DDX1. These DDX1-targeted alternative splicing genes are mainly associated with calcium ion binding, high voltage-gated calcium channel, and transmembrane transporter. Functionally, silencing DDX1 impairs calcium influx and insulin secretion in the pancreatic β cells. These results reveal an important role for DDX1 in the regulation of gene alternative splicing and insulin secretion in pancreatic β cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29679569" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113940" }, "primaryId" : "GEO:GSE113940", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE113940" } ] }, "title" : "Indazole-Cl inhibition of hypoxia-induced cyclooxygenase-2 expression in vascular smooth muscle cells", "dateAssigned" : "2018-05-02T00:00:00.000-05:00", "summary" : "We used RNA-sequencing analysis to identify changes in inflammation-related genes by ER agonist treatment in the hypoxic state.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114031" }, "primaryId" : "GEO:GSE114031", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114031" } ] }, "title" : "Renal congestion (Rattus)", "dateAssigned" : "2018-05-04T00:00:00.000-05:00", "summary" : "We created a rat renal congestion model and investigated the effect of renal congestion on hemodynamics and molecular mechanisms. The inferior vena cava (IVC) between the renal veins was ligated by suture in male Sprague-Dawley rats to increase upstream IVC pressure and induce congestion in the left kidney only. Left kidney congestion reduced renal blood flow, glomerular filtration rate, and increased renal interstitial hydrostatic pressure. Tubulointerstitial and glomerular injury and medullary thick ascending limb hypoxia were observed only in the congestive kidneys. Molecules related to extracellular matrix expansion, tubular injury, and focal adhesion were upregulated in microarray analysis. Renal decapsulation ameliorated the tubulointerstitial injury. Electron microscopy captured pericyte detachment in the congestive kidneys. Transgelin and platelet-derived growth factor receptors, as indicators of pericyte-myofibroblast transition, were upregulated in the pericytes and the adjacent interstitium. With the compression of the peritubular capillaries and tubules, hypoxia and physical stress induce pericyte detachment, which could result in extracellular matrix expansion and tubular injury in renal congestion.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30429498" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114032" }, "primaryId" : "GEO:GSE114032", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114032" } ] }, "title" : "Sperm Epimutation Biomarkers of Obesity and Pathologies following DDT Induced Epigenetic Transgenerational Inheritance of Disease", "dateAssigned" : "2018-05-04T00:00:00.000-05:00", "summary" : "Gestating F0 generational female rats were transiently exposed to DDT during fetal gonadal sex determination and the incidence of adult onset pathologies was assessed in the subsequent F1, F2, and F3 generations. In addition, sperm differential DNA methylation regions (DMRs) that were associated with specific pathologies in the F3 generation males were investigated. No pathology was observed in the F1 generation DDT lineage males or females compared with F1 generation controls (vehicle exposure). There was an increase of testis disease and early onset puberty in the F2 generation DDT lineage males. The F3 generation DDT males had significant increases in testis disease, prostate disease, and late onset puberty. The F3 generation DDT females had significant increases in ovarian and kidney disease. Both the F3 generation males and females had significant increases in the frequency of obesity and multiple disease. The F3 generation sperm was collected to examine DMRs for the ancestrally exposed DDT male population. Unique sets of DMRs were associated with late onset puberty, kidney disease, and multiple disease pathologies.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114088" }, "primaryId" : "GEO:GSE114088", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114088" } ] }, "title" : "Variation of mRNA and lncRNA expression after using AMD3100 in rat chronic allograft nephropathy model.", "dateAssigned" : "2018-05-07T00:00:00.000-05:00", "summary" : "To investigate the variation of mRNA and lncRNA expression after using AMD3100 in rat chronic allograft nephropathy model (CAN) model, we have employed mRNA and lncRNA microarray expression profiling as a discovery platform to identify genes with the potential. CAN rat models were established using male Fisher 344 to Lewis rats. Rats in the experimental group(n=3) were treated with AMD3100 (1 mg/kg/day subcutaneously, 0–12 weeks), rats in the control group(n=3) were treated with saline. The kidney grafts were harvested 12 weeks after modeling for microarray analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114191" }, "primaryId" : "GEO:GSE114191", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114191" } ] }, "title" : "Repurposing of promoters and enhancers during mammalian evolution", "dateAssigned" : "2018-05-08T00:00:00.000-05:00", "summary" : "The spatiotemporal control of gene expression exerted by promoters and enhancers is central for organismal development, physiology and behaviour. These two types of regulatory elements have long been distinguished from each other based on their function, but recent work highlighted common architectural and functional features. It also suggested that inheritable alterations in the epigenetic and sequence context of regulatory elements might underlie evolutionary changes of their principal activity, which could result in changes in the transcriptional profile of genes under their control or even facilitate the birth of new genes. Here, based on integrated cross-mammalian analyses of DNase hypersensitivity, chromatin modification and transcriptional data, we provide support for this hypothesis by detecting 445 regulatory elements with signatures of activity turnover in sister species from the primate and rodent lineages (termed \"P/E\" elements). Through the comparison with outgroup species, we defined the directionality of turnover events, which revealed that most instances represent transformations of putative ancestral enhancers into promoters, leading to the emergence of species-specific transcribed loci or 5' exons. Notably, P/E elements have distinct GC sequence compositions and stabilizing 5' splicing (U1) regulatory motif patterns, which may predispose them to functional repurposing during evolution. Moreover, we trace changes in the U1 and polyadenylation signal densities and distributions that accompanied and likely drove the evolutionary activity switches. Overall, our work highlights functional repurposing as a notable mechanism that likely facilitated regulatory innovation and the origination of new genes and exons during mammalian evolution.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30287902" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114322" }, "primaryId" : "GEO:GSE114322", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114322" } ] }, "title" : "Gene expression analysis of spleens from virus-infected rats", "dateAssigned" : "2018-05-10T00:00:00.000-05:00", "summary" : "Comparison of gene expression between wildtype (WT) and Ifnar1 ko rats following Kilham rat virus (KRV) challenge", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34702762" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114333" }, "primaryId" : "GEO:GSE114333", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114333" } ] }, "title" : "DNA de novo (de)Methylation in the Kidney Contributes to Salt-Induced Hypertension [RRBS-seq]", "dateAssigned" : "2018-05-10T00:00:00.000-05:00", "summary" : "Numerous adult diseases involving tissues that consist primarily of non-dividing cells are associated with changes in DNA methylation. It suggests a role for de novo methylation or demethylation of DNA, which is catalyzed by DNA methyltransferase 3 (Dnmt3) and ten-eleven translocases (Tet). However, the contribution of DNA de novo (de)methylation to these diseases remains nearly completely unproven. Broad changes in DNA methylation occurred within days in the renal outer medulla of Dahl SS rats fed a high-salt diet, a classic model of hypertension. Intra-renal administration of anti-Dnmt3a/Tet3 GapmeR’s attenuated high salt-induced hypertension in SS rats. The high salt diet induced differential expression of 1,712 genes in the renal outer medulla. Remarkably, the differential expression of 76% of these genes were prevented by anti-Dnmt3a/Tet3 GapmeR’s. The genes differentially expressed in response to the GapmeR’s were involved in the regulation of metabolism and inflammation and were significantly enriched for genes showing differential methylation in response to the GapmeR’s. These data indicate DNA de novo (de)methylation in the kidney contributes to the development of hypertension in SS rats. The findings should help to shift the paradigm of DNA methylation research in diseases involving non-dividing cells from correlative analysis to functional and mechanistic studies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30354815" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114334" }, "primaryId" : "GEO:GSE114334", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114334" } ] }, "title" : "DNA de novo (de)Methylation in the Kidney Contributes to Salt-Induced Hypertension [RNA-seq]", "dateAssigned" : "2018-05-10T00:00:00.000-05:00", "summary" : "Numerous adult diseases involving tissues that consist primarily of non-dividing cells are associated with changes in DNA methylation. It suggests a role for de novo methylation or demethylation of DNA, which is catalyzed by DNA methyltransferase 3 (Dnmt3) and ten-eleven translocases (Tet). However, the contribution of DNA de novo (de)methylation to these diseases remains nearly completely unproven. Broad changes in DNA methylation occurred within days in the renal outer medulla of Dahl SS rats fed a high-salt diet, a classic model of hypertension. Intra-renal administration of anti-Dnmt3a/Tet3 GapmeR’s attenuated high salt-induced hypertension in SS rats. The high salt diet induced differential expression of 1,712 genes in the renal outer medulla. Remarkably, the differential expression of 76% of these genes were prevented by anti-Dnmt3a/Tet3 GapmeR’s. The genes differentially expressed in response to the GapmeR’s were involved in the regulation of metabolism and inflammation and were significantly enriched for genes showing differential methylation in response to the GapmeR’s. These data indicate DNA de novo (de)methylation in the kidney contributes to the development of hypertension in SS rats. The findings should help to shift the paradigm of DNA methylation research in diseases involving non-dividing cells from correlative analysis to functional and mechanistic studies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30354815" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114426" }, "primaryId" : "GEO:GSE114426", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114426" } ] }, "title" : "Circular RNA expression alteration in rats after traumatic spinal cord injury (SCI)", "dateAssigned" : "2018-05-14T00:00:00.000-05:00", "summary" : "To determine whether the expression levels of circular RNAs were altered and lay a foundation for future work, we used high-throughput microarray analysis to screen circular RNAs expression patterns in the spinal cord of adult rats after traumatic spinal cord injury (SCI), finally to evaluate the potential rat models as a platform for the development of novel therapeutic targets for spinal cord injury in future clinical studies. Overall six rats at 3 days post-SCI in two groups were used to perform the microarray.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30692912" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114441" }, "primaryId" : "GEO:GSE114441", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114441" } ] }, "title" : "Schwann cell precursor mRNA in normal culture conditions", "dateAssigned" : "2018-05-14T00:00:00.000-05:00", "summary" : "Schwann cell precursor mRNA are carried out in RNAome analyses", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114442" }, "primaryId" : "GEO:GSE114442", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114442" } ] }, "title" : "Comparison of oligodendrocyte miRNAs in normal and differentiated conditions in culture", "dateAssigned" : "2018-05-14T00:00:00.000-05:00", "summary" : "Oligodendrocyte miRNAs in normal and differentiated conditions are compared.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114499" }, "primaryId" : "GEO:GSE114499", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114499" } ] }, "title" : "Unilateral mastication induced alternations of microRNAs expression profiling in synovium of rat temporomandibular joint", "dateAssigned" : "2018-05-15T00:00:00.000-05:00", "summary" : "The present study investigated the alterations of miRNA expression profiling in synovium of temporomandibular joint(TMJ) in a rat model of experimental unilateral mastication. The synovium tissue of TMJ condyles from rats with 4- and 8-weeks unilateral mastication were harvested to extract miRNA for profiling holistic expression alternations. A total of 20 differentially expressed miRNAs were identified. Except for 3 miRNAs with uncertain function, those miRNAs are associated with cell proliferation, invasion, and osteoblast differentiation process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114609" }, "primaryId" : "GEO:GSE114609", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114609" } ] }, "title" : "RNA-seq analysis for mRNA expression change in oxygen/glucose deprivation-treated cultured oligodendrocyte precursor cells", "dateAssigned" : "2018-05-17T00:00:00.000-05:00", "summary" : "Oligodendrocyte precursor cells (OPCs) regulate neuronal, glial and vascular systems in diverse ways and display phenotypic heterogeneity beyond their well-known role as a reservoir for mature oligodendrocytes. Here we demonstrated that perivascular OPCs in cerebral cortex were increased coupling with post-stroke angiogenesis in a mouse model of stroke induced by middle cerebral artery occlusion (MCAO). RNA-seq analysis revealed that primary cultured OPCs notably increased the gene expressions of numerous pro-angiogenic factors, while decreased those related to OPC maturation after oxygen glucose deprivation. The data showed that cerebral ischemia shifts the phenotype of OPCs to perivascular subtypes which can promote angiogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31020902" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114616" }, "primaryId" : "GEO:GSE114616", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114616" } ] }, "title" : "The Signature of Glucocorticoid Receptor -Dependent Hypertrophic Transcriptome in Cardiomyocytes [ChIP-Seq]", "dateAssigned" : "2018-05-17T00:00:00.000-05:00", "summary" : "We examined Glucocorticoid receptor binding sites in isolated neonatal cardiomyocytes treated with Dexamethasone (100nM) for 1hr or Ethanol using GR-ChIP-Seq.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30866692" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114684" }, "primaryId" : "GEO:GSE114684", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114684" } ] }, "title" : "Analysis of delayed changes in expression of miRNA in rat kidneys: role of miR-34a", "dateAssigned" : "2018-05-20T00:00:00.000-05:00", "summary" : "We used a rat model of whole body (except one hind limb that was shielded) x-ray irradiation to profile the microRNA (miRNA) in kidneys at 35 days after radiation. Small RNA from normal and irradiated (with or without lisinopril) Wistar rat kidneys were analyzed by next-generation sequencing and the changes by radiation and lisinopril were identified by deRNA-seq. MiR-34a-5p was increased after irradiation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114766" }, "primaryId" : "GEO:GSE114766", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114766" } ] }, "title" : "The Signature of Glucocorticoid Receptor -Dependent Hypertrophic Transcriptome in Cardiomyocytes [RNA-Seq]", "dateAssigned" : "2018-05-22T00:00:00.000-05:00", "summary" : "We examined Glucocorticoid receptor binding sites in isolated neonatal cardiomyocytes treated with Dexamethasone (100nM) for 1hr or Ethanol using GR-ChIP-Seq. In addition to determine the change in the resulting transcriptional status of genes we performed RNAseq in cardiomyocytes treated with Dexamethasone (100nM) or Ethanol for 1hr or 24hrs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30866692" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114799" }, "primaryId" : "GEO:GSE114799", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114799" } ] }, "title" : "Multiscale analysis of a regenerative therapy for treatment of volumetric muscle loss injury", "dateAssigned" : "2018-05-22T00:00:00.000-05:00", "summary" : "Skeletal muscle possesses a remarkable capacity to regenerate when injured, but when confronted with major traumatic injury resulting in volumetric muscle loss (VML), the regenerative process consistently fails. The loss of muscle tissue and function from VML injury has prompted development of a suite of therapeutic approaches but these strategies have proceeded without a comprehensive understanding of the molecular landscape that drives the injury response. Herein, we administered a VML injury in an established rodent model and monitored the evolution of the healing phenomenology over multiple time points using muscle function testing, histology, and expression profiling by RNA sequencing. The injury response was then compared to a regenerative medicine treatment using orthotopic transplantation of autologous minced muscle grafts (~1 mm3 tissue fragments). A chronic inflammatory and fibrotic response was observed at all time points following VML. These results suggest that the pathological response to VML injury during the acute stage of the healing response overwhelms endogenous and therapeutic regenerative processes. Overall, the data presented delineate key molecular characteristics of the pathobiological response to VML injury that are critical effectors of effective regenerative treatment paradigms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29531830" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114828" }, "primaryId" : "GEO:GSE114828", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114828" } ] }, "title" : "miRNA microarray of rTDSCs under mechanical treatment or not", "dateAssigned" : "2018-05-23T00:00:00.000-05:00", "summary" : "Tendinopathy is a common disease in individuals whose tendons suffer from repetitive strains, such as athletes. The lack of knowledge regarding the pathological mechanisms causes inadequate prevention methods and low cure rate of this disease. Repetitive strain injury is thought to be the source of tendinopathy; therefore, we investigate the effect of mechanical loading on tendon and seek the ways to prevent and treat tendinopathy better. In our study, we found that the expression of a mechanosensitive miRNA, miR-337-3p, decreased in tendon-derived stem cells (TDSCs) under uniaxial cyclical mechanical loading with 10% elongation. In addition, miR-337-3p was negatively related to chondro-osteogenic differentiation of TDSCs, in which lower expression was found in human calcified tendons and rat tendinopathy samples.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114865" }, "primaryId" : "GEO:GSE114865", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114865" } ] }, "title" : "DNA methylation reprogramming after spinal nerve injury [RRBS]", "dateAssigned" : "2018-05-24T00:00:00.000-05:00", "summary" : "Purpose: Nerve injury-induced hyperactivity of primary sensory neurons in the dorsal root ganglion (DRG) contributes critically to chronic pain development, but its underlying mechanisms remain incompletely understood. Chronic neuropathic pain has a clear epigenetic component, however, most studies so far have focused on histone modifications. We determined changes of DNA methylation in the rat DRG, spinal cord, and prefrontal cortex after spinal nerve ligation (SNL).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29875269" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114896" }, "primaryId" : "GEO:GSE114896", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114896" } ] }, "title" : "seekCRIT: detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data", "dateAssigned" : "2018-05-24T00:00:00.000-05:00", "summary" : "Recently, it has been demonstrated that genomes of many species express single stranded RNAs with covalently closed ends, named circular RNAs. Their regulatory potential and functional relevance are just starting to be revealed. Here we present a novel computational tool, seekCRIT (seek for differentially expressed Circular RNAs In Transcriptome), that identifies circular RNAs and detects their differential expression between two conditions. Using seekCRIT we identified the circular RNAs that are expressed in the neural retina and determined that the majority of them (74%) are expressed in both, ischemic and normal conditions. We identified over 40 circular RNAs that were differentially expressed between both conditions and validated these experimentally using qRT-PCR. The high validation rate of 90% with a false discovery rate (FDR) of < 5% demonstrates the accuracy and reliability of seekCRIT.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33079938" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114919" }, "primaryId" : "GEO:GSE114919", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114919" } ] }, "title" : "Differential ageing of growth plate cartilage determines skeletal proportions", "dateAssigned" : "2018-05-25T00:00:00.000-05:00", "summary" : "Bones at different anatomical locations vary dramatically in size. The mechanisms responsible for these size differences are poorly understood. Bone elongation occurs at the growth plates and advances rapidly in early life but then progressively slows due to a developmental program termed growth plate senescence. This developmental program includes declines in cell proliferation and hypertrophy, depletion of cells in all growth plate zones, and extensive underlying changes in the expression of growth-regulating genes. Here we use RNA-Seq to compare changes of gene expression with age in the longer bone (tibia, 1- vs 4-wk) with the difference of gene expression between long and short bones (tibia vs phalanx) at 1wk. We found that the developmental program of growth plate senescence is more advanced in the shorter bone and this differential senescence (or aging) underlies the disparities in bone length.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114957" }, "primaryId" : "GEO:GSE114957", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE114957" } ] }, "title" : "Comparison of oligodendrocyte mRNAs in normal and differentiated conditions in culture", "dateAssigned" : "2018-05-28T00:00:00.000-05:00", "summary" : "Oligodendrocyte mRNAs in control and differentiated conditions are compared.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115061" }, "primaryId" : "GEO:GSE115061", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115061" } ] }, "title" : "ETV1 activates a rapid conduction transcriptional program in rodent and human cardiomyocytes", "dateAssigned" : "2018-05-29T00:00:00.000-05:00", "summary" : "ETV1 (ER81) was identified as a highly enriched transcription factor in rapidly conducting atrial and His-Purkinje cardiomyocytes. Previous work has shown that ETV1 is a critical factor in determining fast conduction physiology in the heart. This high-throughput sequencing project aims to uncover ETV1-dependent gene networks in cardiomyocytes. These results provide insight into the role of ETV1 in the establishment of rapid conduction zones in the heart.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29967479" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115067" }, "primaryId" : "GEO:GSE115067", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115067" } ] }, "title" : "Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury", "dateAssigned" : "2018-05-30T00:00:00.000-05:00", "summary" : "Spinal cord injury (SCI) is a devastating neurological condition for which there are currently no effective treatment options to restore function. A major obstacle to the development of new therapies is our fragmentary understanding of the coordinated pathophysiological processeses triggered by damage to the human spinal cord. An additional challenge to translation of preclinical therapies is the reliance of clinical trials on standardized neurological assessments to enrol and stratify patients, rather than objective injury biomarkers. Here, we describe a systems biology approach to integrate decades of small-scale experiments with unbiased, genome-wide gene expression from the human spinal cord, revealing a gene regulatory network signature of the pathophysiological response to SCI. Our integrative analyses converge on an evolutionarily conserved gene subnetwork enriched for genes associated with the response to SCI by small-scale experiments, and whose expression is upregulated in a severity-dependent manner following injury and downregulated in functional recovery. We validate the severity-dependent upregulation of this subnetwork in prospective transcriptomic and proteomic studies. Our analysis provides a systems-level view of the coordinated molecular processes activated in response to SCI. Further, our results nominate quantitative biomarkers of injury severity and functional recovery, with the potential to facilitate development and translation of novel therapies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30277459" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115156" }, "primaryId" : "GEO:GSE115156", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115156" } ] }, "title" : "Genome wide analysis of upper spinal cords with training after spinal cord hemisection injury", "dateAssigned" : "2018-05-31T00:00:00.000-05:00", "summary" : "The goal of this study is to elucidate the influence of treadmill training on transcriptome of the upper lumbar spinal cord after thoracic spinal cord hemisection. mRNA profiles of spinal cords at 23 days-post injury with/without treadmill training were generated. The expression levels of 650 genes in the trained animal were increased ( > 2-fold) compared to untrained animals. Our study represents the detailed analysis of transcriptomes of spinal cord distal to the hemisected lesion after treadmill training, with biologic replicates, generated by RNA-seq technology.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30782076" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115229" }, "primaryId" : "GEO:GSE115229", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115229" } ] }, "title" : "Genome wide analysis of lower spinal cords with training after spinal cord hemisection injury", "dateAssigned" : "2018-06-01T00:00:00.000-05:00", "summary" : "The goal of this study is to elucidate the influence of treadmill training on transcriptome of the lower lumbar spinal cord after thoracic spinal cord hemisection. mRNA profiles of spinal cords at 23 days-post injury with/without treadmill training were generated. The expression levels of 650 genes in the trained animal were increased ( > 2-fold) compared to untrained animals. Our study represents the detailed analysis of transcriptomes of spinal cord distal to the hemisected lesion after treadmill training, with biologic replicates, generated by RNA-seq technology.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115230" }, "primaryId" : "GEO:GSE115230", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115230" } ] }, "title" : "Genome wide analysis of the upper lumbar spinal cord at 4 days after T9 hemisection injury", "dateAssigned" : "2018-06-01T00:00:00.000-05:00", "summary" : "The goal of this study is to elucidate the influence of hemisection injury at thoracic spinal cord (T9) on the upper transcriptome of the upper lumbar spinal cord at acute phase. mRNA profiles of spinal cord at 4 days-post injury and before injury were generated. 72 Differentially Expressed Genes (DEGs) were observed. Our study represents the detailed analysis of transcriptomes of spinal cord distal to the hemisected lesion at acute phase, with biologic replicates, generated by RNA-seq technology.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115231" }, "primaryId" : "GEO:GSE115231", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115231" } ] }, "title" : "Genome wide analysis of the lower lumbar spinal cord at 4 days after T9 hemisection injury", "dateAssigned" : "2018-06-01T00:00:00.000-05:00", "summary" : "The goal of this study is to elucidate the influence of hemisection injury at thoracic spinal cord (T9) on the transcriptome of the lower lumbar spinal cord at acute phase. mRNA profiles of spinal cord at 4 days-post injury and before injury were generated. 72 Differentially Expressed Genes (DEGs) were observed. Our study represents the detailed analysis of transcriptomes of spinal cord distal to the hemisected lesion at acute phase, with biologic replicates, generated by RNA-seq technology.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115315" }, "primaryId" : "GEO:GSE115315", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115315" } ] }, "title" : "CircRNA-Seq Analysis for Sciatic Nerve Injury of Rat", "dateAssigned" : "2018-06-04T00:00:00.000-05:00", "summary" : "Here, we established a rat sciatic nerve injury model and investigated the circRNA expression profiles by Next-generation sequencing. In all, 7222 distinct circRNA candidates were found in these tissues and 4942 of these circRNAs contained at least two unique back-spliced reads. On the basis of expression of circRNA analysis, we found 131 circRNAs to be significantly (p-value<=0.05, Fold-change>=2) differently expressed in injured sciatic nerve tissues compared with matched normal tissues. All these circRNAs are derived from 21 rat chromosomes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30098504" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115473" }, "primaryId" : "GEO:GSE115473", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115473" } ] }, "title" : "Transcriptome profiles of liver from cirrhotic rat treated with nizatidine", "dateAssigned" : "2018-06-07T00:00:00.000-05:00", "summary" : "Male rats received repeated low-dose diethylnitrosamine (DEN) to induce liver cirrhosis, and were treated with nizatidine to examine change of liver transcriptome and its association with liver cancer chemopreventive effect of nizatidine.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34535664" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115474" }, "primaryId" : "GEO:GSE115474", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115474" } ] }, "title" : "Stretch growth does not alter gene expression", "dateAssigned" : "2018-06-07T00:00:00.000-05:00", "summary" : "Differentiated PC12 cells were magnetically labeled with magnetic nanoparticles (MNP). External magnetic fields were used to mechanically stretch the MNP-labeled neurites. We found that mechanical stretching of the neurites induces mass addition and neurite elongation. We performed RNAseq of MNP-labelled cells in stretched versus non-stretched conditions and we did not found gene expression dysregulation, confirming that the two conditions were identical and excluding cytotoxicity or involvement of nuclear mechanotransdution. Indeed, local mechanisms triggered by the stretching of the MNP-labelled neurite would be responsible for neurite elongation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115534" }, "primaryId" : "GEO:GSE115534", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115534" } ] }, "title" : "APA usage in vaporized cannabis plant matter (CPM) exposure rats", "dateAssigned" : "2018-06-08T00:00:00.000-05:00", "summary" : "Role of alternative polyadenylation (APA) in rat brain after vaporized cannabis plant matter (CPM) exposure remains largely undetermined. Our WTTS-seq approach to capture 3'-end of RNAs clearly revealed alternative polyadenylation events responsible for dominantly down-regulates APA expression on Glutamatergic Transcripts in rats after CPM Exposure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115535" }, "primaryId" : "GEO:GSE115535", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115535" } ] }, "title" : "Maternal obesity has sex dependent effects on liver transcriptome in young adult rat offspring", "dateAssigned" : "2018-06-08T00:00:00.000-05:00", "summary" : "Conclusions: These results improve understanding of the mechanism by which a maternal high fat diet affects their F1. In summary, MO programs sex-dependent F1 changes in insulin, glucose and lipid signaling pathways, leading to liver dysfunction and insulin resistance. Male adult MOF1 livers show global down-regulation of genes that are required for normal function of major liver metabolic pathways. This new knowledge is important for producing sex-specific interventions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29972240" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115614" }, "primaryId" : "GEO:GSE115614", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115614" } ] }, "title" : "Treatment with antidepressant drugs in a rat model of Traumatic Brain Injury", "dateAssigned" : "2018-06-11T00:00:00.000-05:00", "summary" : "Microarray analysis was performed to look at the mRNA and miRNA profiles of several antidepressant drugs in the rat hippocampus after Traumatic Brain Injury to test the hypothesis that antidepressant drugs ameliorate gene and miRNA dysregulation after TBI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31442236" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115662" }, "primaryId" : "GEO:GSE115662", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115662" } ] }, "title" : "Optimizing Personalized Therapy for Rheumatoid Arthritis Using a Novel Drug Combination of Bioactive Chemical Constituents Derived from a Classic Chinese Herbal Formula", "dateAssigned" : "2018-06-12T00:00:00.000-05:00", "summary" : "Microarray analysis based on the adjuvant induced arthritis model combined with characteristics of RA and cold/hot syndromes was performed to screen RA-cold and RA-hot-syndrome-related genes, as well as WTD effect genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115723" }, "primaryId" : "GEO:GSE115723", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115723" } ] }, "title" : "Single-cell RNA sequencing of the mammalian pineal gland identifies two pinealocyte subtypes and cell type-specific daily patterns of gene expression ", "dateAssigned" : "2018-06-13T00:00:00.000-05:00", "summary" : "The vertebrate pineal gland is dedicated to the production of the hormone melatonin, which increases at night to influence circadian and seasonal rhythms. This increase is associated with dramatic changes in the pineal transcriptome. Here, single-cell analysis of the rat pineal transcriptome was approached by sequencing mRNA from ~17,000 individual pineal cells, with the goals of profiling the cells that comprise the pineal gland and examining the proposal that there are two distinct populations of pinealocytes differentiated by the expression of Asmt, which encodes the enzyme that converts N-acetylserotonin to melatonin. In addition, this analysis provides evidence of cell-specific time-of-day dependent changes in gene expression. Nine transcriptomically distinct cell types were identified: ~90% were classified as melatonin-producing α- and β-pinealocytes (1:19 ratio). Non-pinealocytes included three astrocyte subtypes, two microglia subtypes, vascular and leptomeningeal cells, and endothelial cells. α-Pinealocytes were distinguished from β-pinealocytes by ~3-fold higher levels of Asmt transcripts. In addition, α-pinealocytes have transcriptomic differences that likely enhance melatonin formation by increasing the availability of the Asmt cofactor S-adenosylmethionine, resulting from increased production of a precursor of S-adenosylmethionine, ATP. These transcriptomic differences include ~2-fold higher levels of the ATP-generating oxidative phosphorylation transcriptome and ~8-fold lower levels of the ribosome transcriptome, which is expected to reduce the consumption of ATP by protein synthesis. These findings suggest that α-pinealocytes have a specialized role in the pineal gland: efficiently O-methylating the N-acetylserotonin produced and released by β-pinealocytes, thereby improving the overall efficiency of melatonin synthesis. We have also identified transcriptomic changes that occur between night and day in seven cell types, the majority of which occur in β-pinealocytes and to a lesser degree in α-pinealocytes; many of these changes were mimicked by adrenergic stimulation with isoproterenol. The cellular heterogeneity of the pineal gland as revealed by this study provides a new framework for understanding pineal cell biology at single-cell resolution.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30347410" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115835" }, "primaryId" : "GEO:GSE115835", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115835" } ] }, "title" : "Changes in miRNA expression in circulating whole blood resutling from exposure to neurotoxic doses of D-amphetamine", "dateAssigned" : "2018-06-15T00:00:00.000-05:00", "summary" : "Amphetamine effects on gene expression are dependent on body temperature and indicate that many significant changes in genes related to the immune system occur, some likely in response to damage, even when animals remain normothermic during amphetamine exposure. Also, hyperthermia alone produces many changes in immune related genes in blood", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115866" }, "primaryId" : "GEO:GSE115866", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115866" } ] }, "title" : "Gene expression alterations in Danshen-treated rats eye", "dateAssigned" : "2018-06-15T00:00:00.000-05:00", "summary" : "Diabetic rats changes gene expression in Danshen-treated rats eye.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115930" }, "primaryId" : "GEO:GSE115930", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE115930" } ] }, "title" : "RNA-seq transcriptional profiling in sciatic nerves from wildtype and Pmp22 transgenic rats during perinatal development", "dateAssigned" : "2018-06-18T00:00:00.000-05:00", "summary" : "The goal of this study was to identify deregulated genes in Schwann cells of Pmp22 transgenic rats in comparison to wildtype rats. Three timepoints in the course of peripheral nerve myelination were chosen (embryonic day [E] 21, perinatal day [P]6 and P18) in order to reveal mechanistic insight into early pathological processes of Charcot-Marie-Tooth disease 1A (CMT1A).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30072689" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116046" }, "primaryId" : "GEO:GSE116046", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116046" } ] }, "title" : "Integrative analysis of differentially expressed genes and miRNAs predicts complex T3-mediated protective circuits in a rat model of cardiac ischemia reperfusion", "dateAssigned" : "2018-06-20T00:00:00.000-05:00", "summary" : "mRNA and miRNA expression profiling shows that the T3 supplementation reverted the expression of 87 genes and 11 miRNAs that were dysregulated in the untreated group", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30218079" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116397" }, "primaryId" : "GEO:GSE116397", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116397" } ] }, "title" : "Genome-wide analysis of AR binding and transcriptomic analysis of mesenchymal subsets during prostate development", "dateAssigned" : "2018-06-28T00:00:00.000-05:00", "summary" : "Prostate organogenesis is regulated by interactions between mesenchymal and epithelial cells, and via androgen signalling though androgen receptors (AR) expressed in mesenchymal cells. However, there is little knowledge of AR target genes and we have used high resolution genomic methods to examine AR function in subsets of mesenchyme during prostate development. Using ChIP-seq, we defined genomic AR binding sites (ARBS) in microdissected mesenchymal tissues of neonatal male and female rats during prostate growth. By comparing female tissue subsets (ventral mesenchymal pad and urethral smooth muscle) with male tissues (ventral prostate and dorsolateral prostate), we were able to identify sexually dimorphic ARBS. Females had a distinct AR binding profile from males with enrichment of ARBS proximal to gene transcriptional start sites as well as binding to non-classical AR binding sequence motifs. Using both tissue RNA-sequencing and single-cell RNA-sequencing of the same mesenchymal subsets, we identified 128 differentially expressed transcripts between males and females. Comparison of these to ChIP-seq ARBS allowed us to define sexually dimorphic AR target genes. Selected candidates were validated as sexually dimorphic at both the mRNA and protein level in both rat and human developing prostate tissues by qPCR and western blot. Response to testosterone stimulation was examined using ex vivo rat tissue organ cultures and qPCR. In single cell RNAseq data we observed subpopulations of mesenchymal cells in males and females as well as subpopulations common to both. The distribution of AR and target genes did not follow the subpopulation distribution, suggesting that AR action is not restricted by subset identity.Our study is the first to apply multiple transcriptomic approaches to prostate mesenchyme, and we have identified unique AR targets. We have identified sexually dimorphic, androgen responsive mesenchymal target genes that may underlie sexually dimorphic development of the prostate. We suggest that the analysis of transcription factor binding and transcriptomes in cell subsets will be informative when applied to tumour cells and stroma – since these show similar cellular heterogeneity and subset specific activity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116461" }, "primaryId" : "GEO:GSE116461", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116461" } ] }, "title" : "Transcriptome-wide RNA and genome-wide DNA G-Quadruplex mediates alternative transcripts", "dateAssigned" : "2018-06-29T00:00:00.000-05:00", "summary" : "We demonstrate that G4-DNA and G4-RNA may present splicing sites and alternative transcription starting positions on a transcriptome-wide and genome-wide scale by showing widespread effect on alternative transcripts in response to the established intracellular G4 binding ligands PDS.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116653" }, "primaryId" : "GEO:GSE116653", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116653" } ] }, "title" : "Analysis of the role of long non-coding RNAs involved in silica-induced pulmonary fibrosis of rat", "dateAssigned" : "2018-07-05T00:00:00.000-05:00", "summary" : "Mounting evidence suggests that long non-coding RNAs (lncRNAs) are involved in the pathogenesis of silicosis. In this study, Wistar rats were treated with an improved intubation method to ferry silicon dioxide (1mL per rat) into lung. Rats in the control group were injected with normal saline solution (1mL per rat). Twenty eight days after exposure, we examined the rats and found the formation of lung fibrosis in rats treated with silica. We then investigated the lncRNAs expression changes in lungs of silica-exposed rats and compared with that of rats in the control group. Treatment of silica leads to 682 lncRNAs differentially expressed including 300 upregulated and 382 down regulated compared to controls.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116663" }, "primaryId" : "GEO:GSE116663", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116663" } ] }, "title" : "Gestational diabetes adversely affects pancreatic islet development and function in the rat offspring", "dateAssigned" : "2018-07-05T00:00:00.000-05:00", "summary" : "Gestational diabetes mellitus (GDM) exposure and obesity are strong risk factors for type 2 diabetes development; however, the connections between GDM exposure, postnatal diet and islet dysfunction in offspring metabolic health remain unclear. Reduced glucose-stimulated insulin secretion was observed in islets isolated from 15-week-old offspring prenatally exposed to GDM, which was exacerbated by postnatal HFS consumption. In the HFS-fed offspring of Lean dams, islet size and number increased, an adaptation that was not observed in the HFS-fed offspring of GDM dams. Islets from GDM exposed offspring revealed upregulation of 102 genes (e.g. Sod2, Il1b) and 13 downregulated genes. In the GDM offspring that consumed a postnatal HFS-diet, 126 genes were significantly upregulated (e.g. Ccl2, Rps14, Atp5f1) and 17 genes were downregulated (e.g. Hnf1a, Slc2a2). These results demonstrate that GDM exposure induced changes in gene expression in the young adult rat offspring that worsen islet function and whole-body glucose homeostasis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31237608" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116717" }, "primaryId" : "GEO:GSE116717", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116717" } ] }, "title" : "Comparison of epithelial cells from various epithelia and hair follicle stem cells", "dateAssigned" : "2018-07-06T00:00:00.000-05:00", "summary" : "Thepotencyof anadult stem cellisrestricted to certain lineagesduring embryonic life,in response to a specificmicroenvironment (the niche) and it ismaintained for life.Lineage restriction is consideredimmutable.We have investigated if adultstem cells isolated from differentepithelia could change fate by exposing them to ahairy skin niche.We havedemonstrated that clonogenicstem cells restricted to a singleepitheliallineage andculturedfrom various Tp63-expressing tissues e.g, the bladder, the vagina, or the thymuscan acquirenew functionality. When exposed to a hair skinmicroenvironment,thesestem cells acquire thecapacity togeneratehairfolliclesandsebaceous glands,thus behaving likebona fidehairy skinmultipotentstem cells. Genome wide-screen analysis hasdemonstratedthat the stem cellsexpresstranscription factors typical ofhair follicle differentiation,even thoughtheycontinue toexpresssome of thegeneslinked totheirorigin. This increase in potencydemonstrates that lineage restriction is not immutable.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33159086" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116719" }, "primaryId" : "GEO:GSE116719", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116719" } ] }, "title" : "Comparison of epithelial cells from various epithelia and hair follicle stem cells [microarray]", "dateAssigned" : "2018-07-06T00:00:00.000-05:00", "summary" : "Thepotencyof anadult stem cellisrestricted to certain lineagesduring embryonic life,in response to a specificmicroenvironment (the niche) and it ismaintained for life.Lineage restriction is consideredimmutable.We have investigated if adultstem cells isolated from differentepithelia could change fate by exposing them to ahairy skin niche.We havedemonstrated that clonogenicstem cells restricted to a singleepitheliallineage andculturedfrom various Tp63-expressing tissues e.g, the bladder the oralmucous, the oesophagusor the thymuscan acquirenew functionality. When exposed to a hair skinmicroenvironment,thesestem cells acquire thecapacity togeneratehairfolliclesandsebaceous glands,thus behaving likebona fidehairy skinmultipotentstem cells. Genome wide-screen analysis hasdemonstratedthat the stem cellsexpresstranscription factors typical ofhair follicle differentiation,even thoughtheycontinue toexpresssome of thegeneslinked totheirorigin. This increase in potencydemonstrates that lineage restriction is not immutable.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33159086" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116735" }, "primaryId" : "GEO:GSE116735", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116735" } ] }, "title" : "Long noncoding RNAs expression profile in rat extra-synaptic and synaptic NMDAR activation neurons", "dateAssigned" : "2018-07-06T00:00:00.000-05:00", "summary" : "The study revealed differentially expressed lncRNAs in synaptic and extrasynaptic NMDAR activation and suggested that lncRNAs might be responsible for extrasynaptic NMDAR-induced neurodegeneration", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116745" }, "primaryId" : "GEO:GSE116745", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116745" } ] }, "title" : "mRNA expression analysis of radiation-induced skin fibrosis of rats", "dateAssigned" : "2018-07-06T00:00:00.000-05:00", "summary" : "This study aims to compared mRNA expression between radiation-induced fibrotic skin and adjacent normal tissues of rats by RNA-Seq. Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues from nonirradated skin areas and irradietd areas were collected and subjected to mRNA expression analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116746" }, "primaryId" : "GEO:GSE116746", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116746" } ] }, "title" : "ChIP-Sequencing analysis of YY1 binding DNA in radiation-induced skin fibrosis of rats", "dateAssigned" : "2018-07-06T00:00:00.000-05:00", "summary" : "This study aims to compared the genome-wide Ying Yang-1 (YY1) binding DNA sequences in radiation-induced fibrotic skin and adjacent normal tissues of rats by ChIP-Seq. Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues from nonirradated skin areas and irradietd areas were collected and subjected to ChIP of YY1.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116747" }, "primaryId" : "GEO:GSE116747", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116747" } ] }, "title" : "DNA methylation analysis of radiation-induced skin fibrosis of rats", "dateAssigned" : "2018-07-06T00:00:00.000-05:00", "summary" : "This study aims to compared the genome-wide DNA methylation status in radiation-induced fibrotic skin and adjacent normal tissues of rats by methylated DNA immunoprecipitation sequencing (MeDIP-Seq). Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues from nonirradated skin areas and irradietd areas were collected and subjected to DNA methylation analysis by MeDIP.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116760" }, "primaryId" : "GEO:GSE116760", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116760" } ] }, "title" : "RNA-Seq and protein mass spectrometry in microdissected kidney tubules reveal signaling processes initiating lithium-induced nephrogenic diabetes insipidus", "dateAssigned" : "2018-07-07T00:00:00.000-05:00", "summary" : "Results and conclusion: Integration of new data with prior data about lithium effects at a molecular level leads to a signaling model in which lithium increases ERK activation leading to induction of NF-κB signaling and an inflammatory-like response that represses Aqp2 gene transcription.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31146973" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116826" }, "primaryId" : "GEO:GSE116826", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116826" } ] }, "title" : "sRNA sequencing of liver from lean rats and ZDF rats treated with vehicle or colesevelam", "dateAssigned" : "2018-07-09T00:00:00.000-05:00", "summary" : "Colesevelam is a bile acid sequestrant approved to treat both hyperlipidemia and type 2 diabetes, but the mechanism for its glucose lowering effects is not fully understood. The aim of this study was to investigate the role of hepatic microRNA’s as regulators of metabolic disease and to investigate the link between the cholesterol and glucose lowering effects of colesevelam. To quantify the impact of colesevelam treatment in rodent models of diabetes, metabolic studies were performed in Zucker Diabetic Fatty (ZDF) rats and db/db mice. Colesevelam treatments significantly decreased plasma glucose levels and increased glycolysis in the absence of changes to insulin levels in ZDF rats and db/db mice. High-throughput sequencing and real-time PCR were used to quantify hepatic miRNA and mRNA changes, and the cholesterol-sensitive miR-96/182/183 cluster was found to be significantly increased in livers from ZDF rats treated with colesevelam compared to vehicle controls. In summary, these results support that colesevelam likely improves glycemic control through hepatic miR-96/182/183, a mechanism that directly links cholesterol and glucose metabolism.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30160993" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116831" }, "primaryId" : "GEO:GSE116831", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116831" } ] }, "title" : "Deletion of Cdkn1b in ACI rats perturbs mammary progenitor cell proliferation and differentiation through non-cell-autonomous mechanisms", "dateAssigned" : "2018-07-09T00:00:00.000-05:00", "summary" : "Emerging data indicate that breast epithelial stem cells and progenitors, particularly those in the luminal epithelial cell lineage, are the cells-of-origin of breast carcinomas, and factors that influence breast cancer risk may alter the number and/or properties of these cells. We hypothesize that a subset of p27+cells represent hormone-responsive progenitors that are quiescent due to the high activity of TGFβ signaling in these cells. The Estrogen-induced mammary tumor model in ACI inbred rats is physiologically relevant rodent model of breast cancer. In the present study we successfully generatedCdkn1bknockout ACI rats and performed comprehensive phenotypic assessment and RNAseq profiling using FACS sorted basal (CD24+CD29high) and luminal (CD24+CD29low) cell populations to characterizeCdkn1b+/+andCdkn1b-/-females in prepubertal and adult cohorts. We found that p27KO rats exhibited mammary differentiation phenotype and reduced numbers of mammary epithelial progenitor pool, Interestingly, p27 ablation has the most pronounced effect on luminal progenitor cell gene expression, and milk protein genes and pStat5 were dramatically upregulated, while PR and FoxA1 were greatly downregulated inCdkn1b-/-luminal cells. Further characterization of mammary glands of prepubertalCdkn1bknockout rats by fat pad transplantation illustrated p27 deletion in the mammary cancer susceptible ACI rat strain induced mammary epithelial cell differentiation through cell non-autonomous mechanisms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30893315" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116980" }, "primaryId" : "GEO:GSE116980", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE116980" } ] }, "title" : "Unwinding the interplay between brain and liver in the pathophysiology of brain trauma", "dateAssigned" : "2018-07-12T00:00:00.000-05:00", "summary" : "Although clinical evidence indicates that TBI has profound effects on peripheral metabolism, TBI research has primarily focused on the CNS. The liver plays a major role in control of homeostasis and pathogenesis, affecting synthesis of lipids and proteins used across the body and brain. Fructose consumption is common in the Western Society and a major cause of metabolic syndrome, diabetes, and obesity. Results showed that fructose consumption in rodents for 3 weeks, under the threshold for establishment of metabolic syndrome, exacerbates the deleterious effects of fluid percussion injury on glucose metabolism, inflammation, and cell energy homeostasis. These effects of TBI and fructose seem to engage the hypothalamic neuroendocrine axis by involving the growth hormone system with resulting effects on a metabolic/inflammatory cascade in the periphery. Fructose fed TBI animals had elevated markers of inflammation (TLR4), lipid peroxidation (4HNE), and reduced markers of cell energy homeostasis (uMitCK) as well as reduced insulin signaling proteins (InR, IRS1) and growth hormone signaling proteins (GHR, IGF-1) in the liver. Fructose also potentiated the action of TBI on hepatic lipid droplet accumulation involving lipid-promoting factors (FAS, LXRα, CD36, ABCA1). Studies in cultured hepatocytes validated the action of growth hormone and fructose on the synthesis of FAS and CD36. TBI affects the transcriptomic profiling in the hypothalamus and several differentially expressed genes that are primarily associated to lipid metabolism providing cues for peripheral alterations in TBI pathology. These results reveal that the effects caused by TBI are not limited to the CNS, and that fructose promotes a stage of metabolic dysfunction that potentiates the effects of TBI on systemic metabolism.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117046" }, "primaryId" : "GEO:GSE117046", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117046" } ] }, "title" : "Expression of miRNAs in dorsal rat hippocampus: Effect of subchronic and chronic restraint stress", "dateAssigned" : "2018-07-12T00:00:00.000-05:00", "summary" : "Studies conducted in rodents subjected to chronic stress and some observations in humans after psychosocial stress, have allowed to establish a link between stress and the susceptibility to many complex diseases, including mood disorders. The studies in rodents have revealed that chronic exposure to stress negatively affects synaptic plasticity by triggering changes in the production of trophic factors, subunit levels of glutamate ionotropic receptors, neuron morphology and neurogenesis in adult hippocampus. These modifications may account for the impairment in learning and memory processes observed in chronically stressed animals. It is plausible then, that stress modifies the interplay between signal transduction cascades and gene expression regulation in the hippocampus, therefore leading to altered neuroplasticity and functioning of neural circuits. Considering that miRNAs play an important role in post-transcriptional-regulation of gene expression and participate in several hippocampus-dependent functions; we evaluated the consequences of chronic stress in the expression of miRNAs in dorsal (anterior) portion of the hippocampus, which participates in memory formation in rodents. Here, we show that male rats exposed to daily restraint stress (2.5 h/day) during 7 and 14 days display a differential profile of miRNA levels in dorsal hippocampus and remarkably, we found that some of these miRNAs belong to the miR-379-410 cluster. We confirmed a rise in miR-92a and miR-485 levels after 14 days of stress by qPCR, an effect that was not mimicked by chronic administration of corticosterone (14 days). Our in silico study identified the top-ten biological functions influenced by miR-92a, nine of which were shared with miR-485: Nervous system development, Tissue development, Behavior, Embryonic development, Organ development, Organismal development, Organismal survival, Tissue morphology, and Organ morphology. Furthermore, our in silico study provided a landscape of potential miRNA-92a and miR-485 targets, along with relevant canonical pathways related to axonal guidance signaling and cAMP signaling, which may influence the functioning of several neuroplastic substrates in dorsal hippocampus. Additionally, the combined effect of miR-92a and miR-485 on transcription factors, along with histone-modifying enzymes, may have a functional relevance by producing changes in gene regulatory networks that modify the neuroplastic capacity of the adult dorsal hippocampus under stress.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30127715" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117085" }, "primaryId" : "GEO:GSE117085", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117085" } ] }, "title" : "Roux-en-Y Gastric Bypass Reduces Podocyte Injury in Diabetic Kidney Disease", "dateAssigned" : "2018-07-13T00:00:00.000-05:00", "summary" : "Podocyte injury in diabetic kidney disease contributes to the development of albuminuria and subsequent renal decline. Clinically, gastric bypass surgery is associated with reductions in albuminuria, and rodent studies demonstrate coherent improvements in renal histology. We aimed to investigate the mechanisms underpinning remission of albuminuria following gastric bypass focussing on podocyte injury. Firstly, we tracked the evolution of albuminuria and cognate evidence of histological and ultrastructural damage to the glomerulus in male Zucker Diabetic Fatty rats. Secondly, we examined the impact of gastric bypass in these rats, focussing on podocyte injury. Thirdly, we conducted a global transcriptomic study profiling the shift in the renal transcriptome in the Zucker Diabetic Fatty rats rat and its relevance to human disease. Lastly, we explored whether gastric bypass could reverse the changes seen in the disease associated transcriptome. Albuminuria in the Zucker Diabetic Fatty rat developed by 12 weeks of age. This was accompanied by glomerulomegaly, podocyte stress and ultrastructural evidence of podocyte dedifferentiation. When animals underwent gastric bypass at 12 weeks of age, marked reductions in albuminuria in association with normalisation of glomerular tuft size, attenuation of podocyte stress and improvements in podocyte foot process morphology were observed within 2 months of surgery. A characteristic disease associated gene expression signature was observed in the kidneys of Zucker Diabetic Fatty rats, with a core set of alterations conserved in global analysis of the human DKD transcriptome. Many of the shared gene expression alterations were reversed by gastric bypass. Reductions in podocyte injury represent a key mechanism underpinning the remission of albuminuria following gastric bypass.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117319" }, "primaryId" : "GEO:GSE117319", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117319" } ] }, "title" : "Distinct microglial transcriptional responses during opioid exposure or neuropathic pain [rat]", "dateAssigned" : "2018-07-18T00:00:00.000-05:00", "summary" : "In settings of heightened pain sensitivity, such as following peripheral nerve injury (PNI) or opioid-induced hyperalgesia (OIH), microglia take on an activated phenotype. Functional studies have suggested that microglia activated by PNI or chronic opioids then engage common mechanisms to facilitate pain. Here we conducted RNA sequencing of acutely isolated spinal cord microglia to comprehensively interrogate commonality between PNI and OIH. By combining our results with meta-analysis of published datasets, we identify transcriptional signatures of microglial reactivity that differ between PNI models over time, opioid exposure, or CNS pathology, despite similar histological outcomes. Collectively, these results reveal a discrepancy between histological markers of activation and transcriptional response, and provide a resource of pain-associated microglial transcriptomes that caution against a universal signature of microglia activation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117378" }, "primaryId" : "GEO:GSE117378", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117378" } ] }, "title" : "Gastric bypass vs. ‘Medical Bypass’ - Impact on experimental diabetic kidney disease", "dateAssigned" : "2018-07-19T00:00:00.000-05:00", "summary" : "Albuminuria is significantly reduced following Roux-en-Y gastric bypass (RYGB) surgery, suggesting a renoprotective effect of the intervention. Herein, we assess the relative impact of RYGBand RYGB equivalent non-surgical weight loss and glycaemic improvementon glomerularinjury andglobal renal transcriptomic responses in the Zucker diabetic fatty rat (ZDF) model of diabetic nephropathy. We coined the term \"medical bypass\" (MB) to describe the intensive diet and pharmacotherapy based non-surgical interventionAdult ZDF rats underwent sham surgery (n=15) or RYGB (n=9). Nine sham-operated rats were calorie restricted and received insulin, liraglutide, metformin, ramipril, rosuvastatin and fenofibrate for 2 months (MB). Zucker fa/+ rats acted as healthy controls throughout. Bodyweight, glycaemia, albuminuria and glomerular injury specifically podocyte number, density and ultrastructure were assessed at follow up. Renal transcriptomes were compared by RNA-seq. RYGB resulted in 20-30% weight loss, normalized glycaemia and albuminuria and reduced indices of glomerular injury, specifically podocyte injury (foot process effacement). RYGB equivalent outcomes were obtained on all parameters following MB.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117413" }, "primaryId" : "GEO:GSE117413", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117413" } ] }, "title" : "Interleukin-8 modifies the expression profile of microRNA in rat primary skeletal muscle cells", "dateAssigned" : "2018-07-20T00:00:00.000-05:00", "summary" : "Using Target Scan database we found potential targets for all miRNAs with expression modified by IL-8 and focused our further interest on genes and pathways involved in skeletal muscle hypertrophy, that is: myocilin, PKB/Akt and FoxO3.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30945300" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117440" }, "primaryId" : "GEO:GSE117440", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117440" } ] }, "title" : "Transcriptomics analysis of the effects of electrical stimulation on rat denervated gastrocnemius muscle", "dateAssigned" : "2018-07-20T00:00:00.000-05:00", "summary" : "We report the application of RNA sequencing technology for transcriptomics analysis of the effects of electrical stimulation on rat denervated gastrocnemius muscle. Muscle samples were selected for gene expression analyses，corresponding to the following categories: Sham operation rats, (SHAM, n = 3), sciatic nerve injury rats (DN, n = 3), and sciatic nerve injury with electrical stimulation (DN-SM, n = 3). A total of 14,334 genes (DEGs) were detected in this study.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117447" }, "primaryId" : "GEO:GSE117447", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117447" } ] }, "title" : "Hepatic transcriptomic analyses revealing the molecular pathogenesis of T2DM associated NAFLD in the ZDF rats", "dateAssigned" : "2018-07-20T00:00:00.000-05:00", "summary" : "The ZDF rat, with spontaneous homozygous mutation of the leptin receptor gene (fa/fa), is one of the widely used animal model for studying the human type 2 diabetes mellitus (T2DM). Male ZDF rats have the symptoms of obesity and insulin resistance at a young age, accompanying with impaired islet function. However, their hepatic pathogenesis is still unclear. Based on the successive observations and the transcriptomic analyses of the liver tissue at 22 weeks old, we detected the typical clinical indications of T2DM, severe hepatic metabolic remodeling and the inflammatory liver injury in the ZDF rats. The integrin linked kinase signaling, as well as the endoplasmic reticulum stress and its downstream p38 MAPK signaling, seemed to play crucial roles in it. We have proved the ZDF rats could better simulate the pathogenesis of the human T2DM associated nonalcoholic fatty liver disease (NAFLD), and provided targets and reference for future T2DM studies.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117451" }, "primaryId" : "GEO:GSE117451", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117451" } ] }, "title" : "MicroRNAs and histone deacetylase inhibition-mediated protection against inflammatory β-cell damage", "dateAssigned" : "2018-07-20T00:00:00.000-05:00", "summary" : "Inflammatory b-cell failure contributes to type 1 and type 2 diabetes pathogenesis. Proinflammatory cytokines cause b-cell dysfunction and apoptosis, and lysine deacetylase inhibitors (KDACi) prevent b-cell failure in vitro and in vivo, in part by reducing NFkB transcriptional activity. Here we investigated the hypothesis that the protective effect of KDACi involves transcriptional regulation of microRNAs (miRs), potential new targets in diabetes treatment. Insulin-producing INS1 cells were cultured with or without the broad-spectrum KDACi Givinostat prior to exposure to the proinflammatory cytokines IL-1-b and IFN-g for 6h or 24h, and miR expression was profiled with miR array. A shortlist of ten miRs (miR-7a-2-3p, miR-29c-3p, miR-96-5p, miR-101a-3p, miR-140-5p, miR-146a-5p, miR-146b-5p, miR-340-5p, miR-384-5p, and miR-455-5p) regulated by both cytokines and Givinostat was verified by qRT-PCR. MiR-146a-5p was strongly regulated by cytokines and KDACi and analyzed further. MiR-146a-5p expression was induced by cytokines in rat and human islets. Cytokine-induced miR-146a-5p expression was specific for INS1 and β-TC3 cells, whereas α-TC1 cells exhibited a higher basal expression. Transfection of INS1 cells with miR-146a-5p reduced the activity of NFκB and iNOS promoters, decreased NO production, and decreased protein levels of iNOS and its own direct target TNF receptor associated factor 6 (TRAF6). MiR-146a-5p was elevated in diabetes-prone BB-DP rat pancreas at diabetes onset, suggesting that miR-146a-5p could play a role in type 1 diabetes development. The miR array of cytokine-exposed INS1 cells rescued by KDACi revealed several other miRs potentially involved in cytokine-induced b-cell apoptosis, demonstrating the strength of this approach.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30260972" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117467" }, "primaryId" : "GEO:GSE117467", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117467" } ] }, "title" : "The chronological changes of transcriptomic profiles of hepatic macrophages after partial portal vein ligation", "dateAssigned" : "2018-07-22T00:00:00.000-05:00", "summary" : "We compared transcriptomic profiles of hepatic macrophages between sham operated rats, rats 3 days and 10 days after partial portal vein ligation (PPVL) surgery (n=3). The number of genes with a significant change was most numerous in Sham vs 3 days, followed by Sham vs 10 days and 3 days vs 10 days.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117487" }, "primaryId" : "GEO:GSE117487", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117487" } ] }, "title" : "Effect of cell passage number on gene expression in NR8383 macrophages", "dateAssigned" : "2018-07-23T00:00:00.000-05:00", "summary" : "This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117526" }, "primaryId" : "GEO:GSE117526", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117526" } ] }, "title" : "A Transcriptomic Analysis of Neuropathic Pain in Rat Dorsal Root Ganglia Following Peripheral Nerve Injury", "dateAssigned" : "2018-07-23T00:00:00.000-05:00", "summary" : "In this study, we screened the differentially expressed genes (DEGs) in the dorsal root ganglia (DRG) from rats with sham or partial sciatic nerve ligation (pSNL) surgery 7 days using RNAseq technique to explore the molecular mechanisms of neuropathic pain", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31858405" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117679" }, "primaryId" : "GEO:GSE117679", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117679" } ] }, "title" : "In the Setting of Beta Cell Stress, the Pancreatic Duct Gland Transcriptome shows Characteristics of an Activated Regenerative Response", "dateAssigned" : "2018-07-25T00:00:00.000-05:00", "summary" : "The pancreatic duct gland (PDG) compartment has been proposed as a potential stem cell niche. Little is known of the molecular signature of the PDG compartment in either a quiescent state or the potentially activated state during beta cell stress characteristic of diabetes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117835" }, "primaryId" : "GEO:GSE117835", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117835" } ] }, "title" : "Expression data from rats liver", "dateAssigned" : "2018-07-29T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression identified differientially expressed genes during this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117915" }, "primaryId" : "GEO:GSE117915", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117915" } ] }, "title" : "Transcriptional changes during hepatic ischemia-reperfusion in the rat", "dateAssigned" : "2018-07-31T00:00:00.000-05:00", "summary" : "Ischemia-reperfusion (IR) injury, a ubiquitous consequence of liver transplantation, is a cause of early graft rejection and increased morbidity. At present, there are no effective strategies to reduce hepatic IR injury. Molecular mechanisms that promote cell survival under these circumstances are largely undefined. We examined changes in global gene expression at early reperfusion times to identify potential IR-mediated protective responses. Using a rat model of 30 minutes of 70% warm ischemia followed by reperfusion, RNA for microarray analysis was extracted from the non-ischemic and the ischemic-reperfused lobes at four reperfusion times: 0 (no reperfusion), 0.5, 2, and 6 hours. Differentially expressed genes and pathway analyses were used to identify IR-induced events. The transcriptome of the reperfused lobes was unique and discrete at each reperfusion time, showing no evidence of sustained changes of the gene expression alterations seen at 30 minutes of reperfusion. At all reperfusion times, a significant portion of gene expression changes in the reperfused lobes were present in the non-ischemic lobes. However, the earliest reperfusion time, 30 minutes, showed a marked increase in the expression of a set of immediate-early genes (c-Fos, c-Jun, Atf3, Egr1) that was exclusive to the reperfused lobe. Similarities of gene expression changes in the reperfused and the non-ischemic lobes at each time suggest that hemodynamics and/or circulating factors are potent stimuli in an IR model. However, early reperfusion events appear to reflect a cell-autonomous response that may be protective, thereby representing potential targets to ameliorate IR injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31891620" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117961" }, "primaryId" : "GEO:GSE117961", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117961" } ] }, "title" : "RNA-seq datasets for \"A neuron-optimized CRISPR/dCas9 activation system for robust and specific gene regulation\"", "dateAssigned" : "2018-07-31T00:00:00.000-05:00", "summary" : "This dataset contains whole-genome RNA sequencing results from rat embryonic hippocampal neuronal cultures and serves as the basis for characterization of CRISPR/dCas9 gene activation in neuronal systems.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30863790" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117995" }, "primaryId" : "GEO:GSE117995", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE117995" } ] }, "title" : "Developmental Origins of Transgenerational Sperm DNA Methylation Epimutations Following Ancestral Vinclozolin Exposure", "dateAssigned" : "2018-08-01T00:00:00.000-05:00", "summary" : "Previously the agricultural fungicide vinclozolin was found to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs) termed epimutations that help mediate this epigenetic inheritance. The current study was designed to investigate the developmental origins of the transgenerational DMRs during gametogenesis. Male control and vinclozolin lineage F3 generation rats were used as a source of embryonic day 16 (E16) prospermatogonia, postnatal day 10 (P10) spermatogonia, and adult pachytene spermatocytes, round spermatids, caput epididymal sperm, and caudal sperm. The DMRs between the control versus vinclozolin lineage samples were determined for each developmental stage. The top 100 statistically significant DMRs for each stage were compared and the developmental origins of the caudal epididymal sperm DMRs were assessed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118044" }, "primaryId" : "GEO:GSE118044", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118044" } ] }, "title" : "MeDIP Sequencing for 2 rat liver Samples", "dateAssigned" : "2018-08-02T00:00:00.000-05:00", "summary" : "Diabetes exerts adverse effects on the initiation or progression of diabetes and metabolic syndrome of in the next generation. In past studies, limited attention has been given to the fathers’ role in shaping the metabolic landscape of offspring. Our study was designed to investigate how paternal hyperglycemia exerts an intergenerational effect in mammals as well as the underlying mechanisms. Hyperglycemia was introduced in male rats by intraperitoneally injected streptozotocin and these males were bred with healthy female rats to generate offspring. The metabolic profiles of the progeny were assessed, and DNA methylation profiles as well as gene expression related to lipid metabolism were investigated.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118182" }, "primaryId" : "GEO:GSE118182", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118182" } ] }, "title" : "LncRNA expression profile in hepar tissues of 12h after brain death or matched non-brain death donor liver transplantation", "dateAssigned" : "2018-08-06T00:00:00.000-05:00", "summary" : "To determine the LncRNA expression profile in hepar tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation, we uesed LncRNA microArray analysis form Arraystar to examine the expression of LncRNAs and circRNAs in hepar tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31828106" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118306" }, "primaryId" : "GEO:GSE118306", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118306" } ] }, "title" : "Epigenetic Transgenerational Inheritance of Testis Pathology and Sertoli Cell Epimutations: Generational Origins of Male Infertility", "dateAssigned" : "2018-08-08T00:00:00.000-05:00", "summary" : "Environmental toxicant induced epigenetic transgenerational inheritance has been shown to affect testis pathology and sperm count. Sertoli cells have an essential role in spermatogenesis by providing physical and nutritional support for developing germ cells. The current study was designed to further investigate the transgenerational epigenetic changes in the rat Sertoli cell epigenome that are associated with the onset of testis disease.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118323" }, "primaryId" : "GEO:GSE118323", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118323" } ] }, "title" : "Hyperglycemia Alters the Fetal Islet Transcriptome and Leads to Progeny Islet Dysfunction", "dateAssigned" : "2018-08-08T00:00:00.000-05:00", "summary" : "The overall goal of this project is to identify transcriptome alteration in fetal islets exposed to transient maternal hyperglycemia from GD20 to GD22.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30508415" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118381" }, "primaryId" : "GEO:GSE118381", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118381" } ] }, "title" : "Environmental Toxicant Induced Epigenetic Transgenerational Inheritance of Ovarian Pathology and Granulosa Cell Epigenome and Transcriptome Alterations: Ancestral Origins of PCO and POI", "dateAssigned" : "2018-08-09T00:00:00.000-05:00", "summary" : "Previous studies have shown that exposure to a number of environmental toxicants can promote the epigenetic transgenerational inheritance of ovarian disease, including decreases in the primordial follicle pool of oocytes that are similar to what is seen in POI, and increases in ovarian cysts that are similar to what is seen in PCOS. In the current study, transgenerational changes to the epigenome of ovarian granulosa cells are characterized in F3 generation rats after ancestral vinclozolin or DDT exposures compared to controls. In purified granulosa cells from 20 day old F3 generation females 164 differentially methylated regions (DMRs) (p<1e-06) were found in the F3 generation vinclozolin lineage, and 293 DMRs (p<1e-06) in the DDT lineage, compared to controls.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118447" }, "primaryId" : "GEO:GSE118447", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118447" } ] }, "title" : "Environmental Toxicant Induced Epigenetic Transgenerational Inheritance of Prostate Pathology and Stromal-Epithelial Cell Epigenome and Transcriptome Alterations: Ancestral Origins of Prostate Disease", "dateAssigned" : "2018-08-13T00:00:00.000-05:00", "summary" : "The incidence of prostate disease is increasing, and some of this increase may be attributable to ancestral exposure to environmental toxicants and epigenetic transgenerational inheritance mechanisms. The goal of the current study was to determine the effects that exposure of gestating female rats to vinclozolin has on the epigenetic transgenerational inheritance of prostate disease, and to characterize by what molecular epigenetic mechanisms this has occurred. Results indicate that there were changes in DNA methylation in both cell types.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118542" }, "primaryId" : "GEO:GSE118542", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118542" } ] }, "title" : "RNA-seq Quantitative Analysis of Wild Type and Kcnh2-/- day4 cells derived from rESCs", "dateAssigned" : "2018-08-14T00:00:00.000-05:00", "summary" : "Conclusions: Our study represents the detailed analysis of transcriptomes of Kcnh2-/- vs. WT rat embryonic stem cell, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118544" }, "primaryId" : "GEO:GSE118544", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118544" } ] }, "title" : "Chronic hypoxia changes gene expression profile of primary rat carotid body cells: consequences on the expression of NOS isoforms and ET-1 receptors", "dateAssigned" : "2018-08-14T00:00:00.000-05:00", "summary" : "Chronic hypoxia (CH) produces changes not fully understood in morphology and function of the carotid body (CB). To characterize the effect of CH, primary rat CB cells were exposed to 7 days of CH, total RNA was extracted, cDNA-32P synthesized and hybridized with 1185 genes printed on a nylon membrane. Out of 324 differentially expressed genes, 184 were up-regulated and 140 were down-regulated. Since data analyses showed that nitric oxide synthases (NOS) and endothelin-1 (ET-1) pathways were enriched, we studied the effect of CH at protein levels of NOS isoforms and ET-1 receptors. CH induced an increase in all NOS and in ET-1 receptor B (ETB). Combining CH and SNAP, iNOS and ETB were significantly up-regulated, whereas the ET-1 receptor A (ETA) was down-regulated, while Tezosentan up-regulated iNOS and ETA and L-NAME induced up-regulation of all NOS. These results described the changes of CH on the CB gene expression profile, affecting a possible interaction in between NOS and ET-1 receptors, as part of the adaptive CB response to CH.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30822223" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118557" }, "primaryId" : "GEO:GSE118557", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118557" } ] }, "title" : "Glyphosate Induced Epigenetic Transgenerational Inheritance of Pathologies and Sperm Epimutations: Generational Toxicology", "dateAssigned" : "2018-08-15T00:00:00.000-05:00", "summary" : "One of the most widely used agricultural compounds worldwide is the herbicide glyphosate (N-(phosphonomethyl)glycine), commonly known as Roundup. The current study using a transient exposure of gestating F0 generation female rats found negligible impacts of glyphosate on the directly exposed F0 generation or F1 generation offspring, but dramatic increases in pathologies in the F2 generation grand-offspring and F3 transgenerational great-grand-offspring. The transgenerational pathologies observed include prostate disease, obesity, kidney disease, ovarian disease, and parturition (birth) abnormalities. Epigenetic analysis of the F1, F2 and F3 generation sperm identified altered DNA methylation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31011160" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118559" }, "primaryId" : "GEO:GSE118559", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118559" } ] }, "title" : "αKlotho and sTGFBR2 treatment promotes endogenous cartilage regeneration and prevents osteoarthritis progression", "dateAssigned" : "2018-08-15T00:00:00.000-05:00", "summary" : "Osteoarthritis (OA) is the most prevalent musculoskeletal disorder and the most common form of arthritis among the elderly. Despite recent basic biology and clinical progress, the understanding and treatment of this and other cartilage-associated diseases are still a challenge. By using an in vivo rat OA model and in vitro human studies we report the improved homeostasis and repairing capacity of two soluble molecules, αKlotho and sTGFBR2, that in combination are able to prevent the progression of OA and promote cartilage regeneration.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118737" }, "primaryId" : "GEO:GSE118737", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118737" } ] }, "title" : "Loss of voltage dependent anion channel 1 affects mitochondrial bioenergetics in rat dopamine cells", "dateAssigned" : "2018-08-19T00:00:00.000-05:00", "summary" : "Voltage dependent anion channel 1 (VDAC1) is a multi-functional protein that regulates mitochondrial membrane potential, calcium regulation, and apoptosis. VDAC1 also interacts with a number of signaling pathways important for energy homeostasis and proteins involved in neurodegenerative diseases such as alpha-synuclein. To identify novel signaling pathways dependent upon VDAC1 protein in dopamine cells, we used CRISPR-Cas9 gene editing in rat immortalized dopaminergic N27 cells. Western blot confirmed that VDAC1 protein levels were reduced ~90%. Mitochondrial bioenergetics was assessed to determine if there was functional loss of mitochondrial function without VDAC1. Loss of VDAC1 resulted in lower ATP-linked and maximum respiration, and spare respiratory capacity. Transcriptomics was conducted in these cells to identify the pathways perturbed by loss of VDAC. This study sheds novel insight into the different regulatory roles mediated by VDAC1 in dopamine cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118738" }, "primaryId" : "GEO:GSE118738", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118738" } ] }, "title" : "The effects of the pesticide fipronil in rat N27 dopaminergic cells", "dateAssigned" : "2018-08-19T00:00:00.000-05:00", "summary" : "Six samples of N27 cells were treated with 25 uM fipronil, and 6 samples were not treated (control). The treatment proceeded for 24 hours.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118825" }, "primaryId" : "GEO:GSE118825", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118825" } ] }, "title" : "Genomic and proteomic profiling reveals reduced mitochondrial function and disruption of the neuromuscular junction driving rat sarcopenia", "dateAssigned" : "2018-08-21T00:00:00.000-05:00", "summary" : "Molecular mechanisms underlying sarcopenia, the age-related loss of skeletal muscle mass and function, remain unclear. To identify molecular changes that correlated best with sarcopenia and might contribute to its pathogenesis, we determined global gene expression profiles in muscles of rats aged 6, 12, 18, 21, 24, and 27 months. These rats exhibit sarcopenia beginning at 21 months. Correlation of the gene expression versus muscle mass or age changes, and functional annotation analysis identified gene signatures of sarcopenia distinct from gene signatures of aging. Specifically, mitochondrial energy metabolism (e.g., tricarboxylic acid cycle and oxidative phosphorylation) pathway genes were the most downregulated and most significantly correlated with sarcopenia. Also, perturbed were genes/pathways associated with neuromuscular junction patency (providing molecular evidence of sarcopenia-related functional denervation and neuromuscular junction remodeling), protein degradation, and inflammation. Proteomic analysis of samples at 6, 18, and 27 months confirmed the depletion of mitochondrial energy metabolism proteins and neuromuscular junction proteins. Together, these findings suggest that therapeutic approaches that simultaneously stimulate mitochondrogenesis and reduce muscle proteolysis and inflammation have potential for treating sarcopenia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:23109432" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118892" }, "primaryId" : "GEO:GSE118892", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118892" } ] }, "title" : "Screening of Genes Related to Glucose and Lipid Metabolism in Non-alcoholic Fatty Liver Disease by Gene Microarray", "dateAssigned" : "2018-08-22T00:00:00.000-05:00", "summary" : "We used gene expression microarray to explore the correlation between gene expression profiles and find out the target genes related to lipid and glucose metabolism in NAFLD. A rat model of NAFLD was established by feeding male rats with high-fat diet and Agilent DNA microarray was used to detect gene expression profiles of liver tissues. We explored differentially expressed genes and intersection of them by using Gene ontology (GO) and Pathway analyses. Then, target genes were verified by Real-time polymerase chain reaction (RT-PCR). There were 932 genes, including 783 up-regulated and 149 down-regulated, differed in expression compared to those of control rats. The up-regulated genes were involved in biosynthesis, cell development, cell differentiation and down-regulated genes mainly contributed to biological metabolic process and stress reaction. We identified genes involved in insulin signaling pathway, Notch signaling pathway, adipocytokin and linoleic acid metabolism to be closely related to liver fat content and insulin resistance. Among them, genes which supposed to connect glucose and lipid metabolism were screened (IGFBP7, Notch1, HMGCR and ACACB) and then validated by real-time PCR. These data provide innovative information on the whole genome expression profile due to high-fat diet feeding and bring important insights into the mechanism of NAFLD.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118956" }, "primaryId" : "GEO:GSE118956", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118956" } ] }, "title" : "TempO-Seq S1500+ Platform Gene Expression of Rat Liver Mode of Action Samples", "dateAssigned" : "2018-08-23T00:00:00.000-05:00", "summary" : "Using the TempO-Seq rat S1500+ platform we performed gene expression analysis of using 63 purified RNA samples from the livers of rats exposed to controls or chemicals that fall into one of five modes of action (MOAs): constitutive androstane receptor/pregnane X receptor (CAR/PXR) activation, aryl hydrocarbon receptor (AhR) activation, peroxisome proliferator-activated receptor-alpha (PPARA) activation, cytotoxicity or DNA damage. The TempO-Seq data generated was used to compare to gene expression data acquired from the same samples run on Affymetrix microarays (GEO: GSE47875) and Illumina RNA-Seq (GEO: GSE55347, SRA:SRP039021).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30420870" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118978" }, "primaryId" : "GEO:GSE118978", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE118978" } ] }, "title" : "Selective molecular responses of rat white adipose tissue according to the fasting stage", "dateAssigned" : "2018-08-23T00:00:00.000-05:00", "summary" : "White adipose tissue is a central place to energy storage and a major endocrine organ. However, adipose molecular mechanisms have been poorly studied during prolonged fasting. To fill this gap, the aim of this study was to decipher transcriptomic regulations in rat adipose tissue during phase 2 (lipid mobilization) and phase 3 (protein catabolism) of prolonged fasting compared to the fed state. We describe a regulatory transcriptional program in epididymal adipose tissue in line with lipogenesis repression during both phases, and that would favor lipolysis during phase 2 and repress it during phase 3. Such regulations notably involve selective (i.e. phase-dependent) changes in gene expression levels of lipases, lipid droplet-associated factors, and the proteins involved in cAMP-dependent and cAMP-independent regulation of lipolysis. The mRNA levels of adipose-secreted factors were globally consistent with the repression of insulin signalling during prolonged fasting. Regulations of leptin and adiponectin levels could be related to their respective role in triggering refeeding during late fasting and controlling lipid metabolism. Specific responses reflecting adipose tissue inflammation, increased fibrinolysis and a possible protein catabolism-related energy saving mechanism were also recorded during phase 3. These data thus provide a comprehensive molecular basis of adipose tissue responses according to the fasting stage.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31398141" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119095" }, "primaryId" : "GEO:GSE119095", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119095" } ] }, "title" : "Cartilaginous and osteochondral tissue formation by human mesenchymal stem cells on three-dimensionally woven scaffolds", "dateAssigned" : "2018-08-27T00:00:00.000-05:00", "summary" : "The development of mechanically functional cartilage and bone tissue constructs of clinically relevant size, as well as their integration with native tissues, remain important challenges for regenerative medicine. The objective of this study was to assess of adult human mesenchymal stem cells (MSC) in large, three dimensionally woven poly(-caprolactone) (PCL) scaffolds in proximity to viable bone, both in a nude rat subcutaneous pouch model and under simulated conditions in vitro. In Study I, various scaffold permutations: PCL alone, PCL-bone, “point-of-care” seeded MSC-PCL-bone, and chondrogenically pre-cultured Ch-MSC-PCL-bone constructs were implanted in a dorsal, ectopic pouch in a nude rat. After eight weeks, cells in the PCL scaffold exhibited both chondrogenic and osteogenic gene expression profiles. Notably, while both tissue profiles were present, constructs that had been chondrogenically pre-cultured prior to implantation showed a loss of glycosaminoglycan (GAG) as well as the presence of mineralization along with the formation of trabeculae-like structures. In Study II of the study, the GAG loss and mineralization observed in Study I in vivo were recapitulated in vitro by the presence of either nearby bone or osteogenic culture medium additives but were prevented by a continued presence of chondrogenic medium additives. These data suggest conditions under which adult human stem cells in combination with polymer scaffolds synthesize functional and phenotypically distinct tissues based on the environmental conditions, and highlight the potential influence that paracrine factors from adjacent bone may have on MSC fate, once implanted in vivo for chondral or osteochondral repair.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119121" }, "primaryId" : "GEO:GSE119121", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119121" } ] }, "title" : "Expression data from blood of rats", "dateAssigned" : "2018-08-28T00:00:00.000-05:00", "summary" : "Changes over the first day after stroke in rats in order to identy a stroke time signature.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30439964" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119122" }, "primaryId" : "GEO:GSE119122", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119122" } ] }, "title" : "Transcriptomic profiles of tissues from rats treated with drug combinations [Study 1]", "dateAssigned" : "2018-08-28T00:00:00.000-05:00", "summary" : "Combinations of anticancer agents may have synergistic anti-tumor effects, but enhanced toxicity often limit their clinical use. The risk that combinations of two or more drugs will cause adverse effects that are more severe than drugs used as monotherpies can be hypothesized from comprehensive analysis of each compound’s activity. We generated microarray gene expression data following a single dose of agents administered individually with that of the agents administered in a combination. The key objective of this initiative is to generate and make publicly available key high-content gene expression data sets for mechanistic hypothesis generation for several anticancer drug combinations. The expectation is that availability of tissue-based genomic information that are derived from target tissues will facilitate the generation and testing of mechanistic hypotheses. The view is that availability of these data sets for bioinformaticians and other scientists will contribute to analysis of these data and evaluation of the approach.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30620345" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119125" }, "primaryId" : "GEO:GSE119125", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119125" } ] }, "title" : "Expression data of genes in proliferative and differentiated NSCs derived from brain and spinal cord", "dateAssigned" : "2018-08-28T00:00:00.000-05:00", "summary" : "We compared the proliferative and differentiated NSCs derived from brain and spinal cord to investigate the mechanisms of promoting proliferation and differentiation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119129" }, "primaryId" : "GEO:GSE119129", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119129" } ] }, "title" : "Transcriptomic profiles of tissues from rats treated with drug combinations [Study 2]", "dateAssigned" : "2018-08-28T00:00:00.000-05:00", "summary" : "Combinations of anticancer agents may have synergistic anti-tumor effects, but enhanced toxicity often limit their clinical use. The risk that combinations of two or more drugs will cause adverse effects that are more severe than drugs used as monotherpies can be hypothesized from comprehensive analysis of each compound’s activity. We generated microarray gene expression data following a single dose of agents administered individually with that of the agents administered in a combination. The key objective of this initiative is to generate and make publicly available key high-content gene expression data sets for mechanistic hypothesis generation for several anticancer drug combinations. The expectation is that availability of tissue-based genomic information that are derived from target tissues will facilitate the generation and testing of mechanistic hypotheses. The view is that availability of these data sets for bioinformaticians and other scientists will contribute to analysis of these data and evaluation of the approach.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30620345" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119133" }, "primaryId" : "GEO:GSE119133", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119133" } ] }, "title" : "Transcriptomic profiles of tissues from rats treated with drug combinations [Study 3]", "dateAssigned" : "2018-08-28T00:00:00.000-05:00", "summary" : "Combinations of anticancer agents may have synergistic anti-tumor effects, but enhanced toxicity often limit their clinical use. The risk that combinations of two or more drugs will cause adverse effects that are more severe than drugs used as monotherpies can be hypothesized from comprehensive analysis of each compound’s activity. We generated microarray gene expression data following a single dose of agents administered individually with that of the agents administered in a combination. The key objective of this initiative is to generate and make publicly available key high-content gene expression data sets for mechanistic hypothesis generation for several anticancer drug combinations. The expectation is that availability of tissue-based genomic information that are derived from target tissues will facilitate the generation and testing of mechanistic hypotheses. The view is that availability of these data sets for bioinformaticians and other scientists will contribute to analysis of these data and evaluation of the approach.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30620345" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119170" }, "primaryId" : "GEO:GSE119170", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119170" } ] }, "title" : "m6A profile in cardiomyocytes", "dateAssigned" : "2018-08-28T00:00:00.000-05:00", "summary" : "To determine the role of m6A methylation in the heart we isolated primary cardiomyocytes and performed m6A immunoprecipitation followed by RNA sequencing. We measured the level of m6A methylation on cardiomyocyte mRNA, and found a significant increase in response to hypertrophic stimulation, suggesting a potential role for m6A methylation in the development of cardiomyocyte hypertrophy. Analysis of m6A methylation showed significant enrichment in genes that regulate kinases and intracellular signaling pathways. Inhibition of METTL3 completely abrogated the ability of cardiomyocytes to undergo hypertrophy when stimulated to grow, while increased expression of the m6A RNA methylase METTL3 was sufficient to promote cardiomyocyte hypertrophy both in vitro and in vivo. Our study identified METTL3-mediated methylation of mRNA on N6-adenosines as a dynamic modification that is enhanced in response to hypertrophic stimuli and is necessary for a normal hypertrophic response in cardiomyocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30586742" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119235" }, "primaryId" : "GEO:GSE119235", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119235" } ] }, "title" : "Aberrant DNA methylation of hypothalamic angiotensin receptor in prenatal-programmed hypertension", "dateAssigned" : "2018-08-30T00:00:00.000-05:00", "summary" : "Malnutrition during pregnancy, which causes prenatal exposure to excessive glucocorticoid, induces adverse metabolic programming leading to hypertension in offspring. Pregnant rats receiving a low-protein diet exhibited moderate downregulation of 11-beta-dehydrogenase isozyme 2, which inactivates corticosterone, in the placenta, resulting in prenatal exposure to excessive corticosterone. In offspring of pregnant rats receiving a low-protein diet or dexamethasone, mRNA expression of angiotensin receptor type 1a (Agtr1a) in the paraventricular nucleus (PVN) of the hypothalamus was upregulated, concurrent with reduced expression of DNA methyltransferase 3a (Dnmt3a), reduced binding of DNMT3a to the Agtr1a promoter, and DNA demethylation, suggesting hypothalamic Agtr1a expression is epigenetically modulated by excess glucocorticoid. Dexamethasone treatment of PVN cells downregulated DNMT3a while upregulating Agtr1a, and decreased DNMT3a binding and DNA demethylation at the Agtr1a promoter. Consistent with Agtr1a upregulation in the hypothalamus, salt loading increased BP in both types of offspring. Even without dexamethasone treatment, hypothalamic neuron-specific DNMT3a-deficient mice, in which Agtr1a was upregulated, exhibited salt-induced BP elevation. By contrast, dexamethasone-treated Agtr1a-deficient mice failed to show salt-induced BP elevation, despite reduced expression of DNMT3a. Thus, epigenetic modulation of hypothalamic angiotensin signaling contributes to salt-sensitive hypertension induced by prenatal glucocorticoid excess in offspring of mothers that are malnourished during pregnancy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30385711" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119349" }, "primaryId" : "GEO:GSE119349", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119349" } ] }, "title" : "Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures", "dateAssigned" : "2018-08-31T00:00:00.000-05:00", "summary" : "In the central nervous system (CNS), the microRNAs (miRNAs), small endogenous RNAs exerting a negative post-transcriptional regulation on mRNAs, are involved in major functions, such as neurogenesis, and synaptic plasticity. Moreover, they are essential to define the specific transcriptome of the tissues and cell types. However, few studies were performed to determine the miRNome of the different structures of the rat CNS, even through rat is a major model in neuroscience. We determined the miRNome profile of the hippocampus, the cortex, the striatum, the spinal cord and the olfactory bulb, by small RNA-Seq. We found a total of 365 known miRNAs' and 90 novel miRNAs expressed in the CNS of the rat. Novel miRNAs seemed to be important in defining structure-specific miRNomes. Differential analysis showed that several miRNAs were specifically enriched/depleted in these CNS structures. Then, we correlated miRNAs' expression with the expression of their mRNA targets by mRNA-Seq. This analysis suggests that the transcriptomic identity of each structure is regulated by specific miRNAs. Altogether, these results suggest the critical role played by these enriched/depleted miRNAs in the functional identities of CNS structures.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30456375" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119414" }, "primaryId" : "GEO:GSE119414", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119414" } ] }, "title" : "Rat muscle derived stem cells treated with fatty acids or cholesterol", "dateAssigned" : "2018-09-04T00:00:00.000-05:00", "summary" : "RNA was extracted using the RNeasy Plus Micro kit and analyzed at UCLA by the Affymetrix rat Gene 2.0 ST chip.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119434" }, "primaryId" : "GEO:GSE119434", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119434" } ] }, "title" : "Microarray-based miRNA expression in fluid shear stress-stimulated collateral blood vessels", "dateAssigned" : "2018-09-04T00:00:00.000-05:00", "summary" : "A total of ten total RNA samples were processed. 800 ng of total RNA from each sample was subjected to two different labeling reactions (AF665 and AF546). Two differentially labeld reactions were combined into one tube and loaded onto the arrays.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119435" }, "primaryId" : "GEO:GSE119435", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119435" } ] }, "title" : "Transcriptomic analysis reveals new hippocampal gene networks induced by prolactin", "dateAssigned" : "2018-09-04T00:00:00.000-05:00", "summary" : "Prolactin (Prl) is a pleiotropic hormone with multiple functions in several tissues and organs, including the brain. In the hippocampus, Prl has been implicated in several functions, including neuroprotection against excitotoxicity in lactating rats and in Prl-treated ovariectomized animals. However, the molecular mechanisms involved in Prl actions in the hippocampus have not been completely elucidated. The aim of this study was to analyse the hippocampal transcriptome of female Prl-treated ovariectomized rats. Transcriptomic analysis by RNASeq revealed 162 differentially expressed genes throughout 24 h of Prl treatment. Gene Ontology analysis of those genes showed that 37.65% were involved in brain processes that are regulated by the hippocampus, such as learning, memory and behaviour, as well as new processes that we did not foresee, such as glial differentiation, axogenesis, synaptic transmission, postsynaptic potential, and neuronal and glial migration. Immunodetection analysis demonstrated that Prl significantly modified microglial morphology, reduced the expression of Cd11b/c protein, and altered the content and location of the neuronal proteins Tau, Map2 and Syp, which are involved in axogenic and synaptic functions. This novel delineation of Prl activity in the hippocampus highlights its importance as a neuroactive hormone, opens a new avenue for understanding its actions and supports its participation in neuronal plasticity of this brain area.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31551509" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119473" }, "primaryId" : "GEO:GSE119473", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119473" } ] }, "title" : "MicroRNA profiling in male rat germ cells after chronic cyclophosphamide treatment", "dateAssigned" : "2018-09-04T00:00:00.000-05:00", "summary" : "Although numerous miRNAs have been identified in the testis, their roles in regulating the highly specific events that occur in the different germ cell types throughout spermatogenesis remain largely unknown. Furthermore, whether male germ cell miRNA expression is altered in response to or as a consequence of exposure to a toxic agent is unknown. Here we examine miRNA expression profiles in pachytene spermatocytes and round spermatids obtained from control rats and from rats treated with a chronic low dose of cyclophosphamide, a male germ cell toxicant. We observed that pachytene spermatocytes and round spermatids display vastly different miRNA expression profiles, reflecting their different developmental stages and possibly influencing the cellular response to toxic insult. Chronic low dose cyclophosphamide treatment altered the miRNA profiles in both pachytene spermatocytes and round spermatids. Target prediction analyses revealed that miRNAs altered by cyclophosphamide treatment may be involved in the response to cellular stress and damage. However, many are also involved in processes that are crucial for proper germ cell development. This study suggests that pachytene spermatocytes and round spermatids display distinct miRNA profiles that can be altered by cyclophosphamide treatment. The observed changes may be part of a response and repair mechanism to cyclophosphamide-induced damage or a dysregulation that disrupts normal germ cell development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119482" }, "primaryId" : "GEO:GSE119482", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119482" } ] }, "title" : "Methylglyoxal modification of TrkB enhances synaptic plasticity in prefrontal cortex and promotes resilience to chronic stress", "dateAssigned" : "2018-09-05T00:00:00.000-05:00", "summary" : "Major depressive disorder (MDD) is a severe psychiatric illness that affects about 16 percent of the global population. Despite massive efforts, unravelling the pathophysiology of MDD and developing effective treatments is still a huge challenge. Here, we report a novel therapeutic axis of methylglyoxal (MGO)/tropomyosin receptor kinase B (TrkB) for treating MDD. As an endogenous metabolite, MGO was demonstrated directly binding to the extracellular domain of TrkB, provoking its dimerization and autophosphorylation. This rapidly enhances the expression of brain-derived neurotrophic factor (BDNF) and forms a BDNF-positive feedback loop. Low-dose treatment of MGO effectively promotes the hippocampal neurogenesis and exhibits sustained antidepressant effects in chronic unpredictable mild stress rat models. In addition, the modulation on MGO concentration by overexpression or inhibition of Glyoxalase 1 (GLO1) has been demonstrated associated with depression behaviors in rats. Furthermore, we also identified a natural product luteolin and its derivative lutD as potent inhibitors of GLO1 and explored their precise binding modes. Our findings reveal a novel regulatory mechanism underlying MDD and depict principles for the rational design of new antidepressants targeting GLO1.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119524" }, "primaryId" : "GEO:GSE119524", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119524" } ] }, "title" : "Expression data from Tsc2-null cell line ELT3, and the ELT3-derivative rapamycin-resistant cell line ELT3-245", "dateAssigned" : "2018-09-05T00:00:00.000-05:00", "summary" : "Tuberous Sclerosis Complex (TSC) and Lymphangioleiomyomatosis (LAM) are caused by inactivating mutations in TSC1 or TSC2, leading to mTORC1 hyperactivation. The mTORC1 inhibitors rapamycin and analogs (rapalogs) are approved for treating of TSC and LAM. Due to their cytostatic and not cytocidal action, discontinuation of treatment leads to tumor regrowth and decline in pulmonary function. Therefore, life-long rapalog treatment is proposed for the control of TSC and LAM lesions, which increases the chances for the development of acquired drug resistance. Understanding the signaling perturbations leading to rapalog resistance is critical for the development of better therapeutic strategies. We developed the first Tsc2-null rapamycin-resistant cell line, ELT3-245, which is highly tumorigenic in mice, and refractory to rapamycin treatment. In vitro ELT3-245 cells exhibit enhanced anchorage-independent cell survival, resistance to anoikis, and loss of epithelial markers. A key alteration in ELT3-245 is increased β-catenin signaling. We propose that a subset of cells in TSC and LAM lesions have additional signaling aberrations, thus possess the potential to become resistant to rapalogs. Alternatively, when challenged with rapalogs TSC-null cells are reprogrammed to express mesenchymal-like markers. These signaling changes could be further exploited to induce clinically-relevant long-term remissions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30816188" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119557" }, "primaryId" : "GEO:GSE119557", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119557" } ] }, "title" : "Gene expression changes in PC12 cells expressing GFP-mHtt-74Q treated with Guanabenz analogues", "dateAssigned" : "2018-09-06T00:00:00.000-05:00", "summary" : "To gain an overview of the cellular impact of Guanabenz analogues, we analyzed the gene expression changes in PC12 cells expressing GFP-mHtt-74Q utilizing Affimatrix rat genome microarrays. Following exposure of PC12 cells expressing GFP-mHtt-74Q to Compound 6 for 48 hrs, we noted the enhanced expression of over 46 genes and the reduced expression of 8 genes compared to DMSO", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31313908" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119627" }, "primaryId" : "GEO:GSE119627", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119627" } ] }, "title" : "Chromatin remodeler INO80 is essential for cocaine craving during prolonged withdrawal", "dateAssigned" : "2018-09-07T00:00:00.000-05:00", "summary" : "Neuroadaptations in the nucleus accumbens (NAc) underlie cue-induced cocaine craving that intensifies (“incubates”) during withdrawal and contributes to persistent relapse vulnerability. Long-lasting gene changes govern perpetual behavioral abnormalities but the role of epigenetic plasticity in cocaine craving during prolonged withdrawal is poorly understood. Here we show that chromatin remodeler INO80 in the NAc mediates cocaine-induced, withdrawal-dependent plasticity and incubated cocaine craving.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31633032" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119630" }, "primaryId" : "GEO:GSE119630", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119630" } ] }, "title" : "Extraction-Free Whole Transcriptome Profiling from Specific Subareas of Unstained or H&E Stained FFPE Tissues", "dateAssigned" : "2018-09-07T00:00:00.000-05:00", "summary" : "We describe the use of a ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq™, to profile formalin-fixed paraffin-embedded (FFPE) tissue, including H&E stained FFPE tissue, by directly lysing tissue scraped from slides without extracting RNA or converting the RNA to cDNA. The correlation of measured gene expression changes in unfixed and fixed samples using blocks prepared from a pellet of a single cell type was R2 = 0.97, demonstrating that no significant artifacts were introduced by fixation. Fixed and fresh samples prepared in an equivalent manner produced comparable sequencing depth results (+/- 20%), with similar %CV (11.5 and 12.7%, respectively), indicating no significant loss of measurable RNA due to fixation. The sensitivity of the TempO-Seq assay was the same whether the tissue section was fixed or not. The assay performance was equivalent for human, mouse, or rat whole transcriptome. The results from 10 mm2 and 2 mm2 areas of tissue obtained from 5 μm thick sections were equivalent, thus demonstrating high sensitivity and ability to profile focal areas of histology within a section. Replicate reproducibility of separate areas of tissue ranged from R2= 0.83 (lung) to 0.96 (liver) depending on the tissue type, with an average correlation of R2 = 0.90 across nine tissue types. The average %CV’s were 16.8% for genes expressed at greater than 200 counts, and 20.3% for genes greater than 50 counts. Tissue specific differences in gene expression were identified and agreed with the literature. There was negligible impact on assay performance using FFPE tissues that had been archived for up to 30 years. Similarly, there was negligible impact of H&E staining, facilitating accurate visualization for scraping and assay of small focal areas of specific histology within a section.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30794557" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119634" }, "primaryId" : "GEO:GSE119634", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119634" } ] }, "title" : "Modulation of gene expression in rat muscle cells following treatment with nanoceria in different gravity regimes", "dateAssigned" : "2018-09-07T00:00:00.000-05:00", "summary" : "The study evaluates potential protective effects of cerium oxide nanoparticles (nanoceria) against oxidative stress in muscle tissue, both on ground and in space", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30334476" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119640" }, "primaryId" : "GEO:GSE119640", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119640" } ] }, "title" : "Intra-individual methylomics detects the impact of early-life adversity", "dateAssigned" : "2018-09-07T00:00:00.000-05:00", "summary" : "Genetic and environmental factors interact during sensitive periods early in life to influence mental health and disease via epigenetic processes such as DNA methylation. However, it is not known if DNA methylation changes outside the brain provide an 'epigenetic signature' of early-life experiences. Here, we employed a novel intra-individual approach by testing DNA methylation from buccal cells of individual rats before and immediately after exposure to one week of typical or adverse life experience. We find that whereas inter-individual changes in DNA methylation reflect the effect of age, DNA methylation changes within paired DNA samples from the same individual reflect the impact of diverse neonatal experiences. Genes coding for critical cellular–metabolic enzymes, ion channels and receptors were more methylated in pups exposed to the adverse environment, predictive of their repression. In contrast, the adverse experience was associated with less methylation on genes involved in pathways of death and inflammation as well as cell-fate related transcription factors, indicating their potential upregulation. Thus, intra-individual methylome signatures indicate large-scale transcription-driven alterations of cellular fate, growth and function. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30936186" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119748" }, "primaryId" : "GEO:GSE119748", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119748" } ] }, "title" : "Liver tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation.", "dateAssigned" : "2018-09-10T00:00:00.000-05:00", "summary" : "To determine the circRNA expression profile in hepar tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation, we uesed circRNA microArray analysis form Arraystar to examine the expression of circRNAs and circRNAs in hepar tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31828106" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119754" }, "primaryId" : "GEO:GSE119754", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119754" } ] }, "title" : "Transcriptomic Signature of Right Ventricular Failure in Experimental Pulmonary Arterial Hypertension: Deep Sequencing Demonstrates Mitochondrial, Fibrotic, Inflammatory and Angiogenic Abnormalities", "dateAssigned" : "2018-09-10T00:00:00.000-05:00", "summary" : "Abstract: Right ventricular failure (RVF) remains the leading cause of death in pulmonary arterial hypertension (PAH). We investigated the transcriptomic signature of RVF in hemodynamically well-phenotyped monocrotaline (MCT)-treated, male, Sprague-Dawley rats with severe PAH and decompensated RVF (increased right ventricular (RV) end diastolic volume (EDV), decreased cardiac output (CO), tricuspid annular plane systolic excursion (TAPSE) and ventricular-arterial decoupling). RNA sequencing revealed 2547 differentially regulated transcripts in MCT-RVF RVs. Multiple enriched gene ontology (GO) terms converged on mitochondria/metabolism, fibrosis, inflammation, and angiogenesis. The mitochondrial transcriptomic pathway is the most affected in RVF, with 413 dysregulated genes. Downregulated genes included tfam (−0.45-fold), suggesting impaired mitochondrial biogenesis, Cyp2e1 (−3.8-fold), a monooxygenase which when downregulated increases oxidative stress, dehydrogenase/reductase 7C (Dhrs7c) (−2.8-fold), consistent with excessive autonomic activation, and polypeptide N-acetyl-galactose-aminyl-transferase 13 (Galnt13), a known pulmonary hypertension (PH) biomarker (−2.7-fold). The most up-regulated gene encodes Periostin (Postn; 4.5-fold), a matricellular protein relevant to fibrosis. Other dysregulated genes relevant to fibrosis include latent-transforming growth factor beta-binding protein 2 (Ltbp2), thrombospondin4 (Thbs4). We also identified one dysregulated gene relevant to all disordered transcriptomic pathways, Annexin A1. This anti-inflammatory, phospholipid-binding mediator, is a putative target for therapy in RVF-PAH. Comparison of expression profiles in the MCT-RV with published microarray data from the RV of pulmonary artery-banded mice and humans with bone morphogenetic protein receptor type 2 (BMPR2)-mutations PAH reveals substantial conservation of gene dysregulation, which may facilitate clinical translation of preclinical therapeutic and biomarkers studies. Transcriptomics reveals the molecular fingerprint of RVF to be heavily characterized by mitochondrial dysfunction, fibrosis and inflammation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119793" }, "primaryId" : "GEO:GSE119793", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119793" } ] }, "title" : "Gene expression in rat lumbar spinal cord tissues", "dateAssigned" : "2018-09-11T00:00:00.000-05:00", "summary" : "We assessed the transcriptome within lumbar spinal cord tissue of wild-type Lewis rats and attractin-mutant rats (LEWzizi; LEW.SD-Atrn zi/zi).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30704526" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119795" }, "primaryId" : "GEO:GSE119795", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119795" } ] }, "title" : "Jiangya Kangxian Formula attenuates Cardiac Remodeling induced by Hypertension in Spontaneous Hypertensive Rat through modulating Mitochondrial Dysfunction", "dateAssigned" : "2018-09-11T00:00:00.000-05:00", "summary" : "Kangxian formula (KXF), composed of 5 traditional Chinese distinct herbs including Panax Notoginseng, Radix Salviae, Spatholobus Suberectus Dunn, Hedysarum Multijugum Maxim and Citri Grandis Exocarpium, is a proved recipe showing promising outcomes in treating hypertension and cardiac remodeling in clinic. However, the effect of longterm treatment with KXF in such a condition and the related molecular mechanisms remain ambiguous. Here, we evaluated the effect of KXF on the gut microbiota and the prevention of hypertension and cardiac remodeling.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119796" }, "primaryId" : "GEO:GSE119796", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119796" } ] }, "title" : "Expression data of genes and noncoding genes from the ADSCs and adipogenic-induced ADSCs", "dateAssigned" : "2018-09-11T00:00:00.000-05:00", "summary" : "We used microarrays to detail the full transcriptome expression profiles of undifferentiated and adipogenic-induced ADSCs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119814" }, "primaryId" : "GEO:GSE119814", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119814" } ] }, "title" : "Seh1 Interacts with Olig2 and Brd7 to Promote Oligodendrocyte Differentiation and Myelination (ChIP-Seq)", "dateAssigned" : "2018-09-11T00:00:00.000-05:00", "summary" : "Nuclear pore complex components (Nups) are involved in neural development and alterations in Nup genes are linked to human neurological diseases. However, the physiological functions of specific Nups and the underlying mechanisms involved in these processes remain elusive. Here we show that tissue-specific depletion of nucleoporin Seh1 causes dramatic myelination defects in the Central Nervous System (CNS). Seh1-deficient Oligodendrocyte Progenitor Cells (OPCs) proliferate properly, but fail to differentiate into mature oligodendrocytes, which impairs myelin production and remyelination after demyelinating injury. Genome-wide analyses show that Seh1 regulates a core myelinogenic regulatory network and depletion of Seh1 alters open chromatin configurations at its target genes. Mechanistically, Seh1 regulates OPCs differentiation by assembling Olig2 and Brd7 into a transcription complex at nuclear pores. Together, our results reveal that Seh1 is required for oligodendrocyte differentiation and myelination by promoting assembly of an Olig2-dependent transcription complex and expose nucleoporins as key players in the CNS.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119833" }, "primaryId" : "GEO:GSE119833", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119833" } ] }, "title" : "West Virgina Chemical Spill: 5-Day Rat Toxicogenomic Studies", "dateAssigned" : "2018-09-11T00:00:00.000-05:00", "summary" : "As part of the West Virginia Chemical Spill research program, NTP evaluated three chemicals that were spilled into the Elk Rever in West Virginia for their ability to cause toxicity or biological changes in a short-term toxicogenomic study", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119933" }, "primaryId" : "GEO:GSE119933", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119933" } ] }, "title" : "Toxicogenomics directory of rat hepatotoxicants in vivo and in cultivated hepatocytes", "dateAssigned" : "2018-09-13T00:00:00.000-05:00", "summary" : "The raw data for the TGP study are available at https://toxico.nibiohn.go.jp/ For the normalization of the entire set of expression arrays, the RMA algorithm was used. The results are summarized in the publicly available toxicotranscriptomics directory (http://wiki.toxbank.net/toxicogenomics-map/).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30511339" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119955" }, "primaryId" : "GEO:GSE119955", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE119955" } ] }, "title" : "Identification of early transcriptome-based biomarkers related to lipid metabolism in peripheral blood mononuclear cells of rats nutritionally programmed for improved metabolic health", "dateAssigned" : "2018-09-14T00:00:00.000-05:00", "summary" : "Moderate maternal calorie restriction during lactation protects rat offspring against obesity development in adulthood, due to an improved ability to handle and store excess dietary fuel. We used this model to identify early transcriptome-based biomarkers of metabolic health using peripheral blood mononuclear cells (PBMCs), an easily accessible surrogate tissue, by focusing on molecular markers of lipid handling. Male and female offspring of control and 20 % calorierestricted lactating dams (CR) were studied. At weaning, a set of pups was killed, and PBMCs were isolated for whole-genome microarray analysis. The remaining pups were killed at 6 months of age. CR gave lower body weight, food intake and fat accumulation, and improved levels of insulin and leptin throughout life, particularly in females. Microarray analysis of weaned rat PBMCs identified 278 genes significantly differentially expressed between control and CR. Among lipid metabolism-related genes, expression of Cpt1a, Lipe and Star was increased and Fasn, Lrp1 and Rxrb decreased in CR versus control, with changes fully confirmed by qPCR. Among them, Cpt1a, Fasn and Star emerged as particularly interesting. Transcript levels of Cpt1a in PBMCs correlated with their levels in WAT and liver at both ages examined; Fasn expression levels in PBMCs at an early age correlated with their expression levels in WAT; and early changes in Star expression levels in PBMCs correlated with their expression levels in liver and were sustained in adulthood. These findings reveal the possibility of using transcript levels of lipid metabolism-related genes in PBMCs as early biomarkers of metabolic health status.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:24343050" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120002" }, "primaryId" : "GEO:GSE120002", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120002" } ] }, "title" : "Genome-wide analysis of glucocorticoid-responsive transcripts in the hypothalamic paraventricular region of male rats", "dateAssigned" : "2018-09-14T00:00:00.000-05:00", "summary" : "Conclusions: the present study uncovered a broad spectrum of Cort-responsive genes, potentially involved in the regulation of the HPA-axis, as well as other neuroendocrine and pre-autonomic functions of the PVH.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120061" }, "primaryId" : "GEO:GSE120061", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120061" } ] }, "title" : "Distinct Pathogenic Genes Causing Intellectual Disability and Autism Exhibit a Common Neuronal Network Hyperactivity Phenotype", "dateAssigned" : "2018-09-17T00:00:00.000-05:00", "summary" : "Pathogenic mutations in either one of the epigenetic modifiers EHMT1, MBD5, MLL3, or SMARCB1 have been identified to be causative for Kleefstra syndrome spectrum (KSS), a neurodevelopmental disorder with clinical features of both intellectual disability (ID) and autism spectrum disorder (ASD). To understand how these variants lead to the phenotypic convergence in KSS, we employ a loss-of-function approach to assess neuronal network development at the molecular, single-cell, and network activity level. KSS-gene-deficient neuronal networks all develop into hyperactive networks with altered network organization and excitatory-inhibitory balance. Interestingly, even though transcriptional data reveal distinct regulatory mechanisms, KSS target genes share similar functions in regulating neuronal excitability and synaptic function, several of which are associated with ID and ASD. Our results show that KSS genes mainly converge at the level of neuronal network communication, providing insights into the pathophysiology of KSS and phenotypically congruent disorders.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31914384" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120081" }, "primaryId" : "GEO:GSE120081", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120081" } ] }, "title" : "Profiling of gene expression using RNA-Seq in fibroblasts, iPSCs, iPSC-derived neurons and cells overexpressing Onecut transcription factors", "dateAssigned" : "2018-09-17T00:00:00.000-05:00", "summary" : "Remodeling of chromatin accessibility is necessary for successful reprogramming of fibroblasts to neurons. However, it is still not fully known which transcription factors can induce a neuronal chromatin accessibility profile when overexpressed in fibroblasts. To identify such transcription factors, we here used ATAC-sequencing to generate differential chromatin accessibility profiles between human fibroblasts and iNeurons, an in vitro neuronal model system obtained by overexpression of Neurog2 in induced pluripotent stem cells (iPSCs). We found that the ONECUT transcription factor sequence motif was strongly associated with differential chromatin accessibility between iNeurons and fibroblasts. All three ONECUT transcription factors associated with this motif (ONECUT1, ONECUT2 and ONECUT3) induced neuronal morphology and expression of neuronal genes within two days of overexpression in fibroblasts. We observed widespread remodeling of chromatin accessibility; in particular, we found that chromatin regions that contain the ONECUT motif were in- or lowly accessible in fibroblasts and became accessible after the overexpression of ONECUT1, ONECUT2 or ONECUT3. There was substantial overlap with iNeurons, still, many regions that gained accessibility following ONECUT overexpression were not accessible in iNeurons. Our study highlights the potential of ONECUT transcription factors for direct neuronal reprogramming.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31049588" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120083" }, "primaryId" : "GEO:GSE120083", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120083" } ] }, "title" : "Profiling of chromatin accessibility in fibroblasts, iPSCs, iPSC-derived neurons and cells overexpressing Onecut transcription factors (OC1, OC2, OC3)", "dateAssigned" : "2018-09-17T00:00:00.000-05:00", "summary" : "Remodeling of chromatin accessibility is necessary for successful reprogramming of fibroblasts to neurons. However, it is still not fully known which transcription factors can induce a neuronal chromatin accessibility profile when overexpressed in fibroblasts. To identify such transcription factors, we here used ATAC-sequencing to generate differential chromatin accessibility profiles between human fibroblasts and iNeurons, an in vitro neuronal model system obtained by overexpression of Neurog2 in induced pluripotent stem cells (iPSCs). We found that the ONECUT transcription factor sequence motif was strongly associated with differential chromatin accessibility between iNeurons and fibroblasts. All three ONECUT transcription factors associated with this motif (ONECUT1, ONECUT2 and ONECUT3) induced neuronal morphology and expression of neuronal genes within two days of overexpression in fibroblasts. We observed widespread remodeling of chromatin accessibility; in particular, we found that chromatin regions that contain the ONECUT motif were in- or lowly accessible in fibroblasts and became accessible after the overexpression of ONECUT1, ONECUT2 or ONECUT3. There was substantial overlap with iNeurons, still, many regions that gained accessibility following ONECUT overexpression were not accessible in iNeurons. Our study highlights the potential of ONECUT transcription factors for direct neuronal reprogramming.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31049588" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120185" }, "primaryId" : "GEO:GSE120185", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120185" } ] }, "title" : "The pancreatic cancer stem cell marker CD44v6 affects transcription, translation and signaling: consequences on exosome composition and delivery", "dateAssigned" : "2018-09-19T00:00:00.000-05:00", "summary" : "The comparison between the impact of claudin7 and palmitoylation site mutated claudin7 on miRNA and proteins in cells versus exosomes allowed to judge on linked versus independent recruitment of miRNA and proteins and the impact of claudin7 on the recruitment of the mRNA processing machinery into exosomes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31592143" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120195" }, "primaryId" : "GEO:GSE120195", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120195" } ] }, "title" : "In vivo transcriptomic responses to thioacetamide exposure in rat liver, kidney, and heart tissue", "dateAssigned" : "2018-09-19T00:00:00.000-05:00", "summary" : "In this study we tested the ability to predict organ injury from transcriptomics data in Sprague-Dawley rats at early time points after exposure to thioacetmide (8 and 24 hours). We selected thioacetamide, an organosulfur compound extensively used in animal studies as a hepatotoxin and carcinogen for its ability to cause acute liver damage.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30459623" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120445" }, "primaryId" : "GEO:GSE120445", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120445" } ] }, "title" : "Expression data of miRNAs and mRNAs from the fetal rats with anorectal malformations", "dateAssigned" : "2018-09-25T00:00:00.000-05:00", "summary" : "we used microarrays to reveal the global programme of gene expression underlying the development of anorectal malformations.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120516" }, "primaryId" : "GEO:GSE120516", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120516" } ] }, "title" : "Transcriptome profile of RCS chondrocyte wt cell line and RCS chondrocyte obtained from a clone ko for the FGF receptors FGFR3 and FGFR4", "dateAssigned" : "2018-09-26T00:00:00.000-05:00", "summary" : "To understand the transcriptomic effect of FGF18 treatment on Chondrocytes cells from wt rat and on Chondrocytes obtained from a clone ko for the FGF receptors FGFR3 and FGFR4, we performed Quant-seq experiments. Both cell lines were treated with Fibroblast growth factor 18 (FGF18), while untreated cells were used as control.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32716134" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120530" }, "primaryId" : "GEO:GSE120530", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120530" } ] }, "title" : "FGF19 as a Surgical Factor Contributing to the Metabolic Effects of Gastric Bypass Surgery", "dateAssigned" : "2018-09-26T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression affected by gastric bypass surgery in rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29519502" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120679" }, "primaryId" : "GEO:GSE120679", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120679" } ] }, "title" : "Molecular characterization of a precision-cut rat lung slice model for the evaluation of anti-fibrotic drugs", "dateAssigned" : "2018-10-01T00:00:00.000-05:00", "summary" : "The translation of novel pulmonary fibrosis therapies from preclinical models into the clinic represents a major challenge demonstrated by the high attrition rate of compounds that showed efficacy in preclinical models but demonstrated no significant beneficial effects in clinical trials. Precision-cut lung tissue slice (PCLS) contains all major cell types of the lung and preserves the original cell-cell and cell-matrix contacts. It represents a promising ex vivo model to study pulmonary fibrosis. In this study, using RNA sequencing, we demonstrated that TGFβ1 induced robust fibrotic responses in the rat PCLS model as it changed the expression of genes functionally related to extracellular matrix remodeling, cell adhesion, epithelial-to-mesenchymal transition and various immune responses. Nintedanib, pirfenidone and sorafenib each reversed a subset of genes modulated by TGFβ1 and of those genes we identified 229 genes whose expression was reversed by all three drugs. These genes define a molecular signature characterizing many aspects of pulmonary fibrosis pathology and its attenuation in the rat PCLS fibrosis model. A panel of 12 genes and 3 secreted biomarkers including procollagen I, HA and WISP1 were validated as efficacy endpoints for the evaluation of anti-fibrotic activity of experimental compounds. Finally, we showed that blockade of αV integrins suppressed TGFβ1-induced fibrotic responses in the rat PCLS fibrosis model. Overall, our results suggest that the TGFβ1-induced rat PCLS fibrosis model may represent a valuable system for target validation and to determine the efficacy of experimental compounds.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30489156" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120712" }, "primaryId" : "GEO:GSE120712", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120712" } ] }, "title" : "mRNA sequencing analysis of transcripts from CA1 regions 90 minutes after Long-Term Potentiation was induced", "dateAssigned" : "2018-10-01T00:00:00.000-05:00", "summary" : "Conclusions: Our study illustrates the nature of the different transcripts in acute rat hippocampal slices after LTP 90 minutes was induced using field electrophysiology and compares them with control, unstimulated slices. Thius allowed us to identify wich genes are modulated in the hippocampus in order to promote and sustain LTP.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120804" }, "primaryId" : "GEO:GSE120804", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120804" } ] }, "title" : "Molecular Characterization of a Precision-Cut Rat Liver Slice Model for the Evaluation of Anti-Fibrotic Compounds", "dateAssigned" : "2018-10-03T00:00:00.000-05:00", "summary" : "Precision-cut liver tissue slice (PCLS) contains all major cell types of the liver parenchyma and preserves the original cell-cell and cell-matrix contacts. It represents a promising ex vivo model to study liver fibrosis and test the anti-fibrotic effect of experimental compounds in a physiologic environment. In this study using RNAquencing we demonstrated that various pathways functionally related to fibrotic mechanisms were dysregulated in PCLSs derived from rats subjected to bile duct ligation. The Alk5 inhibitor SB525334, nintedanib and sorafenib each reversed a subset of genes dysregulated in fibrotic PCLSs and of those genes we identified 608 genes whose expression was reversed by all three compounds. These genes define a molecular signature characterizing many aspects of liver fibrosis pathology and its attenuation in the model. A panel of 12 genes and 4 secreted biomarkers including procollagen I, HA, IGFBP5 and WISP1, were further validated as efficacy endpoints for the evaluation of anti-fibrotic activity of experimental compounds. Finally, we showed that blockade of αV integrins with a small molecule inhibitor attenuated the fibrotic phenotype in the model. Overall, our results suggest that the rat fibrotic PCLS model may represent a valuable system for target validation and to determine the efficacy of experimental compounds.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30406699" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120934" }, "primaryId" : "GEO:GSE120934", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120934" } ] }, "title" : "Integrated metabolome and transcriptome analyses provide novel insight into colon cancer modulation by the gut microbiota", "dateAssigned" : "2018-10-08T00:00:00.000-05:00", "summary" : "Colon cancer onset and progression is strongly associated with the presence, absence, or relative abundances of certain microbial taxa in the gastrointestinal tract. However, specific mechanisms affecting disease susceptibility related to complex bacterial mixtures are poorly understood. We used a multi-omics approach to determine how differences in the complex gut microbiome (GM) influence the metabolome and host transcriptome and ultimately affect susceptibility to adenoma development. Fecal samples collected from Pirc rats harboring two distinct complex GMs were analyzed using ultra-high performance liquid chromatography mass spectrometry (UHPLC-MS). We identified putative metabolite profiles that predicted future disease severity from samples collected prior to observable disease onset. Transcriptome analyses performed after disease onset on normal epithelium and tumor tissues suggests that the GM also alters the host transcriptome. Integrated pathway (IP) analyses of the metabolome and transcriptome based on putatively identified metabolic features indicate that bile acid biosynthesis was enriched in rats with high tumors (GM:F344) along with increased fatty acid metabolism and mucin biosynthesis. These data emphasize the utility of using untargeted metabolomics to identify metabolites for revealing signatures of susceptibility and resistance.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120978" }, "primaryId" : "GEO:GSE120978", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120978" } ] }, "title" : "Effects of light-at-night on the rat liver - a role for the autonomic nervous system (Experiment 2)", "dateAssigned" : "2018-10-09T00:00:00.000-05:00", "summary" : "Conclusion: One-hour light-at-night acutely affects the liver transcriptome. Part of this effect is mediated via the nervous innervation, as a hepatectomy modulated and reduced the effect of LAN on liver transcripts.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31281239" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120979" }, "primaryId" : "GEO:GSE120979", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE120979" } ] }, "title" : "Effects of light-at-night on the rat liver - a role for the autonomic nervous system (Experiment 1)", "dateAssigned" : "2018-10-09T00:00:00.000-05:00", "summary" : "Conclusion: One-hour light-at-night acutely affects the liver transcriptome. Part of this effect is mediated via the nervous innervation, as a hepatectomy modulated and reduced the effect of LAN on liver transcripts.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31281239" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121036" }, "primaryId" : "GEO:GSE121036", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121036" } ] }, "title" : "Expression data from rat bone marrow mesenchymal stem cells", "dateAssigned" : "2018-10-09T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression bone marrow MSCs (BMSCs) underlying HFD-induced progression of metabolic disorders in rat and identified distinct classes of differentiatilly expressed genes during this process.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121109" }, "primaryId" : "GEO:GSE121109", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121109" } ] }, "title" : "Teriparatide changes the gene expression of dorsal root ganglia in ovariectomized rats", "dateAssigned" : "2018-10-11T00:00:00.000-05:00", "summary" : "Twelve-week-old rats underwent bilateral ovariectomy (OVX) or sham surgery. Four weeks after surgery, the animals underwent the following treatments for 4 weeks: subcutaneous injection of teriparatide (TPTD) or saline 3 times weekly. All rats were anesthetized and sacrificed at the end of the experimental period. The L4-5 dorsal root ganglia (DRG) were harvested.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32210273" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121134" }, "primaryId" : "GEO:GSE121134", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121134" } ] }, "title" : "Triphenyl Phosphate (CAS No. 115-86-6): 5-Day Rat Gavage Toxicogenomic Study", "dateAssigned" : "2018-10-11T00:00:00.000-05:00", "summary" : "Triphenyl phosphate (TPHP) is an organophosphate flame retardant currently on the market and used as a replacement for phased-out polybrominated diphenyl ethers. Toxicity information on this class of chemicals is inadequate. Herein, the NTP use short-term, in vivo transcriptomic studies to inform potential points of departure for TPHP.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121357" }, "primaryId" : "GEO:GSE121357", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121357" } ] }, "title" : "Impact of exosomal miR-92b in hepatocellular carcinoma: its role for cancer immunoediting and clinical value for prognosis", "dateAssigned" : "2018-10-16T00:00:00.000-05:00", "summary" : "To further development of our gene expression approach to HCC development, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish defferent grades of HCC development by real-time PCR, confirming variability betweenHCC grades as well as the predicted HCC biomarkers", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121577" }, "primaryId" : "GEO:GSE121577", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121577" } ] }, "title" : "Expression data from endothelial cells isolated from IL-33 knock-out and wildtype rats", "dateAssigned" : "2018-10-22T00:00:00.000-05:00", "summary" : "We performed here gene-level expression profiling of the endothelial cells isolated from IL-33 knock-out rat dermal blood vessesl and looked for the role of endogenous IL-33 in regulating the endothelial cell phenotype.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121582" }, "primaryId" : "GEO:GSE121582", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121582" } ] }, "title" : "Prenatal alcohol exposure: profiling developmental DNA methylation patterns in central and peripheral tissues", "dateAssigned" : "2018-10-22T00:00:00.000-05:00", "summary" : "Prenatal alcohol exposure (PAE) alters the development of neurobiological systems, leading to lasting neuroendocrine, neuroimmune, and neurobehavioral deficits. Although the etiology of this reprogramming remains unknown, emerging evidence suggests DNA methylation as a potential mediator and biomarker for the effects of PAE due to its responsiveness to environmental cues and relative stability over time. Here, we utilized a rat model of PAE to examine the DNA methylation profiles of rat hypothalami and leukocytes at four time points during early development to assess the genome-wide impact of PAE on the epigenome and identify potential biomarkers of PAE. Our model of PAE approximates to 1-2x the legal limit of drunk driving in most jurisdictions (blood alcohol 80-150 mg/dl) throughout the equivalent of the first two trimesters of human pregnancy. Hypothalami were analyzed on postnatal (P) days 1, 8, 15, 22 and leukocytes at P22 to compare central and peripheral markers. Genome-wide DNA methylation analysis was performed by methylated DNA immunoprecipitation followed by next-generation sequencing. PAE resulted in lasting changes to DNA methylation profiles across all four ages, with 118 differentially methylated regions (DMRs) displaying persistent alterations across the developmental profile at a false-discovery rate (FDR) <0.05. By contrast, 299 DMRs showed the same direction of change in the hypothalamus and leukocytes of P22 pups at an FDR<0.05, with some genes overlapping with the developmental profile findings. The majority of these DMRs were located in intergenic regions, which contained several computationally-predicted transcription factor binding sites. Differentially methylated genes were generally involved in immune function, epigenetic remodeling, metabolism, and hormonal signaling, as determined by gene ontology analyses. Persistent DNA methylation changes in the hypothalamus may be associated with the long-term deficits observed in PAE. Furthermore, correlations between epigenetic alterations in peripheral tissues and those in the brain will provide a foundation for the development of biomarkers of fetal alcohol spectrum disorder (FASD). Finally, findings from studies of PAE provide important insight into the etiology neurodevelopmental and mental health disorders, as they tend to share numerous symptoms and comorbidities.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30568673" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121585" }, "primaryId" : "GEO:GSE121585", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121585" } ] }, "title" : "Developmental Origins of Transgenerational Sperm DNA Methylation Epimutations Following Ancestral DDT Exposure", "dateAssigned" : "2018-10-22T00:00:00.000-05:00", "summary" : "In previous studies, the pesticide DDT was shown to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs), also called epimutations, which can mediate this epigenetic inheritance. In the current study, the developmental origins of the transgenerational DMRs during gametogenesis have been investigated. Male control and DDT lineage F3 generation rats were used to isolate embryonic day 16 (E16) prospermatogonia, postnatal day 10 (P10) spermatogonia, adult pachytene spermatocytes, round spermatids, caput epididymal spermatozoa, and caudal sperm. The DMRs between the control versus DDT lineage samples were determined at each developmental stage. The top 100 statistically significant DMRs at each stage were compared and the developmental origins of the caudal epididymal sperm DMRs were assessed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30500333" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121695" }, "primaryId" : "GEO:GSE121695", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121695" } ] }, "title" : "Intestinal toxicity in rats following administration of CDK4/6 inhibitors is independent of primary pharmacology", "dateAssigned" : "2018-10-23T00:00:00.000-05:00", "summary" : "We used microarrays to analyze changes in gene expression in gastrointestinal tissue (musocal scrapings) after 4 days of dosing. Total RNA was extracted from tissues of 3 rats per experimental group for analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30401694" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121736" }, "primaryId" : "GEO:GSE121736", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121736" } ] }, "title" : "The effect of DZNeP-exposure on activation of hepatic stellate cells analyzed by RNA-sequencing.", "dateAssigned" : "2018-10-24T00:00:00.000-05:00", "summary" : "DZNeP is the inhibitor of Ezh2 and paly negative roles on activation of hepatic stellate cells. We used RNA sequencing to identify the effective genes of DZNeP in rat HSCs. The primary rat HSCs was isolated and purified from SD rats, and cultured in DMEM culture medium with 20% FBS for 24 hours. Then the rat HSCs was administrated with DZNeP at 1μM concentration, or with similar volume of DMSO as negative control. 48 hour later, the cells were harvested and cell lysis was subjected to RNA-sequencing. This study identified that DZNeP regulated HSC activation through upregulating the expression of many key anti-fibrotic factors including Tgfβ signaling inhibitor: Bambi; cell cycle inhibitors: p21, Gadd45s; and immunomodulatory cytokine IL10.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33391480" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121792" }, "primaryId" : "GEO:GSE121792", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121792" } ] }, "title" : "Expression data from the kidney of Sprague-Dawley rats given colistin methanesulfonate sodium", "dateAssigned" : "2018-10-25T00:00:00.000-05:00", "summary" : "Affymetrix GeneChip microarrays indicated 894 differentially expressed genes in groups treated with CMS (ANOVA, FDR < 0.05, fold change ≥ 1.3).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30628653" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121839" }, "primaryId" : "GEO:GSE121839", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121839" } ] }, "title" : "Microarray expression profile analysis of long non-coding RNAs and mRNAs in A Rat Carotid Artery Balloon Injury Model", "dateAssigned" : "2018-10-26T00:00:00.000-05:00", "summary" : "Restenosis after angioplasty or stent is a major clinical problem. While long noncoding RNAs (lncRNAs) are implicated in a variety of diseases, their role in restenosis is not well understood. This study aims to investigate how dysregulated lncRNAs and mRNAs contribute to restenosis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121924" }, "primaryId" : "GEO:GSE121924", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121924" } ] }, "title" : "Transcriptome-Wide Identification of Differentially Expressed Genes and Long Non-coding RNAs in Nitroglycerin Tolerant Rat Aorta", "dateAssigned" : "2018-10-29T00:00:00.000-05:00", "summary" : "We investigated comprehensive transcriptomic change in rat aorta tolerant to nitroglycerin (GTN) with a focus on lncRNAs. We employed RNA sequencing (RNA-seq) technique and identified 22788 genes (RPKM > 0.1, 14720 protein coding and 4408 lncRNA). And 115 differentially expressed (DE) mRNAs (65 upregulated and 50 downregulated) and 104 DE lncRNAs (56 upregulated and 48 downregulated) were found in GTN-tolerant aortas. Many DE mRNAs and cis-target genes of DE lncRNAs have been implicated in regulation of blood pressure or cell contraction. Collectively, these results suggested that dysregulated mRNAs and lncRNAs contribute to the development of GTN tolerance and might be used as novel potential targets to prevent and reverse GTN tolerance.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121929" }, "primaryId" : "GEO:GSE121929", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121929" } ] }, "title" : "siRNA knockdown in neonatal rat cardiac myocytes", "dateAssigned" : "2018-10-29T00:00:00.000-05:00", "summary" : "Primary neonatal rat cardiac myocytes were isolated and subjected to siRNA mediated Yap knockdown", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121975" }, "primaryId" : "GEO:GSE121975", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE121975" } ] }, "title" : "Protein phosphorylation profiling of rat sciatic nerve stumps", "dateAssigned" : "2018-10-30T00:00:00.000-05:00", "summary" : "Examine protein phosphorylation status during peripheral nerve regeneration when using autologous nerve graft or tissue engineered nerve graft to bridge nerve gap.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122006" }, "primaryId" : "GEO:GSE122006", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122006" } ] }, "title" : "Profiling of 18 - 45 nt small RNAs in the cauda epididymal sperm of mice and rats.", "dateAssigned" : "2018-10-31T00:00:00.000-05:00", "summary" : "Total RNAs were extracted from the purified cauda epididymal spermatozoa of mouse (C57BL/6, 2 months old) and rats (Sprague Dawley, 450g young adult), and the 18 - 45 nt fraction small RNAs were subjected to library construction and deep sequencing, using Illumina GAIIx.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31044548" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122020" }, "primaryId" : "GEO:GSE122020", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122020" } ] }, "title" : "Gene expression data from remote ischemic postconditioning in rat model of ischemia reperfusion injury", "dateAssigned" : "2018-10-31T00:00:00.000-05:00", "summary" : "Here, the cardioprotective effect of remote ischemic postconditioning (RPostC) was investigated, based on our in vitro rat model of myocardial IRI. Three groups, including Sham, IRI, and IRI+ RPostC, were utilized for the analysis of Affymetrix Rat Gene 2.0 ST chip.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31072368" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122025" }, "primaryId" : "GEO:GSE122025", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122025" } ] }, "title" : "Profiling of 18 - 45 nt small RNAs in the caput epididymal sperm of mice and rats", "dateAssigned" : "2018-10-31T00:00:00.000-05:00", "summary" : "Total RNAs were extracted from the purified caput epididymal spermatozoa of mouse (C57BL/6, 2 months old) and rats (Sprague Dawley, 450g young adult), and the 18 - 45 nt fraction small RNAs were subjected to library construction and deep sequencing, using Illumina HiSeq 2000.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31044548" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122044" }, "primaryId" : "GEO:GSE122044", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122044" } ] }, "title" : "MiR-29 Regulates de novo Lipogenesis in the Liver and Circulating Triglyceride Levels in a Sirt1-Dependent Manner", "dateAssigned" : "2018-10-31T00:00:00.000-05:00", "summary" : "Systematic comparison of multiple models of diabetes / insulin resistance reveals miR-29 as a commonality among them, and further analysis reveals it as a key therapeutic target for insulin resistance.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31251698" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122060" }, "primaryId" : "GEO:GSE122060", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122060" } ] }, "title" : "Transcriptome data of rat bladder tissues of chronic bladder ischemia injury mediated detrusor underactive animal model", "dateAssigned" : "2018-11-01T00:00:00.000-05:00", "summary" : "Detrusor underactivity (DUA) is defined as reduced detrusor contraction strength and/or duration, resulting in prolonged bladder emptying and/or a failure to achieve complete bladder emptying within a normal time span. DUA is a frustrating diagnosis for clinicians as well as patients since no effective pharmacological treatment is available. The prevalence of urodynamically confirmed DUA in elderly patients with lower urinary tract symptoms (LUTS) is known to be approximately 28% (40.2% in male and 13.3% in female), and the prevalence of DUA increases with age 65. Vascular endothelial damage (VED) also occurs during the human aging process and is an independent risk factor for atherosclerosis and hypertension. Pelvic arterial insufficiency, a common clinical problem in the elderly population, may lead to impaired lower urinary tract perfusion and have an important role in voiding dysfunction, such as DUA or detrusor overactivity (DO). Thus, to establish a reliable detrusor underactivity (DUA) rat model and to investigate the pathophysiology of chronic bladder ischemia (CBI) on voiding behavior and bladder function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31705030" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122179" }, "primaryId" : "GEO:GSE122179", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122179" } ] }, "title" : "Molecular perturbations of hepatocytes isolated from nonheart-beating donor rats", "dateAssigned" : "2018-11-05T00:00:00.000-06:00", "summary" : "Organs from nonheart-beating donors are attractive for use in cell therapy. Understanding the nature of molecular perturbations following reperfusion/reoxygenation would be highly significant for nonheart-beating donor cells. Nonheart-beating donor rats hepatocytes were studied for global gene expression with Affymetrix microarraays.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:21993967" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122184" }, "primaryId" : "GEO:GSE122184", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122184" } ] }, "title" : "Expression Data from Liver of Rats Dosed with Reference Hepatotoxicants (Microarray)", "dateAssigned" : "2018-11-05T00:00:00.000-06:00", "summary" : "alpha-naphthylisothiocyanate 100mg/kg (vehicle 5ml/kg corn oil); carbon tetrachloride 1582mg/kg (vehicle 5ml/kg corn oil); methylenedianiline 100mg/kg (vehicle 35% ethanol); acetaminophen 1000mg/kg (vehicle 2ml/kg corn oil); diclofenac 10mg/kg (vehicle 10ml/kg water)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30723492" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122242" }, "primaryId" : "GEO:GSE122242", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122242" } ] }, "title" : "Characteristic regulation of Lbp and Sod3 gene expression in peri-implant connective tissue of rats", "dateAssigned" : "2018-11-06T00:00:00.000-06:00", "summary" : "The mucosal penetration area formed by implant placement is critical problems of dental implant treatment, because epithelial barrier is broken and it can become a source of inflammation. To clarify the influence and risk caused by dental implant treatment in peri-implant soft tissue, we compared gene expression profile of peri-implant soft tissue and oral mucosal tissue with microarray analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122315" }, "primaryId" : "GEO:GSE122315", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122315" } ] }, "title" : "Expression Data from Liver of Rats Dosed with Reference Hepatotoxicants_RNASeq", "dateAssigned" : "2018-11-08T00:00:00.000-06:00", "summary" : "Male Sprague Dawley rats were treated orally for 5 days with reference hepatotoxicants, each at a single dose level, alpha-naphthylisothiocyanate 100mg/kg (vehicle 5ml/kg corn oil); carbon tetrachloride 1582mg/kg (vehicle 5ml/kg corn oil); methylenedianiline 100mg/kg (vehicle 35% ethanol); acetaminophen 1000mg/kg (vehicle 2ml/kg corn oil); diclofenac 10mg/kg (vehicle 10ml/kg water)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30723492" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122379" }, "primaryId" : "GEO:GSE122379", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122379" } ] }, "title" : "Characteristics of long non-coding RNAs in the pancreas of rats with acute pancreatitis", "dateAssigned" : "2018-11-09T00:00:00.000-06:00", "summary" : "This study aimed to describe the microarray-based differential expression profile of mRNAs and lncRNAs in acute experimental pancreatitis and identify candidate biomarkers for the diagnosis, prognosis, and treatment of AP.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122494" }, "primaryId" : "GEO:GSE122494", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122494" } ] }, "title" : "Distinct transcriptional profiles of the female, male and finasteride-induced feminized male anogenital region in rat fetuses", "dateAssigned" : "2018-11-13T00:00:00.000-06:00", "summary" : "A short anogential distance (AGD) in males is a marker for incomplete masculinization and a predictor of adverse effects on male reproductive health. For this reason, AGD is used to assess the endocrine disrupting potential of chemicals for risk assessment purposes. The molecular mechanisms underpinning this chemically induced shortening of the AGD, however, remains unclear. Although it is clear that AR-mediated signaling is critical, evidence also suggest the involvement of other signaling pathways. This study present the first global transcriptional profile of the anogenital region in male rats with chemically induced short AGD, also including comparison to normal male and female control animals. The anti-androgenic drug Finasteride (10mg/kg bw/day) was used to induce short AGD by exposing pregnant rats at gestation days (GD) 7-21. The AGD was 37% shorter in exposed male offspring compared to control males. Transcriptomics analysis on anogenital tissues at GD21 revealed a sexually dimorphic transcriptional profile. More than 350 genes were found to be differentially expressed between the three groups. The expression pattern of four genes of particular interest (Esr1, Padi2, Wnt2 and Sfrp4) was verified by RT-qPCR analyses. Our transcriptomics profiles provide a stepping-stone for future studies aimed at characterizing the molecular events governing development of the anogenital region, as well as describing the detailed Adverse Outcome Pathways for short AGD; an accepted biomarker of endocrine effects for chemical regulation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30768126" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122604" }, "primaryId" : "GEO:GSE122604", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122604" } ] }, "title" : "Expression data from hearts (left ventricle apex) of rats with and without metformin treatment", "dateAssigned" : "2018-11-15T00:00:00.000-06:00", "summary" : "In a subacute study, male Wistar rats were treated daily by gavage with 800 mg/kg metformin for 1, 3, or 14 consecutive days, followed by necropsy 24h after the last application. The biguanide metformin is a widely used antidiabetic drug, which has received great interest in oncology research in recent years after an epidemiological study showed a link between metformin treatment and a reduced cancer risk in diabetic patients. Since mitochondrial metabolism has become a target for possible cancer therapeutic approaches, especially for tumors relying on oxidative metabolism, mitochondrial complex I inhibition is under discussion to be responsible for the anti-cancer effect of metformin. The known strong complex I inhibitor Rotenone has also shown anti-cancer activity, however is associated with toxic effects. Therefore, we compared metformin and phenformin, another biguanide withdrawn from the marked as antidiabetic due to safety reasons, with rotenone, to elucidate potential mechanisms rendering biguanides apparently less toxic than rotenone. In this context, various blood and tissue parameters as well as histopathology were measured and/or evaluated. Moreover, gene expression profiling was conducted in liver and heart due to the high metabolic activity and high energy demand. All investigations were based on an experimental design previously described for mechanistic investigations of the effects of rotenone. Our examinations regarding gene expression showed that 1630 transcripts were deregulated by rotenone, metformin and/or phenformin in liver, whereas 777 transcripts were deregulated in heart, indicating that the heart is less affected by these compounds. Overall, the mechanistic profile of phenformin appears to be similar to that of rotenone, yet at a quantitatively reduced level, whereas metformin displayed only transient similarities after one day of treatment. These differences are likely due to differential molecular properties of these compounds, especially concerning their effects on mitochondria: Metformin, in contrast to rotenone, requires a certain mitochondrial potential to allow accumulation in this organelle, thereby self-limiting its entry and thus ability to inhibit mitochondrial function, whereas rotenone and to some extent also phenformin can enter mitochondria freely. Thus, our more detailed molecular characterization of these compounds suggests that inhibition of mitochondrial functions can serve as target for an anti-cancer mode of action, yet should be self-limited or balanced to some extent to avoid exhaustion of all energy stores.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122605" }, "primaryId" : "GEO:GSE122605", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122605" } ] }, "title" : "Expression data from livers of rats with and without metformin treatment", "dateAssigned" : "2018-11-15T00:00:00.000-06:00", "summary" : "In a subacute study, male Wistar rats were treated daily by gavage with 800 mg/kg metformin for 1, 3, or 14 consecutive days, followed by necropsy 24h after the last application. The biguanide metformin is a widely used antidiabetic drug, which has received great interest in oncology research in recent years after an epidemiological study showed a link between metformin treatment and a reduced cancer risk in diabetic patients. Since mitochondrial metabolism has become a target for possible cancer therapeutic approaches, especially for tumors relying on oxidative metabolism, mitochondrial complex I inhibition is under discussion to be responsible for the anti-cancer effect of metformin. The known strong complex I inhibitor Rotenone has also shown anti-cancer activity, however is associated with toxic effects. Therefore, we compared metformin and phenformin, another biguanide withdrawn from the marked as antidiabetic due to safety reasons, with rotenone, to elucidate potential mechanisms rendering biguanides apparently less toxic than rotenone. In this context, various blood and tissue parameters as well as histopathology were measured and/or evaluated. Moreover, gene expression profiling was conducted in liver and heart due to the high metabolic activity and high energy demand. All investigations were based on an experimental design previously described for mechanistic investigations of the effects of rotenone. Our examinations regarding gene expression showed that 1630 transcripts were deregulated by rotenone, metformin and/or phenformin in liver, whereas 777 transcripts were deregulated in heart, indicating that the heart is less affected by these compounds. Overall, the mechanistic profile of phenformin appears to be similar to that of rotenone, yet at a quantitatively reduced level, whereas metformin displayed only transient similarities after one day of treatment. These differences are likely due to differential molecular properties of these compounds, especially concerning their effects on mitochondria: Metformin, in contrast to rotenone, requires a certain mitochondrial potential to allow accumulation in this organelle, thereby self-limiting its entry and thus ability to inhibit mitochondrial function, whereas rotenone and to some extent also phenformin can enter mitochondria freely. Thus, our more detailed molecular characterization of these compounds suggests that inhibition of mitochondrial functions can serve as target for an anti-cancer mode of action, yet should be self-limited or balanced to some extent to avoid exhaustion of all energy stores.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122606" }, "primaryId" : "GEO:GSE122606", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122606" } ] }, "title" : "Expression data from hearts (left ventricle apex) of rats with and without phenformin treatment", "dateAssigned" : "2018-11-15T00:00:00.000-06:00", "summary" : "In a subacute study, male Wistar rats were treated daily by gavage with 800 mg/kg metformin for 1, 3, or 14 consecutive days, followed by necropsy 24h after the last application. The biguanide phenformin was used as antidiabetic drug due to its antihyperglycaemic effect, but was withdrawn from the market in the 1970s for safety reasons. In recent years, biguanides received great interest in oncology research after an epidemiological study showed a link between the treatment with metformin, another biguanide with a better safety profile, and a reduced cancer risk in diabetic patients. Since mitochondrial metabolism has become a target for possible cancer therapeutic approaches, especially for tumors relying on oxidative metabolism, mitochondrial complex I inhibition is under discussion to be responsible for the anti-cancer effect of metformin. The known strong complex I inhibitor Rotenone has also shown anti-cancer activity, however is associated with toxic effects. Therefore, we compared metformin and phenformin, with rotenone, to elucidate potential mechanisms rendering biguanides apparently less toxic than rotenone. In this context, various blood and tissue parameters as well as histopathology were measured and/or evaluated. Moreover, gene expression profiling was conducted in liver and heart due to the high metabolic activity and high energy demand. All investigations were based on an experimental design previously described for mechanistic investigations of the effects of rotenone. Our examinations regarding gene expression showed that 1630 transcripts were deregulated by rotenone, metformin and/or phenformin in liver, whereas 777 transcripts were deregulated in heart, indicating that the heart is less affected by these compounds. Overall, the mechanistic profile of phenformin appears to be similar to that of rotenone, yet at a quantitatively reduced level, whereas metformin displayed only transient similarities after one day of treatment. These differences are likely due to differential molecular properties of these compounds, especially concerning their effects on mitochondria: Metformin, in contrast to rotenone, requires a certain mitochondrial potential to allow accumulation in this organelle, thereby self-limiting its entry and thus ability to inhibit mitochondrial function, whereas rotenone and to some extent also phenformin can enter mitochondria freely. Thus, our more detailed molecular characterization of these compounds suggests that inhibition of mitochondrial functions can serve as target for an anti-cancer mode of action, yet should be self-limited or balanced to some extent to avoid exhaustion of all energy stores.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122608" }, "primaryId" : "GEO:GSE122608", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122608" } ] }, "title" : "Expression data from livers of rats with and without phenformin treatment", "dateAssigned" : "2018-11-15T00:00:00.000-06:00", "summary" : "In a subacute study, male Wistar rats were treated daily by gavage with 800 mg/kg metformin for 1, 3, or 14 consecutive days, followed by necropsy 24h after the last application. The biguanide phenformin was used as antidiabetic drug due to its antihyperglycaemic effect, but was withdrawn from the market in the 1970s for safety reasons. In recent years, biguanides received great interest in oncology research after an epidemiological study showed a link between the treatment with metformin, another biguanide with a better safety profile, and a reduced cancer risk in diabetic patients. Since mitochondrial metabolism has become a target for possible cancer therapeutic approaches, especially for tumors relying on oxidative metabolism, mitochondrial complex I inhibition is under discussion to be responsible for the anti-cancer effect of metformin. The known strong complex I inhibitor Rotenone has also shown anti-cancer activity, however is associated with toxic effects. Therefore, we compared metformin and phenformin, with rotenone, to elucidate potential mechanisms rendering biguanides apparently less toxic than rotenone. In this context, various blood and tissue parameters as well as histopathology were measured and/or evaluated. Moreover, gene expression profiling was conducted in liver and heart due to the high metabolic activity and high energy demand. All investigations were based on an experimental design previously described for mechanistic investigations of the effects of rotenone. Our examinations regarding gene expression showed that 1630 transcripts were deregulated by rotenone, metformin and/or phenformin in liver, whereas 777 transcripts were deregulated in heart, indicating that the heart is less affected by these compounds. Overall, the mechanistic profile of phenformin appears to be similar to that of rotenone, yet at a quantitatively reduced level, whereas metformin displayed only transient similarities after one day of treatment. These differences are likely due to differential molecular properties of these compounds, especially concerning their effects on mitochondria: Metformin, in contrast to rotenone, requires a certain mitochondrial potential to allow accumulation in this organelle, thereby self-limiting its entry and thus ability to inhibit mitochondrial function, whereas rotenone and to some extent also phenformin can enter mitochondria freely. Thus, our more detailed molecular characterization of these compounds suggests that inhibition of mitochondrial functions can serve as target for an anti-cancer mode of action, yet should be self-limited or balanced to some extent to avoid exhaustion of all energy stores.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122664" }, "primaryId" : "GEO:GSE122664", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122664" } ] }, "title" : "Inhibition of the hepatic vitamin B12-dependent methionine-salvage pathway by trichloroethylene metabolites accounts for the formic aciduria in the rat", "dateAssigned" : "2018-11-18T00:00:00.000-06:00", "summary" : "The industrial solvent trichloroethylene (TCE) produces a marked formic aciduria in male and female F344 rats and in male C57Bl mice following single or multiple dosing. The two major metabolites of TCE formed by cytochromes P450 metabolism also produce formic aciduria. The quantity of formic acid excreted was about 2-fold higher following trichloroacetic acid (TCA) compared to trichloroethanol (TCE-OH) or TCE, at similar doses of 16mg/kg/day for 3 days. Prior treatment of male F344 rats with 1-aminobenzotriazole a cytochrome P450 inhibitor, followed by TCE, completely prevented the formic aciduria but had no effect on formic acid excretion produced by TCA, suggesting TCA is the proximate metabolite producing this response. Metabolism of formic acid is largely controlled by the vitamin B12 –dependent methionine salvage pathway. Transcriptomic analysis on the liver of rats dosed with 16mg/kg/day TCE for three days when compared to control liver showed nine differentially expressed genes, of particular interest was the down regulation of LMBRD1 involved in the conversion of vitamin B12 into one of two molecules, methylcobalamin (CH3Cbl) or S-adenosylcobalamin (AdoCbl). Administration of CH3Cbl or hydroxocobalamin for 3 days to rats given a single dose of TCE, lead to a reduction in formic acid in their urine. Similarly, rats given TCE followed by L-methionine for 3 days excreted less formic acid in their urine. These findings suggest an effect on the vitamin B12 –dependent methionine salvage pathway. This was supported by the finding that hepatic methionine synthase, which converts homocysteine to methionine, was inhibited following three large daily dose of TCE. We propose that TCE metabolites interact with the vitamin B12 -dependent methionine salvage pathway leading to tetrahydrofolate deficiency and increased excretion of formic acid in rat urine.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122747" }, "primaryId" : "GEO:GSE122747", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122747" } ] }, "title" : "Identification of cis-regulatory elements affecting pancreatic Islet maturation using chromatin accessibility variations", "dateAssigned" : "2018-11-20T00:00:00.000-06:00", "summary" : "we were able to find several known and unforeseen key transcriptional regulators acting at cis-regulatory sites and promoters which depicted a differential accessibility and induced differential gene expression along maturation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122792" }, "primaryId" : "GEO:GSE122792", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122792" } ] }, "title" : "Transcriptome of c-kit+ cells in rat under stress", "dateAssigned" : "2018-11-21T00:00:00.000-06:00", "summary" : "RNA-sequencing analysis of the c-Kit positive cells under stress to identify novel factors or pathways involved in rat stress erythropoiesis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122822" }, "primaryId" : "GEO:GSE122822", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122822" } ] }, "title" : "Effect of CVX-060 treatment on hepatic gene expression of cirrhotic rats", "dateAssigned" : "2018-11-21T00:00:00.000-06:00", "summary" : "Currently, the therapeutic prospects for cirrhosis patients are limited to liver transplantation and, therefore, there is an urgent need to develop new therapeutic strategies for improved treatments. Cirrhosis was induced in male Wistar rats with CCl4 treatment, and RNA from the complete livers was extracted and quantified through microarray experiments. Angiopoietins signalling is a key pathway in blood vessel normalization. Angiopoietin 1 (Ang1)-Tie2 signalling stabilizes blood vessels, Angiopoietin 2 (Ang2) on the other hand is a context-dependent antagonist of Ang1 and decreases its stabilizing effect giving rise to immature blood vessels. Cirrhotic conditions are characterized by higher expression and activity of Ang2 than healthy conditions, resulting in the loss of blood vessels stability. Previous work showed that inhibition of Ang2 via CVX-060 enhances Ang1-Tie2 signalling, and can stabilize the vascular system in cirrhotic livers. We therefore performed RNA extraction after treatment of cirrhotic rats with CVX-060 during 4 weeks. We observed changes in expression state (expressed/not expressed) in key transcription factors previously implicated in cirrhosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30949696" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122911" }, "primaryId" : "GEO:GSE122911", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122911" } ] }, "title" : "Transcriptional remodeling effects of the nuclear receptor NR4A2 in adult rat ventricular myocytes", "dateAssigned" : "2018-11-26T00:00:00.000-06:00", "summary" : "Sustained elevation of sympathetic activity is an important contributor to pathological cardiac hypertrophy, ventricular arrhythmias, and left ventricular contractile dysfunction in chronic heart failure. The orphan nuclear receptor NR4A2 is an immediate early response gene activated in the heart under beta-adrenergic stimulation. The goal of this study was to identify the transcriptional remodeling events induced by NR4A2 expression in cardiomyocytes, and their impact on the physiological response of those cells to sustained beta-adrenergic stimulation. Treatment of adult rat ventricular myocytes (ARVMs) with isoproterenol induced a rapid (< 4 hours) but transient (< 24 hours) increase in NR4A2 expression levels that was accompanied by increased nuclear localization of the transcription factor. Adenovirus-mediated overexpression of NR4A2 modulated the expression of genes linked to adrenoceptor signaling, calcium signaling, cell growth and proliferation, and counteracted the increase in protein synthesis rate and cell surface area mediated by chronic isoproterenol stimulation. In consistence with those findings, NR4A2 overexpression also blocked the phosphorylative activation of ERK1/2, Akt, and of their downstream effector in protein synthesis p70S6K. Prominent among the transcriptional changes induced by NR4A2 was the > 7-fold up-regulation of the dual-specificity phosphatases DUSP2 and DUSP14, two known inhibitors of ERK1/2. Pre-treatment of NR4A2-overexpressing cardiomyocytes with the DUSPs inhibitor BCI prevented the inhibition of ERK1/2 and p70S6K following isoproterenol stimulation. In conclusion, our results suggest that NR4A2 acts as a novel negative feedback regulator of the beta-adrenergic receptor-mediated growth response in cardiomyocytes, and this at least partly through DUSP-mediated inhibition of ERK1/2 signaling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31188636" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122950" }, "primaryId" : "GEO:GSE122950", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE122950" } ] }, "title" : "Differential expression of antiviral factors in H9c2 cells overexpressing Cacnb4 of the Cav1.2 channel", "dateAssigned" : "2018-11-26T00:00:00.000-06:00", "summary" : "L-type voltage gated Ca channels play a critical role in E-C coupling in cardiac muscle. alpha1C is associated with beta auxiliary subunits (b1-b4), which regulate cardiac Ca channel gating properties. Here we report a preliminary exploratory study suggesting a novel role of beta4 subunit in heart. We observed that overexpression of beta4 subunit increases the expression of a wide variety of endogenous genes related to antiviral activity. This includes genes in the downstream signalling of RIG-1 pathway such as RIG-1, Irf7 and Ifitm3. The increase expression of these factors may have an antiviral protective role against infection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30538175" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123007" }, "primaryId" : "GEO:GSE123007", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123007" } ] }, "title" : "The nerve roots avulsion induced time-specific expression patterns of lncRNA and mRNA occurred before the motoneurons loss of the injured spinal segments", "dateAssigned" : "2018-11-27T00:00:00.000-06:00", "summary" : "In this study, we study the expression pattern of the lncRNAs in rat’s spinal cord of at 3 days and 14 days after the unilateral BPRA. By comparing the expression patterns of mRNAs and lncRNAs, ipsilateral vs contralateral, on the 3rd and the 14th day, in the same spinal segments using microarray analysis. We identified 55 lncRNAs, which were significantly altered at the 3rd day after BPRA. Two weeks after BPRA, 70 lncRNAs which were significantly altered. Among these DE lncRNAs, 17 were consistently over-regulated at 3- and 14- days after injury while 5 lncRNAs were consistently down-regulated. At 3-days after injury, 399 mRNAs were significantly differentially expressed while two weeks after BPRA, 445 were downregulated. Among these mRNAs, 198 were consistently over-regulated, and 15 mRNAs were consistently under-regulated.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123161" }, "primaryId" : "GEO:GSE123161", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123161" } ] }, "title" : "Characterization of the novel spontaneously immortalized rat Müller cell line SIRMu-1", "dateAssigned" : "2018-11-30T00:00:00.000-06:00", "summary" : "Müller cells (MCs) play a crucial role in the retina, and cultured MC lines are an important tool with which to study MC function. Transformed MC lines have been widely used; however, the transformation process can also lead to unwanted changes compared to the primary cells from which they were derived. A monoclonal spontaneously immortalized rat Müller cell line, SIRMu-1, was derived from primary rat MCs and characterized by RNA-sequencing (in addition to immunofluorescence and western blotting) in comparison to primary MCs and the SV40-immortalized MC line, rMC-1.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31372389" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123297" }, "primaryId" : "GEO:GSE123297", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123297" } ] }, "title" : "Klf4 overexpression effect on P0 rat retina", "dateAssigned" : "2018-12-03T00:00:00.000-06:00", "summary" : "Analysis of progenitor cells of P0 rats overexpressing Krüppel-like factor 4 (Klf4). Klf4 is a key transcriptional regulator of differentiation potential. Results provide insight into the role of Klf4 in the retina.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123328" }, "primaryId" : "GEO:GSE123328", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123328" } ] }, "title" : "Open chromatin landscape of rat microglia upon inflammatory or pro-invasive polarization", "dateAssigned" : "2018-12-04T00:00:00.000-06:00", "summary" : "Microglia are brain-resident, myeloid cells that play important roles in health and brain pathologies. While data on chromatin accessibility in activated murine microglia are available, there is no such data on rat microglia subjected to different stimuli. Herein, we report a comprehensive, replicated, FDR-controlled dataset of DNase-hypersensitive (DHS) open chromatin regions for the rat microglia. We compared open chromatin landscapes in untreated primary microglial cultures and cultures stimulated for 6h with either lipopolysaccharide (LPS) or glioma-conditioned medium (GCM). Glioma-secreted factors induce the pro-invasive and immunosuppressive activation of microglia, in which these cells promote tumor growth. The open chromatin landscape of the rat microglia consisted of 126,640 reproducible DHS regions, of which 12,357 and 2,303 significantly changed openness following the stimulation with LPS and GCM, respectively. Active genes had constitutively open promoters, but there was no direct dependence between cumulative openness of DHS regions near to a gene and its expression. LPS-regulated DHS regions were more frequent in introns, while GCM-regulated regions were more frequent away from gene bodies. GCM and LPS treatment differentially affected open chromatin regions mapped to genes in the pathways of Toll-like-receptor signaling and the Axon guidance, suggesting that the molecular machinery used by migrating microglia is similar to that of growing axons and, moreover, that modulation of these pathways is instrumental for glioma to induce a pro-invasive polarization of microglia. Our dataset of open chromatin regions active in rat microglia will constitute a useful resource for studies of the transcriptional regulation in this system.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31339627" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123408" }, "primaryId" : "GEO:GSE123408", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123408" } ] }, "title" : "Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Non-genotoxic Hepatocarcinogens", "dateAssigned" : "2018-12-06T00:00:00.000-06:00", "summary" : "The present study examined hypermethylated and downregulated genes specific to carbon tetrachloride (CCl4) by Methyl-Seq analysis combined with expression microarray analysis in the liver of rats treated with CCl4 or N-nitrosodiethylamine (DEN) for 28 days, by excluding those with DEN.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30690589" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123429" }, "primaryId" : "GEO:GSE123429", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123429" } ] }, "title" : "tert-Butylphenyl Diphenyl Phosphate (CAS No. 56803-37-3): 5-Day Rat Gavage Toxicogenomic Study", "dateAssigned" : "2018-12-06T00:00:00.000-06:00", "summary" : "tert-Butylphenyl Diphenyl Phosphate (BPDP) is an organophosphate flame retardant currently on the market and used as a replacement for phased-out polybrominated diphenyl ethers. Toxicity information on this class of chemicals is inadequate. Herein, the NTP use short-term, in vivo transcriptomic studies to inform potential points of departure for BPDP.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123430" }, "primaryId" : "GEO:GSE123430", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123430" } ] }, "title" : "2-Ethylhexyl Diphenyl Phosphate (CAS No. 1241-94-7): 5-Day Rat Gavage Toxicogenomic Study", "dateAssigned" : "2018-12-06T00:00:00.000-06:00", "summary" : "2-Ethylhexyl Diphenyl Phosphate (EHDP) is an organophosphate flame retardant currently on the market and used as a replacement for phased-out polybrominated diphenyl ethers. Toxicity information on this class of chemicals is inadequate. Herein, the NTP use short-term, in vivo transcriptomic studies to inform potential points of departure for EHDP.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123431" }, "primaryId" : "GEO:GSE123431", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123431" } ] }, "title" : "Isodecyl Diphenyl Phosphate (CAS No. 29761-21-5): 5-Day Rat Gavage Toxicogenomic Study", "dateAssigned" : "2018-12-06T00:00:00.000-06:00", "summary" : "Isodecyl Diphenyl Phosphate (IDDP) is an organophosphate flame retardant currently on the market and used as a replacement for phased-out polybrominated diphenyl ethers. Toxicity information on this class of chemicals is inadequate. Herein, the NTP use short-term, in vivo transcriptomic studies to inform potential points of departure for IDDP.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123432" }, "primaryId" : "GEO:GSE123432", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123432" } ] }, "title" : "Isopropylated Phenol Phosphate (CAS No. 68937-41-7): 5-Day Rat Gavage Toxicogenomic Study", "dateAssigned" : "2018-12-06T00:00:00.000-06:00", "summary" : "Isopropylated Phenol Phosphate (IPP) is an organophosphate flame retardant currently on the market and used as a replacement for phased-out polybrominated diphenyl ethers. Toxicity information on this class of chemicals is inadequate. Herein, the NTP use short-term, in vivo transcriptomic studies to inform potential points of departure for IPP.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123433" }, "primaryId" : "GEO:GSE123433", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123433" } ] }, "title" : "Tricresyl Phosphate (CAS No. 1330-78-5): 5-Day Rat Gavage Toxicogenomic Study", "dateAssigned" : "2018-12-06T00:00:00.000-06:00", "summary" : "Tricresyl Phosphate (TCP) is an organophosphate flame retardant currently on the market and used as a replacement for phased-out polybrominated diphenyl ethers. Toxicity information on this class of chemicals is inadequate. Herein, the NTP use short-term, in vivo transcriptomic studies to inform potential points of departure for TCP.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123542" }, "primaryId" : "GEO:GSE123542", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123542" } ] }, "title" : "Transcriptome Analysis of rat vascular molecular pathways linked to mitochondria in different phase of ischeia", "dateAssigned" : "2018-12-10T00:00:00.000-06:00", "summary" : "Conclusions: variation in mitochondrial morphology and dynamics occurs prior to mitochondrial dysfunctions after ischemic injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32312970" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123598" }, "primaryId" : "GEO:GSE123598", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123598" } ] }, "title" : "Gene expression pattern comparison depend on morphological change in rat pXEN cells", "dateAssigned" : "2018-12-11T00:00:00.000-06:00", "summary" : "pXEN cells have intrinsic property for vacuolation generally and in proper condition, vacuolated cells contribute to cavitation, so call vesiculation, via merge together. So, we want to find meaning of morphogenesis and connection with in vivo gastrulation stage.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31492758" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123687" }, "primaryId" : "GEO:GSE123687", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123687" } ] }, "title" : "Inhibition of the autophagic protein ULK1 attenuates axonal degeneration in vitro and in vivo and modulates differential splicing", "dateAssigned" : "2018-12-12T00:00:00.000-06:00", "summary" : "Several traumatic and neurodegenerative disorders of the CNS show axonal degeneration as a key and early pathological feature. Following a focal axonal lesion, an extended axonal disintegration by acute axonal degeneration (AAD) occurs within several hours. During AAD, activation of autophagic proteins including Unc-51 like autophagy activating kinase 1 (ULK1) has been demonstrated, but its role is incompletely understood. Here, we overexpressed a dominant negative of ULK1 (ULK1.DN) in primary rat cortical neurons in vitro and in the spinal cord (SC) and optic nerve (ON) in vivo. We found a significant inhibitory effect on autophagy in vitro and in vivo. While no effect on cell survival could be observed, ULK1.DN attenuated AAD after axotomy in microfluidic chambers in vitro. Models of SC injury and ON crush in vivo confirmed an attenuation of axonal degeneration by ULK1.DN. In a translational approach, we employed the selective ULK1 inhibitor SBI-0206965 (SBI) and found an attenuation of AAD after ON crush in vivo mediated by a reduction of autophagy by SBI. Quantitative proteomic profiling after ULK1.DN overexpression in vitro revealed a regulation of proteins associated with translation and splicing. A differential exon expression analysis identified the genes kinesin family member 1B (Kif1b), DNA damage inducible transcript 3 (Ddit3) and WD repeat domain 6 (Wdr6) as targets of ULK1.DN and potential mediators of its degeneration-attenuating effect. These findings reveal ULK1 as an important mediator of axonal degeneration and elucidate its function in splicing, defining it as a putative therapeutic target.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32341448" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123721" }, "primaryId" : "GEO:GSE123721", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123721" } ] }, "title" : "Sex differences in the synaptic genomic fabrics of the rat hypothalamic paraventricular node", "dateAssigned" : "2018-12-12T00:00:00.000-06:00", "summary" : "We profiled the whole transcriptomes of male and female rat hypothalamic paraventricular nodes to determine whether there are sex differences in the topology of the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission. Our Genomic Fabric Paradigm (GFP) is proposed as a transformative research approach to enhance the understanding of the brain transcriptomic circuitries. The genomic fabric of a particular synapse is the structured transcriptome associated with the most interconnected and stably expressed gene network responsible for that type of neurotransmission. GFP refines the description of functional pathways by selecting the most prominent genes and determining their networking. Moreover, it quantifies the remodeling of functional pathways and their interplay in disease and recovery in response to a treatment. This experiment provides the absolute controls for a larger study on a rat model of autism spectrum disorder and its treatment with ACTH and PMX53.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123746" }, "primaryId" : "GEO:GSE123746", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123746" } ] }, "title" : "MicroRNAs are important mediators of BMP-7 induced dendritic growth in sympathetic neurons", "dateAssigned" : "2018-12-12T00:00:00.000-06:00", "summary" : "MicroRNA profiling of cultured sympathetic neurons from the superior cervical ganglia of E21 Sprague-Dawley rat pups following growth under control conditions or after treatment with BMP-7 at 50 ng/mL for 6 hours or 24 hours.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31104181" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123776" }, "primaryId" : "GEO:GSE123776", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123776" } ] }, "title" : "microRNA expression profile in renal tissues of rats with doxorubicin nephropathy by Mongolian medicine Narenmandula", "dateAssigned" : "2018-12-13T00:00:00.000-06:00", "summary" : "The biological information of miRNA expression in renal tissues of doxorubicin rats was detected and analyzed using Affymetrix miRNA chip detection technology, which laid a foundation for further elucidating the multi-target regulation effect of the renal function protection and provided data of Mongolian medicine Narenmandula .", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123915" }, "primaryId" : "GEO:GSE123915", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123915" } ] }, "title" : "Rat Schwann cell gene expression analysis after Sox2 overexpression", "dateAssigned" : "2018-12-17T00:00:00.000-06:00", "summary" : "An in vitro microarray analysis of GFP (control) and Sox2/GFP overexpressing Schwann cells", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30726731" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123935" }, "primaryId" : "GEO:GSE123935", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123935" } ] }, "title" : "Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat: Liver Transcriptome Changes in Study 1", "dateAssigned" : "2018-12-17T00:00:00.000-06:00", "summary" : "Conclusions: There were no significant changes in liver gene expression between 5 and 10 h of fasting", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30881311" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123948" }, "primaryId" : "GEO:GSE123948", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123948" } ] }, "title" : "The Effect of Chronic Hypoxia on Cardiac Gene Expression in Rattus Norvegicus", "dateAssigned" : "2018-12-17T00:00:00.000-06:00", "summary" : "To explore the gene expression prolife in the chroniclly hypoxic myocardium, 8 rats were divided randomly into normoxic (n=4) or chroniclly hypoxic (n=4) group, and were exposed to room air (21% O2) or continued hypoxia (10% O2) for 4 weeks. Heart tissues were collected and RNA sequencing was applied to detect the overall gene expression prolife. Genes with adjusted P-value ≤0.01 (corrected by Benjamini-Hochberg) and |log2_ratio|≥0.585 are identified as differentially expressed genes. RNA sequencing identified a total of 2014 gene with statistical significances, among which 1260 genes were significantlly increased and 754 genes were significantlly decreased. The results showed that gene expression profiling was perturbed in chronically hypoxic myocardium.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123987" }, "primaryId" : "GEO:GSE123987", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE123987" } ] }, "title" : "Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat: Liver Transcriptome Changes in Study 3", "dateAssigned" : "2018-12-17T00:00:00.000-06:00", "summary" : "Conclusions: There were no significant changes in liver gene expression between 7 and 13 h of fasting", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30881311" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124002" }, "primaryId" : "GEO:GSE124002", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124002" } ] }, "title" : "Leptin deficiency leads to a unique natural history of NASH in rats", "dateAssigned" : "2018-12-18T00:00:00.000-06:00", "summary" : "Nonalcoholic steatohepatitis (NASH) is an aggressive liver disease threatening public health, however its natural history is poorly understood. Unlike ob/ob mice, Lep∆I14/∆I14 rats develop unique NASH phenotype with an inflection point of inflammation at postnatal week 16. Using Lep∆I14/∆I14 rats, we studied the natural history of NASH progression by performing an integrated analysis of hepatic transcriptome from postnatal week 4 to 48. Leptin deficiency leads to the precipitously increasing expression of genes encoding rate-limiting enzymes in lipid metabolism. However, hepatic inflammation related genes, pathways and immune-cell infiltration are restricted after week 16, implying an essential role of LEPTIN in regulating hepatic inflammation. Lep∆I14/∆I14 rats share more genes with NASH patients than known mouse models, therefore will provide a better genetic platform for studying NASH than mice.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124004" }, "primaryId" : "GEO:GSE124004", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124004" } ] }, "title" : "Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat: Liver Transcriptome Changes in Study 2", "dateAssigned" : "2018-12-18T00:00:00.000-06:00", "summary" : "Conclusions: There were 100 genes that could be mapped to the rat metabolic network iRno, with significant changes in expression between 5 and 10 h of fasting in the top 10% by effect size parameter b (b > 0.6). ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30881311" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124055" }, "primaryId" : "GEO:GSE124055", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124055" } ] }, "title" : "Dopaminylation of Histone H3 in Ventral Tegmental Area Regulates Cocaine-seeking", "dateAssigned" : "2018-12-18T00:00:00.000-06:00", "summary" : "Vulnerability to relapse during periods of attempted abstinence from cocaine use is hypothesized to result from rewiring of brain reward circuitries, particularly ventral tegmental area (VTA) dopamine neurons. How cocaine exposures act on midbrain dopamine neurons to precipitate addiction-relevant changes in gene expression is unclear. We found that histone H3 glutamine 5 dopaminylation (H3Q5dop) plays a critical role in cocaine-induced transcriptional plasticity in midbrain. Rats undergoing withdrawal from cocaine showed an accumulation of H3Q5dop in VTA. By reducing H3Q5dop in VTA during withdrawal, we reversed cocaine-mediated gene expression changes, attenuated cue-induced dopamine release in nucleus accumbens and reduced cocaine-seeking behavior. These findings establish a neurotransmission-independent role for nuclear dopamine in relapse-related transcriptional plasticity in VTA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32273471" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124109" }, "primaryId" : "GEO:GSE124109", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124109" } ] }, "title" : "Graded regulation of cellular quiescence depth between proliferation and senescence by a lysosomal dimmer switch", "dateAssigned" : "2018-12-19T00:00:00.000-06:00", "summary" : "The reactivation of quiescent cells to proliferate is fundamental to tissue repair and homeostasis in the body. Often referred to as the G0 state, quiescence is however not a uniform state but with graded depth. Shallow quiescent cells exhibit a higher tendency to revert to proliferation than deep quiescent cells, while deep quiescent cells are still fully reversible under physiological conditions, distinct from senescent cells. Cellular mechanisms underlying the control of quiescence depth and the connection between quiescence and senescence are poorly characterized, representing a missing link in our understanding of tissue homeostasis and regeneration. Here we measured transcriptome changes as rat embryonic fibroblasts moved from shallow to deep quiescence over time in the absence of growth signals. We found that lysosomal gene expression was significantly upregulated in deep quiescence, and partially compensated for gradually reduced autophagy flux. Reducing lysosomal function drove cells progressively deeper into quiescence and eventually into a senescence-like irreversibly arrested state; increasing lysosomal function, by lowering oxidative stress, progressively pushed cells into shallower quiescence. That is, lysosomal function modulates graded quiescence depth between proliferation and senescence as a dimmer switch. Lastly, we found that a gene expression signature developed by comparing deep and shallow quiescence in fibroblasts can correctly classify a wide array of senescent and aging cell types in vitro and in vivo, suggesting that while quiescence is generally considered to protect cells from irreversible arrest of senescence, quiescence deepening likely represents a common transition path from cell proliferation to senescence, related to aging.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124166" }, "primaryId" : "GEO:GSE124166", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124166" } ] }, "title" : "IL-1 versus p65 overexpression [human, rat]", "dateAssigned" : "2018-12-20T00:00:00.000-06:00", "summary" : "Comparison of cytokine signaling in rat insulinoma cells versus human islets", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124332" }, "primaryId" : "GEO:GSE124332", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124332" } ] }, "title" : "Next Generation Sequencing (NGS) of miRNAs in rat hippocampal tissues", "dateAssigned" : "2018-12-24T00:00:00.000-06:00", "summary" : "We carried out Massive Parallel Sequencing (MPS) to reveal miRNA expression profiles of rats with LiCl-pilocarpine induced epileptic status (SE) in adulthood (Postnatal day 60 -P60) and infancy (P12). Hippocampal tissues were collected at 3 stages of epileptogenesis: acute (24 hours), latent (7 days) and chronic (3 months after SE) from 10 animals after SE and 10 controls in each age group (120 in total). The sequencing platform identified 666 miRNA species, out of which up to 419 miRNAs were present with the coverage of more than 500 reads altogether in individual groups (onset-age epilepsy stage combinations). We discovered that age of SE induction has impact on miRNA profile throughout all stages of epileptogenesis and infantile-onset of epilepsy leads to changes in smaller number of miRNAs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33958654" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124387" }, "primaryId" : "GEO:GSE124387", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124387" } ] }, "title" : "Transcriptome Analysis on Maternal Separation Rats with Depression-related Manifestations Ameliorated by Electroacupuncture", "dateAssigned" : "2018-12-26T00:00:00.000-06:00", "summary" : "Conclusions: Our investigation demonstrates the first analysis of the frontal cortex genome-wide transcriptomes in depression rats under maternal separation by RNA-seq technology. These results suggest that EA at GV20 and GV29 ameliorates depression-related manifestations by regulating the expression of multiple genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31024237" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124431" }, "primaryId" : "GEO:GSE124431", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124431" } ] }, "title" : "PBDE-47 and PBDE mixture (DE-71) toxicities and liver transcriptomic changes at PND 22 after in utero/postnatal exposure in the rat.", "dateAssigned" : "2018-12-27T00:00:00.000-06:00", "summary" : "Test articles used: DE-71 (Pentabromodiphenyl Ether Mixture [Technical Grade), CAS Number 32534-81-9, DTXSID2024246); PBDE-47 (CAS Number 5436-43-1); PB (Phenobarbital, CAS Number 50-06-6 ); PCB (PCB126, CAS Number 57465-28-8)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30206662" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124592" }, "primaryId" : "GEO:GSE124592", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124592" } ] }, "title" : "The translatome of adult cortical axons is regulated by learning in vivo", "dateAssigned" : "2019-01-03T00:00:00.000-06:00", "summary" : "Local protein synthesis has not been believed to occur in adult forebrain axons. We have used translating ribosome affinity purification (TRAP) to capture mRNA from the distal amygdaloid projections of auditory cortical axons. An eYFP-tagged ribosomal protein (rpL10a) was expressed in the adult rat auditory cortex via a lentiviral vector, and rats were given Pavlovian fear conditioning or control training two hours before collection of auditory cortex and amygdala. The eYFP tag alone was used as an IP control. Polysome extraction and eYFP immunoprecipitation were performed according to published protocols (Heiman et al., 2008 Cell 135:78; Kratz et al. 2014 Genome Res. 24:1396).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31825308" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124613" }, "primaryId" : "GEO:GSE124613", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124613" } ] }, "title" : "Prenatal betamethasone remodels the genomic fabrics of the synaptic transmission in the rat hypothalamic paraventricular nucleis", "dateAssigned" : "2019-01-03T00:00:00.000-06:00", "summary" : "We profiled the whole transcriptomes of male and female rat hypothalamic paraventricular nuclei to determine the remodeling of the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission in rats prenatally exposed (G15) to betamethasone. Pups were treated with saline on days 13, 14 and 15. Our Genomic Fabric Paradigm (GFP) is proposed as a transformative research approach to enhance the understanding of the brain transcriptomic alterations in epileptic rats and recovery following various treatments. The genomic fabric of a particular synapse is the structured transcriptome associated with the most interconnected and stably expressed gene network responsible for that type of neurotransmission. GFP refines the description of functional pathways by selecting the most prominent genes and determining their networking. Moreover, it quantifies the remodeling of functional pathways and their interplay in disease and recovery in response to a treatment. We found that priming with betamethasone had substantial consequences on the topology of the genomic fabrics of all kind of synaptic transmission.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124615" }, "primaryId" : "GEO:GSE124615", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124615" } ] }, "title" : "Recovery of the synaptic transmission genomic fabrics in the hypothalamic paraventricular nucleus of a rat model of autism treated with ACTH", "dateAssigned" : "2019-01-03T00:00:00.000-06:00", "summary" : "We profiled the whole transcriptomes of male and female rat hypothalamic paraventricular nuclei to determine the remodeling of the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission in epilepsy and recovery following treatment with ACTH. The rats were prenatally exposed (G15) to betamethasone followed by repeated adiministration of N-Methyl-D-Aspartic acid (NMDA) on postnatal days 12, 13 and 15 which triggered infantile spasms. Pups were treated with ATCH on days 13, 14 and 15 prior to NMDA administration to determine what effects the treatment had on transcriptome recovery. Our Genomic Fabric Paradigm (GFP) is proposed as a transformative research approach to enhance the understanding of the brain transcriptomic alterations in epileptic rats and recovery following various treatments. The genomic fabric of a particular synapse is the structured transcriptome associated with the most interconnected and stably expressed gene network responsible for that type of neurotransmission. GFP refines the description of functional pathways by selecting the most prominent genes and determining their networking. Moreover, it quantifies the remodeling of functional pathways and their interplay in disease and recovery in response to a treatment. We found that priming with betamethasone had substantial consequences on the topology of the genomic fabrics of all kind of synaptic transmission and that NMDA-induced spasms strongly exacerbated the remodeling of these fabrics. ACTH treatment induced a moderate recovery of the normal synaptic transcriptomes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124639" }, "primaryId" : "GEO:GSE124639", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124639" } ] }, "title" : "Investigation of gene expression profiles in a rat adjuvant arthritis model", "dateAssigned" : "2019-01-03T00:00:00.000-06:00", "summary" : "In order to study the molecular biological mechanism underlying the inhibition of RA synovial pannus by triptolide, differentially expressed genes in synovial tissues from an adjuvant arthritis (AA) rat model with and without triptolide treatment were detected and verified by gene transcripts produced by Agilent Technologies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30988781" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124669" }, "primaryId" : "GEO:GSE124669", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124669" } ] }, "title" : "miRNA profiling of urinary exosomes to assess the progression of acute kidney injury", "dateAssigned" : "2019-01-04T00:00:00.000-06:00", "summary" : "Using renal ischemia-reperfusion injury as a model of acute kidney injury, we deteremined temporally-released miRNAs released in urinary exosomes during the injury", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30886169" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124819" }, "primaryId" : "GEO:GSE124819", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124819" } ] }, "title" : "Activity-induced changes in the liver transcriptome after chronic spinal cord injury", "dateAssigned" : "2019-01-08T00:00:00.000-06:00", "summary" : "Spinal cord injury (SCI) is a devastating clinical condition resulting in significant disabilities for affected individuals. Apart from local injury within the spinal cord, SCI patients develop a myriad of complications characterized by multi-organ dysfunction. Disorders, such as lung injury, cardiovascular disease, liver damage, kidney and urinary tract dysfunction, alterations in gut microbiome, neuropathic pain, depression and altered immune responses are common in SCI patients. Such whole body, systemic responses hinder the functional recovery and can be life-threatening in SCI population. Investigations of organ specific gene expression analyses can provide a better understanding of the injury response and identify molecular targets. Consequently, this can be used to develop treatment for SCI, promoting functional recovery and overall quality of life.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31197156" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124833" }, "primaryId" : "GEO:GSE124833", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124833" } ] }, "title" : "Insights from long non-coding RNAs profiling of beta cells undergoing high glucose/palmitate -induced glucolipotoxicity", "dateAssigned" : "2019-01-08T00:00:00.000-06:00", "summary" : "RNA-Seq was performed to compare the control INS-1 cells (rat beta cell line)with the high glucose/palmitate-treated INS-1 cells. According to the expression profiling data, 264 significantly dysregulated lncRNAs were identified with a set filter (fold-change ≥2.0, p < 0.05) in the HG/PA-treated INS-1 cells: 153 were up-regulated, while 111 were down-regulated.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124851" }, "primaryId" : "GEO:GSE124851", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124851" } ] }, "title" : "Alteration of circRNA Expression in rDFCs During Osteogenic Differentiation", "dateAssigned" : "2019-01-09T00:00:00.000-06:00", "summary" : "Circular RNAs (circRNAs) are novel among noncoding RNAs and play crucial roles in various biological processes. However, little is known about the functions of circRNAs during osteogenic differentiation. The current study aimed to investigate the differential expression of circRNAs in rat dental follicle cells (rDFCs) upon osteogenic medium culture. Those potential circRNAs were identified by RNA high-throughput sequencing and quantitative real-time polymerase chain reaction (qRT-PCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to further explore circRNA biofunctions. 266 differentially-expressed circRNAs were revealed and involved in several important signaling pathways, which include MAPK and TGF-β signaling pathways. Among these, circFgfr2 and its predicted downstream targets, miR-133 and BMP6, were identified both in vivo and in vitro. For further validation, circFgfr2 was overexpressed during osteogenic differentiation, bringing about the down-regulation of miR-133 and the up-regulation of BMP6. Taken together, the results revealed the circRNA expression profiles and indicate the importance of circRNAs during the osteogenic differentiation of rDFCs. In addition, circFgfr2 might promote osteogenesis by controlling miR-133/BMP6, which possibly provide new target to manipulate tooth regeneration and bone formation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124870" }, "primaryId" : "GEO:GSE124870", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE124870" } ] }, "title" : "Molecular characterization of the effects of shift work and food consumption on cardiovascular disease in the rat", "dateAssigned" : "2019-01-09T00:00:00.000-06:00", "summary" : "Shift work misaligns the circadian clock and leads to an increased risk of cancer, cardiovascular diseases, and metabolic disorders. Furthermore, food consumed during the rest phase is a major contributor to this misalignment, as food access restricted to the endogenous active phase, at night, prevents against the adverse effects of shift work on obesity and diabetes in rats. In this study, we aimed to investigate the molecular mechanisms by which shift work and food consumption contribute to an increased risk of cardiovascular disorders. To this end, we used a model of shift work in rats, whereby animals are exposed to a 12:12 light:dark cycle and are forced to be active for eight-hours during their natural rest phase during the day, Monday to Friday for five consecutive weeks. Given the preventive effects of temporal restriction of food intake, a group of shift worker rats with food access restricted to the night was included in addition to controls and shift workers. To gain insight into the molecular underpinnings of shift-work associated cardiovascular pathologies, we performed RNA-Seq analysis and Picrosirius Red staining in rat hearts. Our results show that shift work in rats, regardless of the time of food consumption, have an increase in collagen deposition in the heart. In addition, the expression of many genes encoding key fibrotic pathways was found to be up-regulated in shift worker rats that had their food restricted to the active phase. Altogether, our results suggest that five weeks of shift work in rats is capable of inducing cardiovascular disease through an up-regulation of collagen deposition in the heart.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125042" }, "primaryId" : "GEO:GSE125042", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125042" } ] }, "title" : "Effect of landiolol on sex-related transcriptomic changes in myocardium during sepsis", "dateAssigned" : "2019-01-14T00:00:00.000-06:00", "summary" : "We compared the myocardial transcriptional profiles in male and female rats after CLP (Cecal ligation and puncture) induction and landiolol administration. This analysis showed major differences between males and females in the biological processes activated during sepsis. In particular, a very significant decrease in processes related to cell organization, contractile function, ionic transport and PI3K-Akt signaling were observed only in males. Regarding the direct regulation of gene expression of the adrenergic pathway, there was no major differences between male and female. Moreover, our results highlighted the large number of signaling pathways dysregulated during sepsis in males that were reversed by landiolol. In particular, the level of expression of the genes encoding the contractile proteins, TUBA8 and MYH7B, the phosphatase PPP2CA, GRK5 and AKAP6 were close to their basal levels in males. In contrast, in females, only few pathways were affected by the action of landiolol. In addition, adrenergic signaling was decreased while genes potentially involved in calcium overload were overexpressed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31428883" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125084" }, "primaryId" : "GEO:GSE125084", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125084" } ] }, "title" : "RNA-seq-based transcriptome profiling of hawk tea extract (HTE)-fed hypercholesterolemic rat livers", "dateAssigned" : "2019-01-14T00:00:00.000-06:00", "summary" : "The high-fat diet (HFD)-feeding significantly stimulated hypercholesterolemia in male SD rats. Simultaneous feeding of hawk tea extracts (HTE) reversed the hypercholesterolemia in rats by lowering the serum total cholesterol and low-density lipoprotein cholesterol levels. To understand the molecular mechanism underlying the cholesterol-lowering effects of HTE, we performed the RNA-seq analysis. Consequently, the change in mRNA levels of genes invovled in metabolism of lipid and lipoprotein, primary bile acid synthesis, and ABC transporters itriggered by HFD-feeding were reversed by the co-administration of HTE (200 mg/kg/day for 11 weeks).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31098406" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125134" }, "primaryId" : "GEO:GSE125134", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125134" } ] }, "title" : "Analysis of possible mechanisms behind functional recovery following neural progenitor cell transplantation into spinal cord injury.", "dateAssigned" : "2019-01-15T00:00:00.000-06:00", "summary" : "Long-term survival and integration of neural progenitor cells (NPCs) transplanted following spinal cord injury (SCI) have been observed. However, questions concerning the differentiation choice of NPCs, their mechanism of action and their contribution to functional recovery remains unanswered. Therefore, we investigated global transcriptomal changes in transplanted NPCs transplanted into SCI. We found that NPCs transplanted into SCI up-regulate genes related to nerve cell function and signaling and differentiation, and down-regulate genes related to cytokine signaling and apoptosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31031190" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125135" }, "primaryId" : "GEO:GSE125135", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125135" } ] }, "title" : "sRNA sequencing of miRNAs exported to HDL from INS-1 rat insulinoma cells", "dateAssigned" : "2019-01-15T00:00:00.000-06:00", "summary" : "miRNAs are exported to high density lipoproteins (HDL). This study aimed to understand what miRNAs are exported from INS-1 cells to HDL in vitro.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30846744" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125240" }, "primaryId" : "GEO:GSE125240", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125240" } ] }, "title" : "Single base mapping of m6A by an antibody-independent method", "dateAssigned" : "2019-01-17T00:00:00.000-06:00", "summary" : "N6-methyladenosine (m6A) is one of the most abundant mRNA modifications in eukaryotes, related to pivotal RNA metabolism processes. The most popular high-throughput m6A identification method relies on the commercial m6A antibody but suffers from poor reproducibility and limited resolution. Exact location of m6A site is of great vital for understanding the dynamics, functions and machinery of RNA methylation. Here, we developed a precise and high-throughput antibody-independent m6A identification method based on the m6A-sensitive RNA endoribonuclease recognizing ACA motif (m6A-sensitive RNA-Endoribonuclease–Facilitated sequencing or m6A-REF-seq). Whole-transcriptomic single base m6A map generated by m6A-REF-seq displayed a typical distribution pattern with enrichment adjacent to stop codon. Ligase-based and qPCR validation methods were used to confirm the individual m6A sites and quantify the methylation level, reinforcing the high accuracy of m6A-REF-seq. We applied m6A-REF-seq on five tissues from three mammals, showing that m6A sites were conserved and tend to gather together among species. (m6A-REF-seq had been named as Aim-seq.)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31281898" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125276" }, "primaryId" : "GEO:GSE125276", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125276" } ] }, "title" : "Analysis of pathways elicited by empty SV40 capsids (VLPs) in septic rats 24 hours post 2CLP operation", "dateAssigned" : "2019-01-17T00:00:00.000-06:00", "summary" : "During the first hours after infection, before SV40 DNA enters the nucleus, empty capsids (VLPs) and the wild-type virus have the same effect on cellular signaling. VLPs were previously found to ameliorate toxic acute kidney injury (AKI) in a mouse model, counteracting apoptosis by inducing the Akt-1 survival pathway. Here we tested their effect on severe sepsis in rats. VLP pre-treatment increased survival and recovery from zero to 75%. RNAseq studies demonstrated that unlike AKI, here the VLPs did not induce survival pathways. Instead they affected thousands of genes and many cellular functions, eliminating deleterious pathways and inducing beneficial ones: immune response, resolution of inflammation, regeneration and cell and system homeostasis. In contrast, only four genes were affected following VLP administration to healthy rats. We propose that SV40 VLPs respond specifically to perturbation in cellular activities. The study suggests that diseases with complex pathophysiology may require treatments affecting wide-spectrum functions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32110278" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125298" }, "primaryId" : "GEO:GSE125298", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125298" } ] }, "title" : "Next Generation Sequencing Analysis of wild-type and transgenic beta-synuclein reactive T cells", "dateAssigned" : "2019-01-17T00:00:00.000-06:00", "summary" : "We report the expression profile of beta-synuclein reactive CD4+ T cells isolated from blood and brain in animals affected by Experimental autoimmune encephalomyelitis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30867589" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125305" }, "primaryId" : "GEO:GSE125305", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125305" } ] }, "title" : "miRNA profiling of urinary exosomes to assess the progression of acute kidney injury", "dateAssigned" : "2019-01-18T00:00:00.000-06:00", "summary" : "Because exosomes have gained attention as a source of biomarkers, we investigated if miRNAs in exosomes (exo-miRs) can report the disease progression of organ injury. Using renal ischemia-reperfusion injury (IRI) as a model of acute kidney injury (AKI), we determined temporally-released exo-miRs in urine during IRI and found that these exo-miRs could reliably mirror the progression of AKI. From the longitudinal measurements of miRNA expression in kidney and urine, we found that release of exo-miRs was regulated sorting process, rather than simply representing their intracellular biosynthesis. In the injury state, miR-16, miR-24, and miR-200c were increased in the urine. Interestingly, expression of target mRNAs of these exo-miRs was significantly altered in renal medulla. Next, in the early recovery state, urinary exo-miRs (miR-9a, miR-141, miR-200a, miR-200c, miR-429), which shares Zeb1/2 as a common target mRNA, were upregulated, indicating that they reflect TGF--associated renal fibrosis. Finally, release of exo-miRs (miR-125a, miR-351) was regulated by TGF-1 and was able to differentiate the sham and IRI even after the injured kidneys were functionally recovered. Altogether, these data indicate that exo-miRs released in renal IRI are largely associated with TGF- signaling. Temporal release of exo-miRs which share targets might be a regulatory mechanism to control the disease progression of AKI.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125451" }, "primaryId" : "GEO:GSE125451", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125451" } ] }, "title" : "Diabetes severity is reflected by changes in a cardiac gene expression signature characterized by metabolism and cell death processes", "dateAssigned" : "2019-01-22T00:00:00.000-06:00", "summary" : "We tested the impact of a graded reduction in insulin on cardiac gene expression with particular focus on metabolism and energy homeostasis. Wistar rats were made diabetic with a single dose of either 55 (D55) or 100 (D100) mg/kg streptozotocin (STZ). Although both D55 and D100 were equally hyperglycemic compared to control, D100 showed markedly lower plasma insulin and robust increases in plasma FA and TG. D100 demonstrated more significant transcriptomic changes than D55 with enrichment for metabolic processes that direct the heart to use FA, when glucose use is obstructed. Analysis of a protein-protein interaction network identified functional networks in D100 that describe mitochondrial overload, incomplete fatty acid oxidation, and loss of cardiomyocytes. Our data suggests that the differential reduction of insulin produced a dramatic change in cardiac gene expression largely enriched for substrate metabolism functions as well as a gene expression program supporting cell death.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31665961" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125483" }, "primaryId" : "GEO:GSE125483", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125483" } ] }, "title" : "Conservation, acquisition, and functional impact of sex-biased gene expression in mammalian tissues", "dateAssigned" : "2019-01-22T00:00:00.000-06:00", "summary" : "Sex differences are widespread in human health and disease, which are frequently modeled in other mammalian species. However, the extent to which molecular sex differences are conserved across both tissues and species remains unclear. We conducted a 12-tissue, five-species survey of sex differences in gene expression using both publicly available (human) and newly generated (cynomolgus macaque, mouse, rat, and dog) RNA sequencing data. In each of the tissues assessed, we identified between 128 and 805 genes with conserved sex-biased expression. However, most sex bias in gene expression (~77%) – both female and male – has arisen since the last common ancestor of boroeutherian mammals, likely facilitated by reduced selective constraint. Evolutionary gains and losses of regulation by sex-biased transcription factors drove a significant fraction (~27%) of lineage-specific changes in sex bias. Our study suggests caution in the use of other species as models of human sex differences, and that similar selective pressures have driven sex-biased gene expression both within and outside the reproductive tract.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31320509" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125502" }, "primaryId" : "GEO:GSE125502", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125502" } ] }, "title" : "Folate deficiency in vascular smooth muscle cells", "dateAssigned" : "2019-01-23T00:00:00.000-06:00", "summary" : "Folate deficiency promotes differentiation of vascular smooth muscle cells, but shifts the overall phenotype towards skeletal muscle", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31530711" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125507" }, "primaryId" : "GEO:GSE125507", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125507" } ] }, "title" : "CRISPR-Cas9 screening of KSHV-transformed cells identifies XPO1 as a vulnerable target of cancer cells by inducing p62 SQSTM1-mediated p53 activation in PML bodies", "dateAssigned" : "2019-01-23T00:00:00.000-06:00", "summary" : "Mislocalization of oncogenes and tumor suppressors resulting from aberrant nuclear export promotes uncontrolled cell proliferation and growth transformation of cancer cells. We performed a genome-wide CRISPR-Cas9 screening in matched primary and KSHV-transformed cells, and identified genes that were pro-growth and growth-suppressive of both types of cells, of which exportin XPO1 was a critical factor for the survival of transformed cells. Using XPO1 inhibitor KPT-8602 and by siRNA-mediated knockdown, we confirmed the essential role of XPO1 in cell proliferation and growth transformation of KSHV-transformed cells, as well as cell lines of other types of cancer including gastric cancer and liver cancer. XPO1 inhibition induced cell cycle arrest and p53 activation, which depended on the formation of PML nuclear bodies. Furthermore, XPO1 induced relocalization of autophagy adaptor protein p62 (SQSTM1), recruiting p53 for activation in PML nuclear bodies. Our findings highlight a novel mechanism of p53 activation and identify XPO1 as a vulnerable target of cancer cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31088931" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125619" }, "primaryId" : "GEO:GSE125619", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125619" } ] }, "title" : "Regulation of Macrophage Foam Cell Formation during Nitrogen Mustard (NM)-Induced Pulmonary Fibrosis by Lung Lipids", "dateAssigned" : "2019-01-24T00:00:00.000-06:00", "summary" : "Nitrogen mustard (NM) is a vesicant known to target the lung, causing acute injury which progresses to fibrosis. Evidence suggests that activated macrophages contribute to the pathologic response to NM. In these studies, we analyzed the role of lung lipids generated following NM exposure on macrophage activation and phenotype. Treatment of rats with NM (0.125 mg/kg, i.t.) resulted in a time-related increase in enlarged vacuolated macrophages in the lung. At 28 d post exposure, macrophages stained positively for Oil Red O, a marker of neutral lipids. This was correlated with an accumulation of oxidized phospholipids in lung macrophages and epithelial cells, and an increase in bronchoalveolar lavage fluid (BAL) phospholipids. RNA-sequencing analysis revealed that lipid handling pathways under control of the transcription factors LXR, FXR and PPAR-ɣ were significantly altered following NM exposure. Whereas at 1-3 d post NM, FXR and the downstream oxidized low density lipoprotein receptor, Cd36, were increased, Lxr and the lipid extrusion pump targets, Abca1 and Abcg1 were reduced. Treatment of naïve lung macrophages with lipid enriched fractions of BAL collected 3 d after NM resulted in upregulation of Nos2, Apoe and Ptgs2, markers of pro-inflammatory activation, while lipid-enriched BAL collected 28 d post NM upregulated expression of the anti-inflammatory markers, Il10, Cd163, and Cx3cr1, and induced the formation of lipid-laden foamy macrophages. These data suggest that NM-induced alterations in lipid handling and metabolism drive macrophage foam cell formation, potentially contributing to the development of pulmonary fibrosis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125630" }, "primaryId" : "GEO:GSE125630", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125630" } ] }, "title" : "Transcriptome of dorsal root ganglia caudal to a spinal cord injury with modulated behavioral activity", "dateAssigned" : "2019-01-24T00:00:00.000-06:00", "summary" : "Spinal cord injury (SCI) is a devastating clinical condition resulting in significant disabilities for affected individuals. Apart from local injury within the spinal cord, SCI patients develop a myriad of complications characterized by multi-organ dysfunction. Some of the dysfunctions are directly related to the disrupted integrity of sensory afferents from DRGs, which signal to both the spinal cord and peripheral organs. Some classes of DRG neurons undergo axonal sprouting both peripherally and centrally after spinal cord injury. Such physiological and anatomical re-organization of afferent axons after SCI contributes to both adaptive and maladaptive plasticity, which may be modulated by activity/exercise. In this study, we collected comprehensive gene expression data in whole dorsal root ganglia (DRGs) throughout the levels below the injury comparing the effects of SCI with and without activity/exercise.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31175296" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125728" }, "primaryId" : "GEO:GSE125728", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125728" } ] }, "title" : "Oscillatory cAMP Signaling Rapidly Alters H3K4 Methylation", "dateAssigned" : "2019-01-28T00:00:00.000-06:00", "summary" : "In this study we show that cAMP affects gene expression by altering H3K4me3 marks. Note, \"Control\" samples are untreated with cAMP. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31882444" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125762" }, "primaryId" : "GEO:GSE125762", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125762" } ] }, "title" : "The dose- and time-dependent effects of perfluorooctanoic acid on rat liver", "dateAssigned" : "2019-01-28T00:00:00.000-06:00", "summary" : "We reported the hepatic gene expression profiling in male Sprague-Dawley rats treated by different concentrations of perfluorooctanoic acid (PFOA) for 7, 14, and 28 days. We confirmed that PFOA induced liver tumor formation was mainly through the activation of peroxisome proliferator-activated receptor α (PPARα). We identified a panel of 7 genes (Cyp4a1, Nr1d1, Acot2, Vnn, Ehhadh, and Acot1) that might serve as the biomarkers for PPARα activation. We also meausred the apical endpoints of PPARα activation and found a good correlation with the expression level of these biomarker genes. Consitituitive androstane receptor mediated Cyp2b enzymatic activity and gene expression was also upregulated by PFOA in a dose-response manner. On the other hand, acyl hydrocarbon receptor (AhR) target gene Cyp1a2 were significantly downregulated at all time points studied. To our surprise, results of KEGG and Reactome pathway analyses suggested that PFOA did not drive the cell cycles and proliferations in the liver. While some of the DNA replication genes such as Pold2 and Mcm8 were upregulated by PFOA treatment, several key cyclin-dependent cell growth genes, including Ccnd1, Ccne2, Ccnb1, and Ccna2 were all significantly downregulated by PFOA in a dose-dependent manner, especailly at 28 days. Ingenuity Pathway Analysis also indicated that PFOA led to a suppression of liver cancer related pathways at later time points studied. These results suggest that while PFOA clearly induced PPARα activation, the increased cell growth (the second key event in the tumor mode of action), was transient and tightly regulated by feedback mechanisms. Whether such changes will eventually cause the formation of preneoplastic foci and liver tumors in rats remains unclear.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125896" }, "primaryId" : "GEO:GSE125896", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125896" } ] }, "title" : "Transcriptome profiling of the early response to volumetric muscle loss repair strategies", "dateAssigned" : "2019-01-30T00:00:00.000-06:00", "summary" : "We report the transcriptomic profiles of rat tibialis anterior following VML injury and three repair strategies in the early period following injury", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125955" }, "primaryId" : "GEO:GSE125955", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE125955" } ] }, "title" : "Infusion of human amniotic epithelial and mesenchymal stromal stem cells as a new therapeutic option for portal hypertension and cirrhosis", "dateAssigned" : "2019-01-31T00:00:00.000-06:00", "summary" : "Background and aims. Portal hypertension is the main consequence of cirrhosis, responsible for the complications defining clinical decompensation. The only cure for decompensated cirrhosis is liver transplantation, but it is a limited resource and opens the possibility of regenerative therapy. We investigated the potential of human amniotic membrane-derived mesenchymal stromal (hAMSCs) and epithelial (hAECs) stem cells for the treatment of portal hypertension and chronic liver disease. Methods. In vivo: hAMSCs and hAECs were isolated from human amniotic membranes. Cirrhotic rats with ascites (chronic CCl4 inhalation) received 4x10e6 hAMSCs, 4x10e6 hAECs, or vehicle (NaCl 0.9%) (intraperitoneal; n=10 per group). After 2-week we analyzed: a) portal pressure (PP) and liver microcirculatory function; b) liver sinusoidal endothelial (LSECs) and hepatic stellate (HSCs) cells phenotype; c) hepatic fibrosis, inflammation and hepatic function. In vitro: HSCs isolated from CCl4-cirrhotic rats were co-cultured with hAMSCs, hAECs or vehicle for 24h. RNA profile was analyzed by RNAseq. Results. Cirrhotic rats receiving hAMSCs or hAECs had significantly lower PP than vehicle-treated animals, together with improved liver microcirculatory function. This hemodynamic amelioration was associated with improvement in LSECs capillarization and HSCs de-activation, although hepatic collagen/fibrosis was not significantly reduced. Rats that received placenta derived stem cells had markedly reduced hepatic inflammation and oxidative stress. Finally, liver function tests significantly improved in rats receiving hAMSCs. In vitro experiments confirmed HSCs de-activation when co-cultured with stem cells. Conclusion. This pre-clinical study shows that infusion of human amniotic stem cells effectively decreases PP by ameliorating liver microcirculation, suggesting that it may represent a new treatment option for advanced cirrhosis with portal hypertension.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126023" }, "primaryId" : "GEO:GSE126023", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126023" } ] }, "title" : "Proteomic and transcriptional profiling of rat amygdala following social play", "dateAssigned" : "2019-02-01T00:00:00.000-06:00", "summary" : "Social play is a frequently studied behavior and it is the most characteristic form of social interaction observed in adolescent rats. Social play is necessary for adolescents to develop proper cognitive, emotional, and social competency. Deficits in social play have been observed in several neurodegenerative disorders such as autism, schizophrenia, and attention deficit hyperactivity disorder. However, the information available on neural substrates and the mechanism involved in social play is still limited. This study characterized social play by proteomic and transcriptional profiling studies. Social play was performed on male Sprague Dawley rats on postnatal day 38 and protein and gene expression in the amygdala was determined following behavioral testing. The proteomic analysis led to the identification of 170 differentially expressed proteins (p≤0.05) with 67 upregulated and 103 downregulated proteins. The transcriptomic analysis led to the identification of 188 genes (adjusted p≤0.05) with 55 upregulated and 133 downregulated genes. Based on both protein and gene expression data, DAVID analysis revealed that social play altered neurotransmitter signaling including GABAergic and glutamatergic signaling and G-protein coupled receptor (GPCR) signaling. These data suggest that the synaptic levels of GABA and glutamate increased during play. Ingenuity Pathway Analysis (IPA) confirmed these alterations. IPA also revealed that differentially expressed genes/proteins in our data had significant over representation of additional neurotransmitter signaling systems, including the opioid, serotonin, and dopamine systems, suggesting that play alters the systems involved in the regulation of reward. In addition, corticotropin-releasing hormone signaling was altered indicating that an increased level of stress occurs during play. Our data suggest that increased inhibitory GPCR signaling in these neurotransmitter pathways occurs following social play as a physiological response to regulate the induced level of reward and stress and to maintain the excitatory-inhibitory balance in the neurotransmitter systems.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31673590" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126032" }, "primaryId" : "GEO:GSE126032", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126032" } ] }, "title" : "Gloable gene expression is affected by loss of CSB function in the rat model for Cockayne syndrome", "dateAssigned" : "2019-02-04T00:00:00.000-06:00", "summary" : "Cockayne syndrome (CS) is a rare genetic neurodevelopmental disorder, characterized by a deficiency in the transcription-coupled nucleotide excision repair pathway. Mutation of Cockayne syndrome B (CSB) affects basal transcription which is considered a major cause of CS neurological dysfunction. Here, we generated a rat model by mimicking a nonsense mutation in the CSB(ERCC6) gene of CS-B patients. CSB-deficient rats exhibit the well-known CS repair characteristics: inability to resume RNA synthesis from stalled RNA polymerase II (RNAP II) and persistent gamma H2AX overexpression after UV damage. In contrast to that of the Csb-/- mouse models, the cerebella of the CSB-deficient rats are more profoundly affected. Both the molecular and the granular layers of the cerebellum cortex showed significant atrophy. The white matter of the cerebellum demonstrated high GFAP staining indicative of reactive astrogliosis. RNA-seq analysis of CSB-deficient rat cerebella revealed that even in the absence of UV damage, CSB affects the expression of hundreds of genes, many of which are neuronal genes, suggesting that transcription dysregulation could contribute to the neurological features in CSB rat models.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31644904" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126057" }, "primaryId" : "GEO:GSE126057", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126057" } ] }, "title" : "Deletion of the KH1 domain coding sequence of Fmr1 leads to transcriptional alterations and attentional deficits in rats", "dateAssigned" : "2019-02-04T00:00:00.000-06:00", "summary" : "We found that the previously published Fmr1 knockout rat model of FXS expresses an Fmr1 transcript with an in-frame deletion of exon 8, which encodes for the K-homology (KH) RNA-binding domain, KH1. We observed that the deletion of exon 8 in 10 male rats within the medial prefrontal cortex (mPFC) led to transcriptional alterations compared to 12 WT rats using RNAseq. Additionally, we used weighted gene co-expression network analysis to generate 23 modules specific to the mPFC with tissue from 35 WT rat samples.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30877790" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126059" }, "primaryId" : "GEO:GSE126059", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126059" } ] }, "title" : "Changes in mRNA in the dorsal root ganglion after stroke and subcutaneous neurotrophin-3 infusion in elderly rats", "dateAssigned" : "2019-02-04T00:00:00.000-06:00", "summary" : "Brain and spinal injury often impair sensorimotor processing in the spinal cord and reduce mobility. Cortical stroke in rats leads to long-term deficits in dexterity and walking. Subcutaneous neurotrophin-3 infusion initiated at a clinically-feasible time-point after injury improved walking and dexterity. We discovered that Neurotrophin-3 is transported in sensory afferents from muscles to the dorsal root ganglia. Using genome-wide RNA sequencing of the whole cervical level 6-8 dorsal root ganglia, we sought gene changes in afferent neurons that were present at two timepoints after stroke.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126062" }, "primaryId" : "GEO:GSE126062", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126062" } ] }, "title" : "Expression data from healthy and diastolic heart failure rats", "dateAssigned" : "2019-02-04T00:00:00.000-06:00", "summary" : "Heart failure (HF) with preserved ejection fraction (HFpEF) is rising, whose morbidity, mortality and healthcare costs are similar to HF with reduced ejection fraction (HFrEF). Although substantial molecular pathways lead to the changes in organ and tissue levels, there are still lack of successful treatments for HFpEF given the complexity molecular networks remaining unknown. Here we report that the significantly changed genes of HFpEF rats associates positively with inflammatory processes and immune responses while negatively with calcium ion transport into cytosol. GSEA analysis shows several KEGG pathways are significantly enriched in HFpEF rats including p53 signaling pathway, Toll like receptor signaling pathway and so on. Our study provides new insights into HFpEF pathogenesis and a new therapeutic against HFpEF.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126063" }, "primaryId" : "GEO:GSE126063", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126063" } ] }, "title" : "Self-renewal capability of hepatocytic parental progenitor cells derived from an adult rat liver is maintained for a long term in the chemically defined medium cultured on lamini111", "dateAssigned" : "2019-02-04T00:00:00.000-06:00", "summary" : "We analyzed gene expression of hepatocytic parental progenitor cells cultured on laminin (LN) 111, LN511 and Matrigel (Mat) in a population of small hepatocytes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126087" }, "primaryId" : "GEO:GSE126087", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126087" } ] }, "title" : "α1ACT is essential for survival and early cerebellar programming in a critical neonatal window [RNA-Seq]", "dateAssigned" : "2019-02-05T00:00:00.000-06:00", "summary" : "Previous study has shown that alpha1ACT is a transcription factor involved with regulating neuronal gene expression. We performed a time-series RNA-seq study using pc12 cell lines stably expressing pcDNA3-alpha1ACT at 4 time points (6hr, 24hr, 3day, and 10day) to explore the transcriptional profiles that capture transient and prolonged dynamic changes regulated by alpha1ACT during cell cycle and differentiation", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30922876" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126088" }, "primaryId" : "GEO:GSE126088", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126088" } ] }, "title" : "α1ACT is essential for survival and early cerebellar programming in a critical neonatal window [ChIP-Seq]", "dateAssigned" : "2019-02-05T00:00:00.000-06:00", "summary" : "Previous study has shown that alpha1ACT is a transcription factor involved with regulating neuronal gene expression. We further performed ChIP-seq using pc12 cell lines stably expressing pcDNA3-alpha1ACT or control pcDNA3 vectors to identify genomic locus directly occupied by alpha1ACT", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30922876" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126104" }, "primaryId" : "GEO:GSE126104", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126104" } ] }, "title" : "Identification of candidate genes and pathways in dexmedetomidine-induced cardioprotection in the rat heart by bioinformatics analysis [mRNA]", "dateAssigned" : "2019-02-05T00:00:00.000-06:00", "summary" : "Differentially expressed miRNAs and mRNAs after dexmedetomidine administration in rat hearts were successfully identified by conducting microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30939728" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126105" }, "primaryId" : "GEO:GSE126105", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126105" } ] }, "title" : "Identification of candidate genes and pathways in dexmedetomidine-induced cardioprotection in the rat heart by bioinformatics analysis [miRNA]", "dateAssigned" : "2019-02-05T00:00:00.000-06:00", "summary" : "Differentially expressed miRNAs and mRNAs after dexmedetomidine administration in rat hearts were successfully identified by conducting microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30939728" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126216" }, "primaryId" : "GEO:GSE126216", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126216" } ] }, "title" : "Transcriptomic impact of IMA-08401, a novel AHR-agonist resembling laquinimod, on rat liver", "dateAssigned" : "2019-02-07T00:00:00.000-06:00", "summary" : "IMA-08401 (C2) represents a novel AHR agonist and selective AHR modulator (SAHRM) that is structurally similar to laquinimod (LAQ). Although both compounds produce an identical AHR-active metabolite, IMA-06201 (DELAQ) in vivo, C2 generates it to a far greater degree. SAHRMs have been proposed as therapeutic options for autoimmune disorders, including multiple sclerosis. So far, clinical trials on LAQ have not reported any significant toxic outcomes and C2 has shown low toxicity in rats; however, more research is required due to the functional resemblance of these compounds to the highly toxic AHR agonist, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Here, we report transcriptomic profiling of rat liver following acute (single-dose) and sub-acute exposure (repeated dosing for 5 days followed by a 5-day recovery period) to high doses of C2. Exposure to C2 leads to activation of the AHR, as shown by changes in mRNA abundance of the prototypical AHR-response gene Cyp1a1. We identify a heightened response early after exposure (1 day) that drops off considerably by day 10. Acute exposure to C2 produces a significant immune response, with a focus on antiviral and antibacterial responses that highlights the dual effects of AhR agonists as immunomodulators. Sub-acute exposure leads to an increase in oxidative stress in the liver, the consequences of which require further study on sensitive tissues, such as the CNS and immune system which may be compromised in patients with the target autoimmune disorders.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30893768" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126237" }, "primaryId" : "GEO:GSE126237", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126237" } ] }, "title" : "Interleukin-6 modifies the expression profile of microRNA in rat primary skeletal muscle cells", "dateAssigned" : "2019-02-07T00:00:00.000-06:00", "summary" : "In order to verify the microarray data, qRT-PCR analysis was performed to quantify miRNA expression. We confirmed the increased expression of miR-154-3p (fold change =3.25) and miR-338-3p (fold change =3.37). Using Target Scan database we found potential targets for these miRNAs with expression modified by IL-6 and focused our further interest on genes involved in cytoskeleton organization and cell migration, that is: ephrinA4, pacsin3, actin, alpha-actinin, dyneins and desmin.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126246" }, "primaryId" : "GEO:GSE126246", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126246" } ] }, "title" : "Effect of liposome on gene expression of splenic macrophages", "dateAssigned" : "2019-02-07T00:00:00.000-06:00", "summary" : "Myeloid-derived suppressor cells (MDSC) are induced in various situations. Generation of MDSC has been investigated extensively. Several cytokines are involved in regulating MDSC. Cellular microvesicles, which comprise cellular membrane (single lipid bilayer) are involved in the induction of MDSC. Especially, proteins or nucleic acids encapsulated in them or expressed on their surface are thought to play a role in the induction of MDSC. Nevertheless, the role of lipid components remains to be investigated. Our earlier study using WKAH rat revealed that MDSC-like cells can be induced in the rat spleen by intravenous injection of liposomal microparticles. They comprise a single lipid bilayer of approximately 250 nm diameter, with no cellular component. Therefore, they resemble cellular microvesicles, Cells capable of suppressing T cell proliferation were liposome-internalized cells. The cell surface phenotype was class II low/-, CD11b/c+. Nitric oxide was responsible for their suppression. In this study, we showed that they express B7-H3 molecule on their surface, removal of B7-H3 positive cells restored T cell proliferation. Western blot analysis confirmed that they are positive for iNOS and NFkB was activated 4 hr after liposomal injection. These results indicate that these cells in question belongs to a subset of MDSCs. Furthermore, we elucidated that vesicular form of lipid is important for the induction of T cell suppressive function. Based on these data, we concluded that liposomal microparticles can induce B7-H3 positive MDSC in vivo and the vesicular formation of lipid is essential for the induction of MDSC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33070657" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126424" }, "primaryId" : "GEO:GSE126424", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126424" } ] }, "title" : "Cross-species association of microRNA expression in mammary epithelial cells with stem/progenitor characteristics and cancer susceptibility", "dateAssigned" : "2019-02-12T00:00:00.000-06:00", "summary" : "Comparison of mammosphere-derived epithelial cells across breast cancer susceptible and resistant species", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126510" }, "primaryId" : "GEO:GSE126510", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126510" } ] }, "title" : "Glucocorticoid action in the hippocampus revealed by integrated genome-wide ChIP and RNA analysis [ChIP-seq]", "dateAssigned" : "2019-02-13T00:00:00.000-06:00", "summary" : "Glucocorticoid hormones (GCs) play a critical role in physiological regulation and behavioural adaptation through mineralocorticoid (MR)- and glucocorticoid receptor (GR)-mediated actions in the hippocampus. We conducted genome-wide MR and GR ChIP-Seq studies on rat hippocampus to elucidate MR- and GR-regulated genes under physiological conditions like acute stress and circadian variation. Rat hippocampus tissue was collected under early morning baseline conditions, at 30 min after the start of a 15-min forced swim session (acute stress), or under late afternoon baseline conditions. We identified many genomic loci in which MR and/or GR binds following acute stress or due the circadian rise in GC secretion.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36942087" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126556" }, "primaryId" : "GEO:GSE126556", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126556" } ] }, "title" : "CREB mediates transient and sustained genomic responses to cAMP via distinct mechanisms [ChIP-seq]", "dateAssigned" : "2019-02-14T00:00:00.000-06:00", "summary" : "We investigated genome-wide occupancy of CREB, CREB coactivators, lineage determining transcription factors and histone acetylation to uncover mechanisms behind tissue-specific gene induction by cAMP in pancreatic islets. CREB mediates effects of cAMP on cellular gene expression. Most core CREB target genes are ubiquitously induced following recruitment of CREB and its coactivators to promoter proximal binding sites. We found that CREB stimulates the expression of pancreatic beta cell genes by binding to sites within distal enhancers. By contrast with its transient effects on core target genes, CREB stimulates pancreatic beta cell specific gene expression in a sustained manner, reflecting increases in the CBP-mediated acetylation of resident nucleosomes that recruit the chromatin reader BRD4. CREB cooperates with the lineage specific activator Neurod1 in establishing cAMP-responsive enhancers in beta cells. As deletion of a CREB-Neurod1 bound enhancer within the Lrrc10b-Syt7 super-enhancer locus disrupted the expression of both genes and decreased glucose-induced insulin secretion, our results demonstrate how cooperativity between signal dependent and lineage determining factors promotes the expression of cell type-specific gene programs in response to extracellular cues.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31182641" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126557" }, "primaryId" : "GEO:GSE126557", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126557" } ] }, "title" : "CREB mediates transient and sustained genomic responses to cAMP via distinct mechanisms [RNA-seq]", "dateAssigned" : "2019-02-14T00:00:00.000-06:00", "summary" : "We investigated genome-wide occupancy of CREB, CREB coactivators, lineage determining transcription factors and histone acetylation to uncover mechanisms behind tissue-specific gene induction by cAMP in pancreatic islets. CREB mediates effects of cAMP on cellular gene expression. Most core CREB target genes are ubiquitously induced following recruitment of CREB and its coactivators to promoter proximal binding sites. We found that CREB stimulates the expression of pancreatic beta cell genes by binding to sites within distal enhancers. By contrast with its transient effects on core target genes, CREB stimulates pancreatic beta cell specific gene expression in a sustained manner, reflecting increases in the CBP-mediated acetylation of resident nucleosomes that recruit the chromatin reader BRD4. CREB cooperates with the lineage specific activator Neurod1 in establishing cAMP-responsive enhancers in beta cells. As deletion of a CREB-Neurod1 bound enhancer within the Lrrc10b-Syt7 super-enhancer locus disrupted the expression of both genes and decreased glucose-induced insulin secretion, our results demonstrate how cooperativity between signal dependent and lineage determining factors promotes the expression of cell type-specific gene programs in response to extracellular cues.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31182641" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126627" }, "primaryId" : "GEO:GSE126627", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126627" } ] }, "title" : "Oligonucleotide Microarrays Identified Potential Regulatory Genes Related To Early Outward Arterial Remodeling Induced By Tissue Plasminogen Activator", "dateAssigned" : "2019-02-15T00:00:00.000-06:00", "summary" : "Constrictive vascular remodeling limiting blood flow, as well as compensatory outward remodeling, have been observed in many cardiovascular diseases; however, the underlying mechanisms regulating the remodeling response of the vessels remain unclear. Plasminogen activators (PA) are involved in many of the processes of vascular remodeling. We have shown previously that increased tissue-type PA (tPA) contributes to outward vascular remodeling. To elucidate the mechanisms involved in the induction of outward remodeling we characterized changes in the expression profiles of 8799 genes in injured rat carotid arteries one and four days after recombinant tPA treatment compared to vehicle. Periadventitial tPA significantly increased lumen size and vessel area, encompassed by the external elastic lamina, at both one and four days after treatment. Among 41 differentially expressed known genes one day after tPA application, 5 genes were involved in gene transcription, 5 genes were related to the regulation of vascular tone (for example, thromboxane A2 receptor (D32080) or nonselective-type endothelin receptor (S65355)), and 8 genes were identified as participating in vascular innervation (for example, calpain (D14478) or neural cell adhesion molecule L1 (X59149)). Four days after injury in tPA-treated arteries, 4 genes, regulating vascular tone, were differentially expressed. Thus, tPA promotes outward arterial remodeling after injury, at least in part, by regulating expression of genes in the vessel wall related to function of the nervous system and vascular tone.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126705" }, "primaryId" : "GEO:GSE126705", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126705" } ] }, "title" : "Glucocorticoid action in the hippocampus revealed by integrated genome-wide ChIP and RNA analysis (RNA-seq)", "dateAssigned" : "2019-02-18T00:00:00.000-06:00", "summary" : "We conducted Ribo-Zero RNA-Seq studies on rat hippocampus to elucidate changes in RNA expression in the hippocampus under physiological conditions such as acute stress and circadian variation. Rats were subjected to 15-min forced swim (FS) session and hippocampus tissue was collected at 30, 60, 120, 180 or 360 minutes after the onset of swimming. Tissues were also collected under early morning baseline (BL AM) or late afternoon baseline (BL PM) conditions. Based on this analysis, we have identified many genes that are differentially expressed as a result of acute stress exposure and circadian variation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36942087" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126709" }, "primaryId" : "GEO:GSE126709", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126709" } ] }, "title" : "Expression data from myocardial tissue from Spontaneously hypertensive rat (SHR) and its minimal congenic strain PD5", "dateAssigned" : "2019-02-18T00:00:00.000-06:00", "summary" : "We used microarray aproach to unravel gene expression differences between SHR and PD5 responsible for the different phenotypes in our rat strains.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126711" }, "primaryId" : "GEO:GSE126711", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126711" } ] }, "title" : "Left atrial tissue of rats exposed to rapid atrial pacing", "dateAssigned" : "2019-02-18T00:00:00.000-06:00", "summary" : "The effects of atrial tachypacing are well documented in large mammals but very little is know regarding the effects of tacypacing on the rodent atria.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31616316" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126773" }, "primaryId" : "GEO:GSE126773", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126773" } ] }, "title" : "Chemotherapy neurotoxicity is codependent on cancer", "dateAssigned" : "2019-02-19T00:00:00.000-06:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying neurologic dysfunction following chemotherapy treatment in animals bearing and not bearing cancer.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126796" }, "primaryId" : "GEO:GSE126796", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126796" } ] }, "title" : "Next Generation Sequencing Facilitates Quantitative Analysis of control, NDEA, NDEA + CFT-1 and NDEA+FYT Transcriptomes", "dateAssigned" : "2019-02-20T00:00:00.000-06:00", "summary" : "Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31428352" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126835" }, "primaryId" : "GEO:GSE126835", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126835" } ] }, "title" : "Goto-Kakizaki rats with Roux-en-Y gastric bypass surgery", "dateAssigned" : "2019-02-20T00:00:00.000-06:00", "summary" : "Roux-en-Y gastric bypass (RYGB), as one of the most effective metabolic operations, excludes a portion of stomach with the proximal intestine (biliopancreatic limb, BL) and rearranges the distal end of the intestine into a Y-configuration, in which food can flow from the upper stomach pouch through the Roux limb (RL). To address the above questions to RYGB surgery, we designed a series of surgical procedures in Goto-Kakizaki （GK） rats to assess the relationship between glycemic control independent of weight loss and RL length in the RYGB procedure and studied the molecular mechanism of the RL from a systematic and comprehensive view.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32025334" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126841" }, "primaryId" : "GEO:GSE126841", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126841" } ] }, "title" : "Intracellular Zn2+ transients modulate global gene expression in dissociated rat hippocampal neurons", "dateAssigned" : "2019-02-20T00:00:00.000-06:00", "summary" : "Zinc (Zn2+) is an integral component of many proteins and has been shown to act in a regulatory capacity in different mammalian systems, including as a neurotransmitter in neurons throughout the brain. While Zn2+ plays an important role in modulating neuronal potentiation and synaptic plasticity, little is known about the signaling mechanisms of this regulation. In dissociated rat hippocampal neuron cultures, we used fluorescent Zn2+ sensors to rigorously define resting Zn2+ levels and stimulation-dependent intracellular Zn2+ dynamics, and we performed RNA-Seq to characterize Zn2+-dependent transcriptional effects upon stimulation. We found that relatively small changes in cytosolic Zn2+ during stimulation altered expression levels of 931 genes, and these Zn2+ dynamics induced transcription of many genes implicated in neurite expansion and synaptic growth. Additionally, while we were unable to verify the presence of synaptic Zn2+ in these cultures, we did detect the synaptic vesicle Zn2+ transporter ZnT3 and found it to be substantially upregulated by cytosolic Zn2+ increases. These results provide the first global sequencing-based examination of Zn2+-dependent changes in transcription and identify genes that may mediate Zn2+-dependent processes and functions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31253848" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126883" }, "primaryId" : "GEO:GSE126883", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126883" } ] }, "title" : "Expression data from young and old nucleus pulposus stem cells", "dateAssigned" : "2019-02-21T00:00:00.000-06:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying NPMSCs aging and identified distinct classes of up and down-regulated genes during this process", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31379949" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126946" }, "primaryId" : "GEO:GSE126946", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE126946" } ] }, "title" : "Neonatal intermittent hypoxia exposure sex-specifically augments rat microglial cytokine expression acutely and long-term", "dateAssigned" : "2019-02-22T00:00:00.000-06:00", "summary" : "We analyzed gene expression via RNA-sequencing in microglia isolated from postnatal day 9 rats exposed to normoxia or intermittent hypoxia, in the presence or absence of lipopolysaccharide", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127000" }, "primaryId" : "GEO:GSE127000", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127000" } ] }, "title" : "Transcriptomic Analysis in Renal T Lymphocytes Exposes Sodium-Independent Dietary Differences in Dahl Salt-Sensitive Rats", "dateAssigned" : "2019-02-25T00:00:00.000-06:00", "summary" : "Conclusions. These functional and transcriptomic T-cell differences between SS/MCW and SS/CRL show that sodium-independent dietary effects may influence the immune response and infiltration of immune cells into the kidney, ultimately impacting susceptibility to salt-induced hypertension and renal damage.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31476910" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127214" }, "primaryId" : "GEO:GSE127214", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127214" } ] }, "title" : "Dynamic chromatin targeting of BRD4 stimulates cardiac fibroblast activation [ChIP-seq]", "dateAssigned" : "2019-02-26T00:00:00.000-06:00", "summary" : "Small molecule inhibitors of the acetyl-histone binding protein BRD4 have been shown to block cardiac fibrosis in pre-clinical models of heart failure (HF). However, the mechanisms by which BRD4 promotes pathological myocardial fibrosis remain unclear. Here, we demonstrate that BRD4 functions as an effector of TGF-b signaling to stimulate conversion of quiescent cardiac fibroblasts into Periostin (Postn)-positive cells that express high levels of extracellular matrix. BRD4 undergoes stimulus-dependent, genome-wide redistribution in cardiac fibroblasts, becoming enriched on a subset of enhancers and super-enhancers, and leading to RNA polymerase II activation and expression of downstream target genes. Employing the SERTA domain-containing protein 4 (Sertad4) locus as a prototype, we demonstrate that dynamic chromatin targeting of BRD4 is controlled, in part, by p38 mitogen-activated protein kinase, and provide evidence of a novel function for Sertad4 in TGF-b-mediated cardiac fibroblast activation. These findings define BRD4 as a central regulator of the pro-fibrotic cell state of cardiac fibroblasts, and establish a signaling circuit for epigenetic reprogramming in HF.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31409188" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127229" }, "primaryId" : "GEO:GSE127229", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127229" } ] }, "title" : "Dynamic chromatin targeting of BRD4 stimulates cardiac fibroblast activation [RNA-seq]", "dateAssigned" : "2019-02-26T00:00:00.000-06:00", "summary" : "Small molecule inhibitors of the acetyl-histone binding protein BRD4 have been shown to block cardiac fibrosis in pre-clinical models of heart failure (HF). However, the mechanisms by which BRD4 promotes pathological myocardial fibrosis remain unclear. Here, we demonstrate that BRD4 functions as an effector of TGF-b signaling to stimulate conversion of quiescent cardiac fibroblasts into Periostin (Postn)-positive cells that express high levels of extracellular matrix. BRD4 undergoes stimulus-dependent, genome-wide redistribution in cardiac fibroblasts, becoming enriched on a subset of enhancers and super-enhancers, and leading to RNA polymerase II activation and expression of downstream target genes. Employing the SERTA domain-containing protein 4 (Sertad4) locus as a prototype, we demonstrate that dynamic chromatin targeting of BRD4 is controlled, in part, by p38 mitogen-activated protein kinase, and provide evidence of a novel function for Sertad4 in TGF-b-mediated cardiac fibroblast activation. These findings define BRD4 as a central regulator of the pro-fibrotic cell state of cardiac fibroblasts, and establish a signaling circuit for epigenetic reprogramming in HF.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31409188" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127248" }, "primaryId" : "GEO:GSE127248", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127248" } ] }, "title" : "DMSO cryopreservation: the method of choice for droplet-based single-cell RNA sequencing of preserved cells [10X Genomics]", "dateAssigned" : "2019-02-27T00:00:00.000-06:00", "summary" : "Recently, combining single-cell RNA sequencing (scRNA-seq) with upstream cell preservation procedures such as cryopreservation or methanol fixation has become more common. By separating cell handling and preparation, from downstream library generation, scRNA-seq workflows are more flexible and manageable. However, the inherent transcriptomics changes associated with cell preservation and how they may bias further downstream analysis remain unknown. Here, we present a side-by-side droplet-based scRNA-seq analysis, comparing the gold standard – fresh cells – to three different cell preservation workflows: dimethyl sulfoxide based cryopreservation, methanol fixation and CellCover reagent. Cryopreservation proved to be the most robust protocol, maximizing both cell integrity and low background ambient RNA. Importantly, gene expression profiles from fresh cells correlated most with those of cryopreserved cells. Such similarities were consistently observed across the tested cell lines (R≥0.97), monocyte-derived macrophages (R=0.97) and immune cells (R=0.99). In contrast, both methanol fixation and CellCover preservation showed an increased ambient RNA background and an overall lower gene expression correlation to fresh cells. Thus, our results demonstrate the superiority of cryopreservation over other cell preservation methods. We expect our comparative study to provide single cell omics researchers invaluable support when integrating cell preservation into their scRNA-seq studies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31337793" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127254" }, "primaryId" : "GEO:GSE127254", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127254" } ] }, "title" : "Maternal cadmium exposure during pregnancy changes DNA methylation patterns in adult F1 rats ovarian granulosa cells.", "dateAssigned" : "2019-02-27T00:00:00.000-06:00", "summary" : "Cadmium is a heavy metal pollutant and environmental endocrine disruptor. Studies have shown that cadmium exposure, whether it occurs in adulthood, in puberty or during the period from weaning to sexual maturity, can produce notable toxic effects on ovarian cells, especially ovarian granulosa cells. However, the effects of prenatal cadmium exposure on the morphology, function and its epigenetic mechanism of ovarian granulosa cells in offspring during adulthood have not been reported.In this study,the promoter methylation was assessed using MeDIP-Chip and Several methods were used to analyze the scanned genes, including the Gene Ontology Consortium tools, hierarchical clustering and KEGG pathway analysis.The results indicated that multiple signaling pathways, including apoptosis and hormone synthesis related pathways were affected,besides, some genes DNA methylation status of apoptosis and hormone synthesis pathways were changed.In summary, our results provide a scientific basis for subsequent analyses of cadmium-induced ovarian granulosa cell damage and its epigenetic mechanism.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127272" }, "primaryId" : "GEO:GSE127272", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127272" } ] }, "title" : "Mating enhances expression of hormonal and trophic factors in the midbrain of female rats", "dateAssigned" : "2019-02-27T00:00:00.000-06:00", "summary" : "Microarrays revealed 53 target genes that were significantly up-regulated (> 2.0-fold change) in response to mating. Mating significantly enhanced midbrain mRNA expression of genes involved in hormonal and trophic actions: Gh1, S100g, and Klk1b3 in proestrous, but not OVX and/or ADX, rats; Fshb in all but OVX/ADX rats; and Lhb and Tshb in all rats. Thus, mating enhances midbrain gene expression, independent and dependent of, peripheral glands.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127793" }, "primaryId" : "GEO:GSE127793", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127793" } ] }, "title" : "Characterization of Npas4 and heterodimer DNA binding in stimulated and silenced rat neurons", "dateAssigned" : "2019-03-04T00:00:00.000-06:00", "summary" : "We evaluated genome-wide DNA binding of NPAS4, ARNT1, ARNT2, H3K27ac, and RNAPII by chromatin immunoprecipitation sequencing (ChIP-seq) in mature primary hippocampal neurons (rat, DIV 28) that were pharmacologically silenced (“–”; 24 hours in TTX, CPP, and NBQX) or silenced and then treated with PTX for two hours (“+”) to trigger the production of AP- and EPSP-induced NPAS4.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31585079" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127794" }, "primaryId" : "GEO:GSE127794", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127794" } ] }, "title" : "RNAseq analysis of primary differentiated rat aorta tissue compared to proliferative cultured cells", "dateAssigned" : "2019-03-04T00:00:00.000-06:00", "summary" : "Investigation of alternative splicing changes in rat smooth muscle aorta differentiated tissue compared to dedifferentiated proliferative aorta smooth muscle cells in culture.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31283468" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127799" }, "primaryId" : "GEO:GSE127799", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127799" } ] }, "title" : "RBPMS knockdown and overexpression in rat PAC1 pulmonary artery smooth muscle cells (SMCs)", "dateAssigned" : "2019-03-04T00:00:00.000-06:00", "summary" : "Investigation of RBPMS role in post-transcriptional control of mRNAs in rat PAC1 pulmonary artery smooth muscle cells (SMCs). PolyA mRNA-Seq was carried out after RBPMS knockdown in differentiated PAC1 cells and after inducible RBPMS-A overexpression in dedifferentiated (proliferative) PAC1 cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31283468" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127945" }, "primaryId" : "GEO:GSE127945", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127945" } ] }, "title" : "Printer emitted particles (PEPs) exposed rat blood mRNA expression profiling", "dateAssigned" : "2019-03-06T00:00:00.000-06:00", "summary" : "The rats were exposed to printer emitted particles PEPs (exposed) and high efficiency particulate air (HEPA) filtered air (control). Animals were sacrificed on 1, 5, 9, 13, 17 and 21 days for blood collection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31888290" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127947" }, "primaryId" : "GEO:GSE127947", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127947" } ] }, "title" : "Printer emitted particles (PEPs) exposed rat blood miRNA expression profiling", "dateAssigned" : "2019-03-06T00:00:00.000-06:00", "summary" : "The rats were exposed to printer emitted particles PEPs (exposed) and high efficiency particulate air (HEPA) filtered air (control). Animals were sacrificed on 1, 5, 9, 13, 17 and 21 days for blood collection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31888290" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127949" }, "primaryId" : "GEO:GSE127949", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127949" } ] }, "title" : "Printer emitted particles (PEPs) exposed rat lung mRNA expression profiling", "dateAssigned" : "2019-03-06T00:00:00.000-06:00", "summary" : "The rats were exposed to printer emitted particles PEPs (exposed) and high efficiency particulate air (HEPA) filtered air (control). Animals were sacrificed on 1, 5, 9, and 21 days for lung tissue collection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31888290" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127950" }, "primaryId" : "GEO:GSE127950", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE127950" } ] }, "title" : "Printer emitted particles (PEPs) exposed rat lung miRNA expression profiling", "dateAssigned" : "2019-03-06T00:00:00.000-06:00", "summary" : "The rats were exposed to printer emitted particles PEPs (exposed) and high efficiency particulate air (HEPA) filtered air (control). Animals were sacrificed on 1, 5, 9, and 21 days for lung tissue collection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31888290" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128090" }, "primaryId" : "GEO:GSE128090", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128090" } ] }, "title" : "Recovery of the synaptic transmission genomic fabrics in the hypothalamic paraventricular nucleus of a rat model of autism treated with PMX53", "dateAssigned" : "2019-03-11T00:00:00.000-05:00", "summary" : "We profiled the whole transcriptomes of male and female rat hypothalamic paraventricular nuclei to determine the remodeling of the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission in epilepsy and recovery following treatment with PMX53. The rats were prenatally exposed (G15) to betamethasone followed by repeated adiministration of N-Methyl-D-Aspartic acid (NMDA) on postnatal days 12, 13 and 15 which triggered infantile spasms and autistic behavior. Pups were treated with PMX53 (a potent C5ar1 antagonist) on days 13, 14 and 15 prior to NMDA administration to determine what effects the treatment had on transcriptome recovery. Our Genomic Fabric Paradigm (GFP) is proposed as a transformative research approach to enhance the understanding of the brain transcriptomic alterations in epileptic rats and recovery following various treatments. The genomic fabric of a particular synapse is the structured transcriptome associated with the most interconnected and stably expressed gene network responsible for that type of neurotransmission. GFP refines the description of functional pathways by selecting the most prominent genes and determining their networking. Moreover, it quantifies the remodeling of functional pathways and their interplay in disease and recovery in response to a treatment. We found that priming with betamethasone had substantial consequences on the topology of the genomic fabrics of all kind of synaptic transmission, that NMDA-induced spasms strongly exacerbated the remodeling of these fabrics and that PMX53 treatment recovered partially the the normal synaptic transcriptomes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128091" }, "primaryId" : "GEO:GSE128091", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128091" } ] }, "title" : "Remodeling of synaptic transmission genomic fabrics in the hypothalamic paraventricular nucleus of a rat model of autism", "dateAssigned" : "2019-03-11T00:00:00.000-05:00", "summary" : "We profiled the whole transcriptomes of male and female rat hypothalamic paraventricular nuclei to determine the remodeling of the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission in autism. The rats were prenatally exposed (G15) to betamethasone followed by repeated adiministration of N-Methyl-D-Aspartic acid on postnatal days 12, 13 and 15 which triggered the infantile spasms and autism spectrum disease behavior. Pups were treated with saline on days 13, 14 and 15 prior to NMDA administration. Our Genomic Fabric Paradigm (GFP) is proposed as a transformative research approach to enhance the understanding of the brain transcriptomic alterations in autistic rats . The genomic fabric of a particular synapse is the structured transcriptome associated with the most interconnected and stably expressed gene network responsible for that type of neurotransmission. GFP refines the description of functional pathways by selecting the most prominent genes and determining their networking. Moreover, it quantifies the remodeling of functional pathways and their interplay in disease and recovery in response to a treatment. We found that priming with betamethasone had substantial consequences on the topology of the genomic fabrics of all kind of synaptic transmission and that NMDA-induced spasms strongly exacerbated the remodeling of these fabrics.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128093" }, "primaryId" : "GEO:GSE128093", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128093" } ] }, "title" : "A small molecule promotes cartilage extracellular matrix generation and inhibits osteoarthritis development", "dateAssigned" : "2019-03-11T00:00:00.000-05:00", "summary" : "These observations identify SOD3 as a relevant drug target, and BNTA as a potential therapeutic agent in osteoarthritis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31015473" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128136" }, "primaryId" : "GEO:GSE128136", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128136" } ] }, "title" : "Full-length transcriptome reconstruction reveals large diversity of RNA isoforms and open reading frames in rat hippocampus", "dateAssigned" : "2019-03-11T00:00:00.000-05:00", "summary" : "We developed a hybrid-sequencing workflow, combining next-generation and third-generation sequencing, to reconstruct full-length transcriptomes. Integrating with polysome profiling and ribosome footprinting data, we predicted isoform–specific translational status and reconstructed ORFeome. Moreover, we identified isoforms with specific subcellular localization pattern in neurons.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31676752" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128167" }, "primaryId" : "GEO:GSE128167", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128167" } ] }, "title" : "Different Gene Expression Profile in Spontaneously Hypertensive Rats Treated with Songling Xuemaikang Capsule", "dateAssigned" : "2019-03-12T00:00:00.000-05:00", "summary" : "To study in vivo action of Songling Xuemaikang Capsule (SXC), SHRs were orally administration with high- or low-dose of SXC for 28 days.Valsartan, an angiotensin receptor antagonist, is used as a positive control drug in this study and orally administrated for 28 days. The levels of AngII, Aldosterone in serum of SHRs from different groups were analyzed, and gene expression profiling were performed in the thoracic aortakidney of SHRs, using the Whole Rat Genome Oligonucleotide Microarray. The integrated causal network analysis is performed to understand the mechanism of antihypertensive effect of SXC. The results showed that expression of 706 unique genes (p<0.05) were changed (fold change >2.0) in SHRs at a dose of 472.5 mg/kg day SXC when compared with control rats, whereas the expression of 920 unique genes were changed (fold change>2.0) at a dose of 1417.5 mg/kg/day. Those genes are involved in lipid metabolism, complement system induced immune response, inflammation and vascular and endothelial dysfunction.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128451" }, "primaryId" : "GEO:GSE128451", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128451" } ] }, "title" : "Expression data of lung tissues of rats exposed to chronic hypoxia", "dateAssigned" : "2019-03-18T00:00:00.000-05:00", "summary" : "We used microarrays to screen out miRNAs related to VEGF/Notch pathway in hypoxic exposure, and in this process, we found genes with a downregulation trend with prolonged exposure time.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128618" }, "primaryId" : "GEO:GSE128618", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128618" } ] }, "title" : "Activation of β-adrenoceptor signaling inhibits extracellular matrix deposition of human bladder smooth muscle cells", "dateAssigned" : "2019-03-20T00:00:00.000-05:00", "summary" : "To extensively explore its underlying mechanism, our study aims to investigate the effect of β-adrenoceptor (ADRB) signaling on the ECM of human bladder smooth muscle cells (hBSMCs) exposed to pathological hydrostatic pressure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128777" }, "primaryId" : "GEO:GSE128777", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128777" } ] }, "title" : "Transcriptome analysis of the brain and testis of the human-derived DNMT3A transgenic rat", "dateAssigned" : "2019-03-25T00:00:00.000-05:00", "summary" : "We performed global gene expression profiling of transgenic rat brain and testis tissues using mRNA sequencing (mRNA-seq) to investigate the impact of epigenetic modifier overexpression on tissue gene expression patterns.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128824" }, "primaryId" : "GEO:GSE128824", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128824" } ] }, "title" : "Transcriptional Profiling of Maternal and Fetal Organs following Rat In Utero TCDD or TCDF Exposure", "dateAssigned" : "2019-03-25T00:00:00.000-05:00", "summary" : "We report the RNAseq-based transcriptome profiles of rat gestation day 20 dam liver, fetal male and female liver, fetal male pituitary, and fetal testis following in utero exposure to either 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) or 2,3,7,8-tetrachlorodibenzofuran (TCDF). Two exposure models were examined: 1) pregnant rats exposed to either a dose response series of TCDD or TCDF from gestation day 6 - 20 or 2) pregnant rats exposed to a single dose of TCDD or TCDF on gestation day 15. These data support a mode-of-action for dioxin-induced rat male reproductive toxicity involving key events in both the fetal pituitary (reduced gonadotropin production) and fetal testis (reduced Leydig cell cholesterologenesis and steroidogenesis) which are hypothesized to decrease perinatal Sertoli cell proliferation and culminate in reduced spermatogenesis. The lack of a TCDF effect on proposed key events may be due to a higher rate of metabolic clearance relative to TCDD.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128973" }, "primaryId" : "GEO:GSE128973", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128973" } ] }, "title" : "Neuron-astrocyte metabolic coupling protects against activity-induced fatty acid toxicity", "dateAssigned" : "2019-03-28T00:00:00.000-05:00", "summary" : "Gene expression profiling of cultured glia with low or high levels of lipid droplets", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31130380" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128992" }, "primaryId" : "GEO:GSE128992", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE128992" } ] }, "title" : "Identification of renal resident macrophages across species [10X]", "dateAssigned" : "2019-03-28T00:00:00.000-05:00", "summary" : "We use single cell RNA sequencing to identify an evolutionarily conserved gene expression signature in resident macrophages. Based on our single cell data, we show the presence of a core gene expression signature in a cluster of innate immune cells in mouse, rat, pig, and human kidney tissue. Further, using this gene expression signature, we identify novel candidate markers for resident macrophages that span all 4 species tested.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30948627" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129015" }, "primaryId" : "GEO:GSE129015", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129015" } ] }, "title" : "Distinct Hippocampal Expression Profiles of Long Non-coding RNAs in an Alzheimer’s Disease Model", "dateAssigned" : "2019-03-28T00:00:00.000-05:00", "summary" : "In the present study, we applied microarray technology to analyse the expression profiles of lncRNAs and messenger RNAs (mRNAs) in the hippocampus of rats in a validated AD model. Additionally, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the biological roles and potential signalling pathways of these differentially expressed lncRNAs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:27501805" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129051" }, "primaryId" : "GEO:GSE129051", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129051" } ] }, "title" : "Identifying circRNA-associated-ceRNA networks in the hippocampus of Aß1-42-induced Alzheimer's disease-like rats using microarray analysis (mRNA)", "dateAssigned" : "2019-03-29T00:00:00.000-05:00", "summary" : "In the present study, we used microarray analysis technology to characterize the expression patterns of circular RNAs (circRNAs), microRNAs (miRNAs), and mRNAs in hippocampal tissue from Aβ1‐42‐induced AD model rats, to integrate interaction data and thus provide novel insights into the mechanisms underlying AD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29706607" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129053" }, "primaryId" : "GEO:GSE129053", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129053" } ] }, "title" : "Identifying circRNA-associated-ceRNA networks in the hippocampus of Aß1-42-induced Alzheimer's disease-like rats using microarray analysis (miRNA)", "dateAssigned" : "2019-03-29T00:00:00.000-05:00", "summary" : "In the present study, we used microarray analysis technology to characterize the expression patterns of circular RNAs (circRNAs), microRNAs (miRNAs), and mRNAs in hippocampal tissue from Aβ1‐42‐induced AD model rats, to integrate interaction data and thus provide novel insights into the mechanisms underlying AD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29706607" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129054" }, "primaryId" : "GEO:GSE129054", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129054" } ] }, "title" : "Identifying circRNA-associated-ceRNA networks in the hippocampus of Aß1-42-induced Alzheimer's disease-like rats using microarray analysis (circRNA)", "dateAssigned" : "2019-03-29T00:00:00.000-05:00", "summary" : "In the present study, we used microarray analysis technology to characterize the expression patterns of circular RNAs (circRNAs), microRNAs (miRNAs), and mRNAs in hippocampal tissue from Aβ1‐42‐induced AD model rats, to integrate interaction data and thus provide novel insights into the mechanisms underlying AD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29706607" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129313" }, "primaryId" : "GEO:GSE129313", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129313" } ] }, "title" : "Inhalation exposure of hexanal in rats (DNA methylation)", "dateAssigned" : "2019-04-04T00:00:00.000-05:00", "summary" : "To further development of insight into the mechanism of toxicity, it is important to employ whole genome microarray expression profiling to identify and characterize DNA methylation profiles as a discovery platform relevant for toxicologic mechanisms of hexanal. DNA methylation have prominent epigenetic role in regulation of gene expression, cell cycle control, apoptosis, cancer development and proliferation-related processes. However, few reports have described the effect of hexanal on DNA methylation expression profiles using animal model. In this respect, we studied the expression profiles of DNA methylation in hexanal-exposed in rats by DNA methylation microarray analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129399" }, "primaryId" : "GEO:GSE129399", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129399" } ] }, "title" : "Therapeutic benefit of rapamycin combined with clorgyline or rasagiline in an immunodeficient LAM model", "dateAssigned" : "2019-04-05T00:00:00.000-05:00", "summary" : "Inhibition of mechanistic target of rapamycin (mTOR) constitutes the standard of care of lymphangioleiomyomatosis (LAM). However, this treatment does not eradicate diseased cells and some patients show progressive decline of lung function. This study provides preclinical evidence for beneficial therapeutic approaches in combination with rapamycin. LAM tumorigenesis is reduced in vivo (ELT3-V3 tumor xenografts) using approved drugs for other human diseases and targeting monoamine oxidase A (MAO-A; clorgyline) or MAO-B (rasagiline).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129458" }, "primaryId" : "GEO:GSE129458", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129458" } ] }, "title" : "Notch signaling controls periodontal ligament maturation through regulating Lamin A", "dateAssigned" : "2019-04-08T00:00:00.000-05:00", "summary" : "Tooth eruption is a continuous biological proces with dynamic changes at cellular and tissue levels particularly within the periodontal ligament (PDL). Occlusion completion is a significant physiological landmark of dentintion establishment. However the implication and molecular networks engaging in of this event on the the final PDL maturation are still largely unknown. In this study, using rat and mouse molar teeth and transgenic approaches, as well as a human PDL cell line by combining RNAseq and proteomic analysis systematically, we screened the key molecular links in regulating PDL maturation before and after occlusion establishiment. We discovered Notch, a key molecular pathway in regulating stem cell fate and differentiation, is a major player in the event. Intercepting Notch pathway by deleting its key canonical transtripitonal factor: RBP-Jkappa using conditional knocking out strategy in the mice delayed PDL maturation. We also identified that Lamin A, a cell nuclear lamina member, is one unique marker of PDL maturation and its expression is under the control of Notch signalling. Our study therefore provides a deep insight of how PDL maturation is regulated molecularly and we expect the outcomes to be applied to better understand the molecular regulation networks and physiological conditions such as tooth eruption and movement, and also for periodontal diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31461625" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129466" }, "primaryId" : "GEO:GSE129466", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129466" } ] }, "title" : "Effects of the Co-Administration of MK-801 and Clozapine on MiRNA Expression Profiles in Rats", "dateAssigned" : "2019-04-08T00:00:00.000-05:00", "summary" : "Conclusion: Our results suggested the altered miRNA expressions might play an important role in the complex pathophysiology of schizophrenia, and subsequently impacted on brain functions.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129525" }, "primaryId" : "GEO:GSE129525", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129525" } ] }, "title" : "Introducing a new pre-clinical rat model of advanced NASH by combining carbon tetrachloride with high fat & cholesterol diet", "dateAssigned" : "2019-04-09T00:00:00.000-05:00", "summary" : "NASH is a severe form of NAFLD that can progress to cirrhosis and hepatocellular carcinoma and, its incidence has markedly increased in recent years. Current available animal models fail to reflect the whole spectrum of the disease. We herein designed a Barcelona NASH (BarNa) rat model using the combination of high fat & cholesterol diet with CCl4 inhalation for 10 weeks (NASH) or 24 weeks (NASH-CH). This model reflects the full spectrum of human NASH and present the main characteristics of the disease including: steatosis and metabolic syndrome, lipotoxicity, cellular death, inflammation, hepatic fibrosis and portal hypertension. Moreover, the molecular signature of the BarNa model shared the most important pathways involved in the pathophysiology of the human disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31510105" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129539" }, "primaryId" : "GEO:GSE129539", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129539" } ] }, "title" : "MiR-29 regulates de novo lipogenesis and controls circulating triglyceride levels in a Sirt1-dependent manner", "dateAssigned" : "2019-04-09T00:00:00.000-05:00", "summary" : "Investigation of the effect of miR-29 on de novo lipogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31736786" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129545" }, "primaryId" : "GEO:GSE129545", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129545" } ] }, "title" : "Transcriptome analysis of Tbx18-induced pacemaker cells (TBX18-iPMs) in comparison to ventricular cardiomyocytes", "dateAssigned" : "2019-04-09T00:00:00.000-05:00", "summary" : "To understand the transcriptional landscape of Tbx18-induced cardiac pacemaker cells. The control cells were ventricular myocytes expressing GFP.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36006872" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129561" }, "primaryId" : "GEO:GSE129561", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129561" } ] }, "title" : "Differential gene expressions for androgen-induced benign prostatic hyperplysia rat underwent oral treatment of metabolic peptide ghrelin", "dateAssigned" : "2019-04-10T00:00:00.000-05:00", "summary" : "To preliminary distinguish differential gene expressions in BPH-rat prostate after oral treatment of ghrelin.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31885795" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129598" }, "primaryId" : "GEO:GSE129598", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129598" } ] }, "title" : "Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation", "dateAssigned" : "2019-04-10T00:00:00.000-05:00", "summary" : "Loss of functional cardiomyocytes is a major determinant of heart failure after myocardial infarction. Previous high throughput screening studies have identified a series of microRNAs that induce cardiomyocyte proliferation and stimulate cardiac regeneration after myocardial infarction. Here we investigate the mechanism of action of the top ten most effective of these miRNAs. Analysis of the transcriptional profile of miRNA-treated cardiomyocytes revealed an involvement of the Hippo-YAP pathway in their action. All the investigated miRNAs activated YAP-mediated transcription, nuclear localization of active YAP and increased expression of YAP responsive genes. In particular, miR-199a-3p, one of the most effective miRNAs, directly downregulated two mRNA targets impinging on the Hippo pathway, the upstream inhibitory kinase TAOK1and the E3 ubiquitin ligase destroying YAP, b-TrCP. Most of the miRNAs that promoted proliferation also modulated the dynamics of the cardiomyocyte actin cytoskeleton. In particular, four miRNAs targeted Cofilin2 and increased the ratio between polymerized F-actin and monomeric G-actin. Cells treated with the most effective miRNAs (including miR-199a-3p) were round-shaped, with formation of gross bundles of actin fibers at the cytoplasm periphery. During mitosis, these miRNA-treated cardiomyocytes displayed disruption of the sarcomeric architecture. Downregulation of Cofilin2 itself was sufficient to promote cardiomyocyte proliferation, activate nuclear translocation of YAP and stimulate transcription of TEAD-responsive genes. Inhibition of F-actin polymerization decreased YAP activation. Collectively, these results indicate that activation of YAP and modulation of the acting cytoskeleton are major components of the pro-proliferative effect of miR-199a-3p and other miRNAs inducing cardiomyocyte proliferation", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31141697" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129685" }, "primaryId" : "GEO:GSE129685", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129685" } ] }, "title" : "tRNA-derived small non-coding RNAs as novel epigenetic molecules regulating adipogenesis", "dateAssigned" : "2019-04-11T00:00:00.000-05:00", "summary" : "tRNA-derived fragments (tRFs) are a novel class of non-coding RNA that play an vital role in regulating gene expression at post-transcriptional level. To date, it is completely unknown the regulatory mechanism of tRFs governing fat deposition and adipogenesis. In this study, we used high fat diet successfully induced obese rat model, and used tRFs transcriptome sequencing to select differentially expressed tRFs that response to obesity. We found tRFGluTTC was the highest fold change in the 296 differentially expressed tRFs, which promoted preadipocytes proliferation by increasing the expression of cell cycle regulatory factors. Moreover, tRFGluTTC also suppressed preadipocytes differentiation by reducing lipid accumulation and triglyceride content, and decreasing the expression of genes related to fatty acid synthesis. According to luciferase activity assays, tRFGluTTC directly targeted KLF9, KLF11, and KLF12, and could significantly suppressed the mRNA expression of these target genes. Besides, tRFGluTTC suppressed adipogenesis also accompanied by decreasing the expression of adipogenic transcription factors (AP2, C/EBPα, and PPARγ). Taken together, these results imply that tRFGluTTC may take as a novel epigenetic molecules governing adipogenesis and could be a target for therapeutic intervention in obesity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31336727" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129694" }, "primaryId" : "GEO:GSE129694", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129694" } ] }, "title" : "Transcriptional changes in soleus muscle for rats exposed to different activities after contusion injury to the spinal cord and transcriptional changes in soleus muscle with complete spinal cord transection injury", "dateAssigned" : "2019-04-11T00:00:00.000-05:00", "summary" : "Spinal cord injury (SCI) is a devastating clinical condition resulting in significant disabilities for affected individuals. Apart from local injury within the spinal cord, SCI patients develop a myriad of complications characterized by multi-organ dysfunction. Disorders, such as lung injury, cardiovascular disease, liver damage, kidney and urinary tract dysfunction, alterations in gut microbiome, neuropathic pain, depression and altered immune responses are common in SCI patients. Such whole body, systemic responses hinder the functional recovery and can be life-threatening in SCI population. Investigations of organ specific gene expression analyses can provide a better understanding of the injury response and identify molecular targets. Consequently, this can be used to develop treatment for SCI, promoting functional recovery and overall quality of life.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32226812" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129814" }, "primaryId" : "GEO:GSE129814", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129814" } ] }, "title" : "Genome-Scale Characterization of Toxicity-Induced Metabolic Alterations in Primary Hepatocytes", "dateAssigned" : "2019-04-15T00:00:00.000-05:00", "summary" : "Context-specific Genome-scale Metabolic Network Reconstructions (GENREs) provide a means to understand cellular metabolism at a deeper level of physiological detail. Here, we use transcriptomics data from chemically exposed rat hepatocytes to constrain a GENRE of rat hepatocyte metabolism and predict biomarkers of liver toxicity using the Transcriptionally Inferred Metabolic Biomarker Response (TIMBR) algorithm. We profiled alterations in cellular hepatocyte metabolism following in vitro exposure to three toxicants (acetaminophen, 2,3,7,8-tetrachlorodibenzodioxin, and trichloroethylene) for six hours. TIMBR predictions were compared with paired metabolomics data from the same exposure conditions. Agreement between computational model predictions and experimental data led to the identification of specific metabolites and thus metabolic pathways associated with toxicant exposure; where predictions and experimental data disagreed, we identified testable hypotheses to reconcile differences between the model predictions and experimental data. The presented pipeline for using paired transcriptomics and metabolomics data provides a framework for interrogating multiple omics datasets to generate mechanistic insight of metabolic changes associated with toxicological responses.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31501904" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129848" }, "primaryId" : "GEO:GSE129848", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129848" } ] }, "title" : "Prenatal hypoxia exposure induced methylomic and transcriptomic alterations in rat hearts [RNA-seq]", "dateAssigned" : "2019-04-15T00:00:00.000-05:00", "summary" : "Antenatal hypoxia has critial impacts on fetal heart development. The molecular mechanism of the antenaltal hypoxia effect on the heart development is still unknown. We performed DNA methylome and transcriptome analyses of antenatal hypoxia induced rat fetal and adult offspring hearts to understand the hypoxia-mediated epigenomic programming in the heart development. Heart tissue from fetal (E21) and adult rat (5 months old) were collected. mRNA and genomic DNA methylation profiles of the heart tissue were generated by RNAseq and reduced representation bisulfite seuqencing (RRBS) techniques. We found 323 and 112 differential expressed genes between control and hypoxia groups in the fetal and adult hearts, respectively. Meanwhile, 2828 and 2193 differential methylated regions were identified in the fetal and adult hearts. Furthermore, opposite gobal DNA methylation pattern changes in transcription start site regions (TSS ± 1kb) were observed between fetal and adult hearts. Combining transcriptome, data indicates a significant difference in the responding genes and pathways between fetal and adult hearts in responding to the antenatal hypoxia. Our study provides an initial framework and new insights into fetal hypoxia-mediated epigenetic programming of pro-inflammatory phenotype in the heart development, linking antenatal stress, and developmental programming of heart vulnerability to disease later in life.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31664036" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129874" }, "primaryId" : "GEO:GSE129874", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129874" } ] }, "title" : "Prenatal hypoxia exposure induced methylomic and transcriptomic alterations in rat hearts [BiSulfite-seq]", "dateAssigned" : "2019-04-16T00:00:00.000-05:00", "summary" : "Antenatal hypoxia has critial impacts on fetal heart development. The molecular mechanism of the antenaltal hypoxia effect on the heart development is still unknown. We performed DNA methylome and transcriptome analyses of antenatal hypoxia induced rat fetal and adult offspring hearts to understand the hypoxia-mediated epigenomic programming in the heart development. Heart tissue from fetal (E21) and adult rat (5 months old) were collected. mRNA and genomic DNA methylation profiles of the heart tissue were generated by RNAseq and reduced representation bisulfite seuqencing (RRBS) techniques. We found 323 and 112 differential expressed genes between control and hypoxia groups in the fetal and adult hearts, respectively. Meanwhile, 2828 and 2193 differential methylated regions were identified in the fetal and adult hearts. Furthermore, opposite gobal DNA methylation pattern changes in transcription start site regions (TSS ± 1kb) were observed between fetal and adult hearts. Combining transcriptome, data indicates a significant difference in the responding genes and pathways between fetal and adult hearts in responding to the antenatal hypoxia. Our study provides an initial framework and new insights into fetal hypoxia-mediated epigenetic programming of pro-inflammatory phenotype in the heart development, linking antenatal stress, and developmental programming of heart vulnerability to disease later in life.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129908" }, "primaryId" : "GEO:GSE129908", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129908" } ] }, "title" : "C6 glioblastoma microRNA regulation induced by haloperidol, risperidone and clozapine", "dateAssigned" : "2019-04-16T00:00:00.000-05:00", "summary" : "Antipsychotic drugs (APDs) have been reported to ease psychotic symptoms in the clinic. miRNAs have also been identified that can regulate the expression of genes/proteins related to possible molecular mechanisms of drug action. To reveal APD-induced miRNA modulations in glial cells, we analyzed miRNA expression in subchronically APD-treated C6 cells by using a miRNA microarray.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129924" }, "primaryId" : "GEO:GSE129924", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129924" } ] }, "title" : "Free circular introns with an unusual branchpoint in neuronal projections", "dateAssigned" : "2019-04-16T00:00:00.000-05:00", "summary" : "In eukaryotic cells, most introns are degraded soon after splicing in the nucleus but some persist either due to lack of splicing (detained/retained introns) or because they contain important functional elements, for example, sno/scaRNAs. Few introns are detectable outside the nucleus. To hunt for interesting new phenomena in cytoplasmic introns and splicing, we conducted a multimodal study of total RNA within projections (axons, dendrites, glial projections) of rat hippocampal neurons and discovered a class of free circular introns enriched in distal projections.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31697236" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129991" }, "primaryId" : "GEO:GSE129991", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129991" } ] }, "title" : "Gene expression profiling of Fischer rat thyroid (FRT) cells", "dateAssigned" : "2019-04-17T00:00:00.000-05:00", "summary" : "The purpose of the study was to define the global expression profile of FRT cells, with a particular focus on genes involved in ion transport", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31622498" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129995" }, "primaryId" : "GEO:GSE129995", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE129995" } ] }, "title" : "microRNA expression profile in retina and choroid in oxygen-induced retinopathy model", "dateAssigned" : "2019-04-17T00:00:00.000-05:00", "summary" : "Using Next Generation Sequencing (NGS) we profiled miRNA expression in the retina and choroid during degenerative and NV phases of oxygen-induced retinopathy (OIR).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31188886" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130102" }, "primaryId" : "GEO:GSE130102", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130102" } ] }, "title" : "Spontaneous Superimposed Preeclampsia: Chronology and Expression Unveiled by Temporal Transcriptomic Analysis", "dateAssigned" : "2019-04-19T00:00:00.000-05:00", "summary" : "Preeclampsia (PE), a multifactorial pregnancy-specific syndrome accounting for up to 8% of pregnancy complications, is a leading cause of maternal and fetal morbidity and mortality and PE is also associated with long-term risk of hypertension and stroke for both the mother and fetus. Currently, the only “cure” is delivery of the baby and placenta, largely because the pathogenesis of preeclampsia is not yet fully understood. Preeclampsia is associated with impaired vascular remodeling at the maternal-fetal interface and placental insufficiency; however, the specific factors that contribute to this impairment have not been identified. To identify potential contributing pathways, we examined temporal transcriptomic changes occurring within the uterus, uterine implantation sites, and placentae from the Dahl salt-sensitive (Dahl S) rat model of superimposed preeclampsia compared to Sprague Dawley (SD) rats. We hypothesized that the Dahl S maternal-fetal interface would exhibit a unique temporal transcriptomic profile unveiling novel biomarkers, therapeutic targets, and mechanistic pathways regarding the development of PE. Our initial study focused on evaluation of genes previously linked to the development PE from using real time quantitative PCR (RT qPCR) and total RNA was isolated from uterus (day 0), uterine implantation sites (days 7, 10, 14), and placenta (days 14 and 20). Subsequently, an unbiased transcriptome analysis was performed at each time point using whole genome microarray to identify novel factors involved in PE. 624, 332, 185 , and 366 genes were found to be differentially expressed on days 0, 7, 10 and 14 respectively, with a Reactome Pathway enrichment for “Fatty acid metabolism, Metabolism of water-soluble vitamins and cofactors, Metabolism, Synthesis of substrates in N-glucan biosynthesis on Day 7”; ”Glycerophospholipid biosynthesis, Phospholipid metabolism, and Metabolism of lipids on Day 10”; and “Metabolism of lipids, Phospholipid metabolism, degradation of the extracellular matrix, Fatty acid metabolism, and Collagen degradation on Day 14” in the Dahl S rat vs. SD. Our data revealed numerous pathways that may play a role in the pathophysiology of spontaneous superimposed PE and allow for further investigation of novel therapeutic targets and biomarker development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31125289" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130121" }, "primaryId" : "GEO:GSE130121", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130121" } ] }, "title" : "RNA-seq analysis of mRNA profiles in β-Gal-overexpressing, NIK-overexpressing, and NIK(KA)-overexpressing INS-1 832/13 cells", "dateAssigned" : "2019-04-22T00:00:00.000-05:00", "summary" : "Conclusion: Our study represents the first detailed analysis of mRNA profiles in NIK-overexpressing and NIK(KA)-overexpressing INS-1 832/13 cells, generated by RNA-seq technology. Our results show that 471 genes were upregulated and 249 genes were downregulated following NIK overexpression. GO analysis indicated that the upregulated genes were primarily related to the immune response. KEGG pathway enrichment analysis showed that immune signaling pathways, including the TNF, NF-κB, antigen processing and presentation signaling pathways, were significantly activated by NIK overexpression in INS-1 832/13 cells, whereas genes related to insulin secretion and regulation of secretion were significantly decreased. NIK(KA), the dominant-negative mutant of NIK, does not induce the expression of genes related to immune response in INS-1 832/13 cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32730745" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130150" }, "primaryId" : "GEO:GSE130150", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130150" } ] }, "title" : "Selective Class IIa HDAC inhibitor alters gene expression in NRVMs", "dateAssigned" : "2019-04-22T00:00:00.000-05:00", "summary" : "Expression profiling of neonatl rat ventricular cardiomyocytes (NRVMs) upon the treatement of Class IIa HDAC inhibitor", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30962285" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130258" }, "primaryId" : "GEO:GSE130258", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130258" } ] }, "title" : "Epigenetic Transgenerational Inheritance of Parent-of-Origin Allelic Transmission of Outcross Pathology and Sperm Epimutations Following Ancestral Toxicant Exposures", "dateAssigned" : "2019-04-24T00:00:00.000-05:00", "summary" : "Previous observations have demonstrated that the agricultural fungicide vinclozolin and the pesticide DDT (dichlorodiphenyltrichloroethane) induce transgenerational sperm epimutations involving DNA methylation. These two environmental toxicants were used to investigate the impacts of parent-of-origin outcross on the epigenetic transgenerational inheritance of disease. Male and female rats were collected from a paternal outcross (POC) or a maternal outcross (MOC) F4 generation control and exposure lineages for pathology and epigenetic analysis. This model allows the parental allelic transmission of disease and epimutations to be investigated. There was increased pathology incidence in MOC outcross F4 generation male prostate, kidney, obesity and multiple diseases through a maternal allelic transmission. The POC outcross F4 generation female offspring had increase pathology incidence for kidney, obesity and multiple diseases through the paternal allelic transmission. Some disease such as testis or ovarian pathology appear to be transmitted through the combined actions of both male and female alleles. Analysis of the F4 generation sperm epigenomes identified differential DNA methylated regions (DMRs) in a genome-wide analysis. Observations demonstrate that DDT and vinclozolin have the potential to promote the epigenetic transgenerational inheritance of disease and sperm epimutations to the outcross F4 generation in a sex specific and exposure specific manner.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31682807" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130276" }, "primaryId" : "GEO:GSE130276", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130276" } ] }, "title" : "Prostaglandin D2 Signaling in Tendon Healing", "dateAssigned" : "2019-04-24T00:00:00.000-05:00", "summary" : "We report RNA sequencing data from the plantaris tendons of 3-month old Sprague Dawley rats that were treated with vehicle or GSK2894631A to inhibit the HPGDS enzyme. Rats underwent a bilateral plantaris tendon tear followed by immediate repair, and samples were obtained either 7 or 21 days after surgical intervention.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31782241" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130338" }, "primaryId" : "GEO:GSE130338", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130338" } ] }, "title" : "Genome-Wide RNA Pol II Initiation and Pausing in Neural Progenitors of the Rat.", "dateAssigned" : "2019-04-25T00:00:00.000-05:00", "summary" : "CONCLUSIONS: Our study has produced the first Start-seq dataset for the rat. Apart from profiling transcription initiation, our data reaffirm the prevalence of Pol II pausing across the rat genome and indicate conservation of pausing mechanisms across metazoan genomes. We suggest that pausing location, at least in mammals, is constrained by a distance from initiation of transcription, whether it occurs at or outside of a gene promoter. Abundant antisense transcription initiation around protein coding genes indicates that Pol II recruited to the vicinity of a promoter is distributed to available start sites of transcription at either DNA strand. Transcriptome profiling of neural progenitors presented here will facilitate further studies of other rat cell types as well as other organisms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31185909" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130409" }, "primaryId" : "GEO:GSE130409", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130409" } ] }, "title" : "Genome wide anaylsis of histone modifications in rats exposed to endocrine disruptors. [ChIP-Seq]", "dateAssigned" : "2019-04-28T00:00:00.000-05:00", "summary" : "Our early life environment has a profound influence on developing organs and tissues that impacts metabolic function, and determines health and disease susceptibility across the life-course. We show an adverse early-life exposure that causes metabolic dysfunction in adulthood reprograms active and repressive histone marks in the developing liver to accelerate acquisition of an adult epigenomic signature at specific genes and chromatin states. This epigenomic reprogramming persists long after the initial exposure, but remarkably, can remain transcriptionally- and metabolically-silent until later-life exposure to a Western-style (high fat-fructose-cholesterol) diet. These findings reveal the importance of epigenome:environment interactions across the life-course, which early in life accelerate epigenomic aging and reprogram the epigenome, and later in adulthood, can unlock metabolically restriced epigenetic reprogramming to drive metabolic dysfunction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32385268" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130434" }, "primaryId" : "GEO:GSE130434", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130434" } ] }, "title" : "Genome wide anaylsis of transcriptome modifications in rats exposed to endocrine disruptors. [RNA-Seq]", "dateAssigned" : "2019-04-29T00:00:00.000-05:00", "summary" : "Our early life environment has a profound influence on developing organs and tissues that impacts metabolic function, and determines health and disease susceptibility across the life-course. We show an adverse early-life exposure that causes metabolic dysfunction in adulthood reprograms active and repressive histone marks in the developing liver to accelerate acquisition of an adult epigenomic signature at specific genes and chromatin states. This epigenomic reprogramming persists long after the initial exposure, but remarkably, can remain transcriptionally- and metabolically-silent until later-life exposure to a Western-style (high fat-fructose-cholesterol) diet. These findings reveal the importance of epigenome:environment interactions across the life-course, which early in life accelerate epigenomic aging and reprogram the epigenome, and later in adulthood, can unlock metabolically restriced epigenetic reprogramming to drive metabolic dysfunction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32385268" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130481" }, "primaryId" : "GEO:GSE130481", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130481" } ] }, "title" : "Bcl-2 overexpression effects in rat neural precursor cells.", "dateAssigned" : "2019-04-30T00:00:00.000-05:00", "summary" : "Bcl-2 is highly enriched in the nervous system during neural development and plays an important role in modulating cell survival. In addition to its anti-apoptotic function, Bcl-2 has previously been suggested as a mediator of neuronal differentiation. However, the mechanism by which Bcl-2 might influence neurogenesis is not sufficiently understood. We aimed to determine the non-apoptotic functions of Bcl-2 during neuronal differentiation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130486" }, "primaryId" : "GEO:GSE130486", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130486" } ] }, "title" : "microRNA expression profile in vascular smooth muscle cells (VSMCs) after inducing calcification", "dateAssigned" : "2019-04-30T00:00:00.000-05:00", "summary" : "Vascular calcification, the ectopic deposition of calcium in blood vessels, develops in association with various metabolic diseases and atherosclerosis. Because it often causes stiffness and remodeling of the blood vessels, vascular calcification increases morbidity and mortality. Both miRNA and mRNA microarrays (Series GSE74755) were performed with rat VSMCs and reciprocally regulated pairs of miRNA and mRNA were selected after bioinformatic analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130573" }, "primaryId" : "GEO:GSE130573", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130573" } ] }, "title" : "Maternal antioxidant treatment prevents the adverse effects of prenatal stress on the offspring's brain and behavior [NanoString nCounter rat miRNA]", "dateAssigned" : "2019-05-01T00:00:00.000-05:00", "summary" : "The results highlight placental oxidative stress as a key mediator in transmitting the maternal social stress effects on the offspring's brain and behaviour, and offer a potential intervention to prevent stress-induced fetal programming of affective disorders.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33344732" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130610" }, "primaryId" : "GEO:GSE130610", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130610" } ] }, "title" : "Transcriptome profiling of the rat retina following ischemia-reperfusion injury", "dateAssigned" : "2019-05-02T00:00:00.000-05:00", "summary" : "Transcriptomics has played valuable roles in deciphering differences between normal and diseased conditions at the molecular level. Herein is presented a transcriptome profile of ischemia-reperfusion (I/R) injury in adult Sprague-Dawley rat model and control group. Following acute I/R induction, a pool of the rats’ retinas at 12hr post I/R was made. RNA sequencing was performed on both the model and the control groups, followed by their transcriptomic analyses. Sample validation and quality control were done in accordance with standard protocols. Comparison of the sequenced data revealed significant variations in genes expression between the I/R model and their sham counterparts. These differentially expressed genes may provide valuable information to understanding the molecular mechanisms underlying retinal cell dysfunction, cell death and structure collapse in adult rats, and may help characterize or develop therapeutic interventions for visual impairment.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130651" }, "primaryId" : "GEO:GSE130651", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130651" } ] }, "title" : "Identification of Scrt1, a new transcriptional regulator of beta-cell maturation using chromatin accessibility variations", "dateAssigned" : "2019-05-02T00:00:00.000-05:00", "summary" : "Pancreatic beta-cells are highly specialized cells that produce and release insulin in response to nutrients, hormones and neurotransmitters. Glucose-induced insulin secretion, a unique feature of fully differentiated beta-cells, is only acquired after birth and is preceded by a phase of intense beta-cell proliferation. These events occurring in the neonatal period are critical for the establishment of an appropriate functional beta-cell mass covering the insulin needs throughout life. However, key regulators of gene expression and cis-regulatory elements involved in the cellular reprogramming along maturation remain to be elucidated. This project addresses this issue by using ATAC-seq (Assay for Transposase-Accessible Chromatin with high throughput sequencing) permitting a fine genome-wide mapping of chromatin accessibility. This approach is used to compare open chromatin regions in newborn and adult rat beta-cells. We obtained a genome-wide picture of chromatin accessible sites (100000) among which 20% were differentially accessible during maturation. Nearly 60% of these sites were in the proximity of significantly differentially expressed genes. An analysis of transcription factor binding sites revealed key known and unforeseen transcription factors which could explain these changes. We validated a transcriptional repressor named SCRT1, that depicted a significant effect on beta-cell proliferation and targeted several genes implicated in the acquisition of glucose-stimulated insulin secretion function. Thus, we were able to find several known and unforeseen key transcriptional regulators acting at cis-regulatory sites and promoters which depicted a differential accessibility and induced differential gene expression along maturation. These findings could be of interest to induce maturation of surrogate insulin-producing cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130744" }, "primaryId" : "GEO:GSE130744", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130744" } ] }, "title" : "Expression profile of rat kidney of fetuses with 19 days of gestation under chronic rotation of the photoperiod.", "dateAssigned" : "2019-05-06T00:00:00.000-05:00", "summary" : "We investigated whether the chronic rotation of the photoperiod (CPS) during gestation can modify the fetal kidney expression profile at gestational day 19 by Affymetrix microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31244775" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130795" }, "primaryId" : "GEO:GSE130795", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130795" } ] }, "title" : "Co-expression Analysis Reveals Dysregulated miRNAs and miRNA-mRNA Interactions in the Development of Contrast-induced Acute Kidney Injury [mRNA]", "dateAssigned" : "2019-05-07T00:00:00.000-05:00", "summary" : "Conclusions:In conclusion, our present study contributes to the first evidence of miRNA-mRNA regulations in the development of kidney injury following an intra-arterial contrast injection route. These novel findings provide insights into the underlying mechanisms of CI-AKI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31306435" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130796" }, "primaryId" : "GEO:GSE130796", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE130796" } ] }, "title" : "Co-expression Analysis Reveals Dysregulated miRNAs and miRNA-mRNA Interactions in the Development of Contrast-induced Acute Kidney Injury [miRNA]", "dateAssigned" : "2019-05-07T00:00:00.000-05:00", "summary" : "Conclusions: In conclusion, our present study contributes to the first evidence of miRNA-mRNA regulations in the development of kidney injury following an intra-arterial contrast injection route. These novel findings provide insights into the underlying mechanisms of CI-AKI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31306435" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131012" }, "primaryId" : "GEO:GSE131012", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131012" } ] }, "title" : "Microarray and qPCR Analysis of Mitochondrial Metabolism Activation during Prenatal and Early Postnatal Development in Rats and Humans with Emphasis on CoQ10 Biosynthesis", "dateAssigned" : "2019-05-10T00:00:00.000-05:00", "summary" : "We used microarrays to detail the orchestration of gene expression underlying perinatal metabolic shift and identified up- and down-regulated genes during this process.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34066731" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131034" }, "primaryId" : "GEO:GSE131034", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131034" } ] }, "title" : "Thyroid hormone inhibits hepatocellular carcinoma progression via induction of differentiation and metabolic reprogramming", "dateAssigned" : "2019-05-10T00:00:00.000-05:00", "summary" : "T3 induces a global shift of the expression profile of KRT-19+ lesions towards that of fully differentiated hepatocytes", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31954205" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131040" }, "primaryId" : "GEO:GSE131040", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131040" } ] }, "title" : "Maternal antioxidant treatment prevents behavioural and neurological changes in offspring exposed to prenatal social stress [RNA-seq]", "dateAssigned" : "2019-05-10T00:00:00.000-05:00", "summary" : "Maternal exposure to social stress during pregnancy is associated with an increased risk of psychiatric disorders in the offspring in later life. How the effects of maternal social stress are transmitted to the developing foetus is unclear. Using a rat model of maternal social stress during pregnancy, we explored the mechanisms by which maternal stress is conveyed to the foetus and the potential for targeted treatment to prevent disease in the offspring. Maternal stress induced oxidative stress in the placenta, but not in the foetal brain, which was prevented by a single administration of nanoparticle-bound antioxidant prior to the stress exposure. Moreover, this antioxidant treatment prevented prenatal stress-induced anxiety-like behaviour in juvenile male offspring, along with neurological and gene expression changes in the offspring brain. In vitro, placental conditioned medium or foetal plasma from stressed pregnancies caused changes to cultured cortical neurons, similar to those observed in the brains of juvenile offspring exposed to prenatal stress, and were found to contain altered levels of extracellular microRNAs but not corticosterone. The present study highlights the crucial role of the placenta, and molecules secreted from the placenta, in foetal brain development and provides evidence of the potential for treatment that can prevent maternal stress-induced foetal programming of neurological disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33344732" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131044" }, "primaryId" : "GEO:GSE131044", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131044" } ] }, "title" : "Circular RNA expression profiling and selection of key circular RNAs in the hypothalamus of heat-acclimated rats", "dateAssigned" : "2019-05-10T00:00:00.000-05:00", "summary" : "Circular RNAs (circRNAs) play crucial roles in diverse biological processes. However, expression levels and functions of circRNAs related to heat acclimation (HA) are poorly understood. we, for the first time, used comprehensive circRNA expression profiling to investigate circRNA–miRNA interactions in HA rats, to provide a better understanding of mechanisms underlying HA. CircRNA expression profile was performed in rats’ hypothalamus of HA and control group with microarray assays. Bioinformatics analysis was conducted to predict their functions. And differential circRNAs and their regulated downstream miRNAs and mRNAs were quantitatively validated using real-time quantitative polymerase chain reaction (RT-qPCR ). Predicted proteins expression were determined using enzyme-linked immunosorbent assay (ELISA). In total, 53 circRNAs were differentially expressed between the HA and C group; 28 of these circRNAs were upregulated, while 25 were downregulated in HA (Fold change >1.5; P < 0.05). Three circRNAs and two miRNAs and three predicted mRNAs were obviously regulated after validated by RT-qPCR in HA rats. Two proteins expression were proportional to their mRNA changes. Further analysis indicated the circRNAs mostly close to HA were grouped into 3 signal pathways: including rno_circRNA_014301-vs-rno-miR-3575-vs-Hif-1α, rno_circRNA_014301-vs-rno-miR-3575-vs-Lppr4, rno_circRNA_010393-vs-rno-miR-20b-3p-vs-Mfap4 in hypoxia response pathways, substance/energy metabolism and inflammatory response pathways. Our findings implicate that many circRNAs regulate expressions of genes that interact with each other to exert their functions during HA.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131103" }, "primaryId" : "GEO:GSE131103", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131103" } ] }, "title" : "Analysis of a long noncoding RNAs that modulate neurotransmitter release", "dateAssigned" : "2019-05-13T00:00:00.000-05:00", "summary" : "We report the application of a novel integrated screening strategy to identify lncRNAs that regulate synaptic vesicle release. We identified one of these lncRNAs, which is conserved across mammals, neuron-specific and strictly nuclear. Modulations of this lncRNA influence synaptic vesicle release, presynaptic calcium influx, neurite elongation and neuronal migration. We have characterized the DNA, RNA and protein inteactors of this lncRNA and clarified its involvement in the stabilization of mRNAs for synaptic vesicle proteins.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31897430" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131144" }, "primaryId" : "GEO:GSE131144", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131144" } ] }, "title" : "A comprehensive comparison of differential accessibility analysis methods for ATAC-seq data", "dateAssigned" : "2019-05-13T00:00:00.000-05:00", "summary" : "Conclusions: It is important to use PCA to check the samples distribution, and the Remove Unwanted Variation strategy can be used to correct the data to improve the sensitivity when strong batch effects are found in the data. Finally, BeCorrect can be used to correct the batch-effect of ATAC-seq data signal based on DARs analysis, and generate a proper visualization on a genome browser.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32576878" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131221" }, "primaryId" : "GEO:GSE131221", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131221" } ] }, "title" : "Enarodustat, hypoxia-inducible factor stabilizer, counteracts the diabetic renal energy metabolism alterations in streptozotocin-induced diabetic rats", "dateAssigned" : "2019-05-14T00:00:00.000-05:00", "summary" : "We analyzed the effects of enarodustat (JTZ-951; HIF stabilizer) on renal energy metabolism in streptozotocin-induced diabetic rat model. Transcriptome analysis of renal cortex revealed that genes related to fatty acid metabolism and amino acid metabolism were upregulated in diabetes and downregulated by enarodustat, whereas genes related to glucose metabolism were upregulated by enarodustat. Thus, HIF stabilization counteracts the renal energy metabolism alterations occurring in the early stages of diabetic kidney disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32171449" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131289" }, "primaryId" : "GEO:GSE131289", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131289" } ] }, "title" : "Effects of social isolation stress on miRNA expression in the bed nucleus of stria terminalis (BNST) in male and female rats", "dateAssigned" : "2019-05-15T00:00:00.000-05:00", "summary" : "Conclusions: The current study shows that housing conditions (either SI or GH) during adolescence regulates miRNA expression in a sex-specific manner in the sexually dimorphic area of the adBNST", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31636537" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131435" }, "primaryId" : "GEO:GSE131435", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131435" } ] }, "title" : "Hippocampus-Cerebellum Axis Specific Transcriptomic Stratification to Discriminate Mild from Moderate TBI", "dateAssigned" : "2019-05-17T00:00:00.000-05:00", "summary" : "The variations of psycho- and physiological deficits caused by TBI correlate with the degree of brain injury. However, the objective stratification of TBI is yet elusive. A modified closed-head injury Marmarou model was used based on the release of a 500 gram steel slug on top of the rat skull from a height of 100 cm or 120 cm to induce differential injury models for mild TBI and moderate TBI, respectively. The skull was covered by a helmet to mimic the warfighter’s condition in theater. The hippocampus was at the focal point of injury, and the cerebellum, was susceptible to diffused shock (secondary injury). The HC-CB axis coordinates visuomotor performance, which is known to be vulnerable to TBI. The rats that received moderate TBI showed deficient visuomotor performance by the Barnes maze test for longer time periods than those inflicted with mild TBI. The time resolved and HC-CB specific transcriptomic analysis focused on genes that enabled discrimination of mild from moderate TBI at 14d post injury which is equivalent to nearly 1.5 years of human lifetime. The functional analysis elucidated an active healing mechanism in the HC exposed to mild TBI. In contrast, moderate TBI caused delayed healing and active cell death in the HC. In conclusion, the graded brain injuries differentially implicated the HC-CB axis, despite the use of a helmet to reduce the impact. Time resolved functional dynamics informed the distinct consequences of mild vs. moderate TBI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33172833" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131544" }, "primaryId" : "GEO:GSE131544", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131544" } ] }, "title" : "Arsenic is more potent than cadmium or manganese in disrupting the INS-1 beta cell microRNA landscape", "dateAssigned" : "2019-05-21T00:00:00.000-05:00", "summary" : "Diabetes is a metabolic disorder characterized by fasting hyperglycemia and impaired glucose tolerance. Laboratory and population studies have shown that inorganic arsenic (iAs) can impair these pathways. Other metals including cadmium (Cd) and manganese (Mn) have also been linked to diabetes phenotypes. MicroRNAs, short non-coding RNAs that regulate gene expression, have emerged as potential drivers of metabolic dysfunction. MicroRNAs responsive to metal exposures in vitro have also been reported in independent studies to regulate insulin secretion in vivo. We hypothesize that microRNA dysregulation may associate with and possibly contribute to insulin secretion impairment upon exposure to iAs, Cd, or Mn. We exposed insulin secreting rat insulinoma cells to non-cytotoxic concentrations of iAs (1 µM), Cd (5 µM), and Mn (25 µM) for 24 h followed by small RNA sequencing to identify dysregulated microRNAs. RNA sequencing was then performed to further investigate changes in gene expression caused by iAs exposure. While all three metals significantly inhibited glucose-stimulated insulin secretion, high-throughput sequencing revealed distinct microRNA profiles specific to each exposure. One of the most significantly upregulated microRNAs post-iAs treatment is miR-146a (~ + 2-fold), which is known to be activated by nuclear factor κB (NF-κB) signaling. Accordingly, we found by RNA-seq analysis that genes upregulated by iAs exposure are enriched in the NF-κB signaling pathway and genes down-regulated by iAs exposure are enriched in miR-146a binding sites and are involved in regulating beta cell function. Notably, iAs exposure caused a significant decrease in the expression of Camk2a, a calcium-dependent protein kinase that regulates insulin secretion, has been implicated in type 2 diabetes, and is a likely target of miR-146a. Further studies are needed to elucidate potential interactions among NF-kB, miR-146a, and Camk2a in the context of iAs exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31555879" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131560" }, "primaryId" : "GEO:GSE131560", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131560" } ] }, "title" : "Uropathogenic E. coli mediated ACLY dependent acetyl-CoA change control IL 8 expression", "dateAssigned" : "2019-05-21T00:00:00.000-05:00", "summary" : "Furthermore, using H3 Lysine9 acetylation (H3K9ac) immunoprecipitation coupled next generation sequencing (ChIP-seq), we found that UPEC cause site specific regulation of H3K9ac which correlates with the expression of pro-inflammatory cytokines and chemokines. To be more specific, the expression of pro-inflammatory cytokines and chemokines like IL 8, CXCL2, and IL-1α are suppressed by UPEC mediated decreasing of H3K9ac at TSS-promoter region. Thus, this study established that UPEC manipulate host cell metabolism to impact histone acetylation at specific loci, correlating with cytokines and chemokines expression, as a means to inhibit NF-κB signaling.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131693" }, "primaryId" : "GEO:GSE131693", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131693" } ] }, "title" : "Salt-deficient diet exacerbates cystogenesis in ARPKD via epithelial sodium channel (ENaC)", "dateAssigned" : "2019-05-23T00:00:00.000-05:00", "summary" : "We report the changes in miRNA expression in the renal cortex od the PCK rats fed diets with different sodium content", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131704" }, "primaryId" : "GEO:GSE131704", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131704" } ] }, "title" : "microRNA expression in rat hippocampus up to 1 year after fluid percussion brain injury", "dateAssigned" : "2019-05-23T00:00:00.000-05:00", "summary" : "Methods: miRNA-Seq analysis of microRNA expression in the hippocampus of TBI and sham surgery rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32094409" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131750" }, "primaryId" : "GEO:GSE131750", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131750" } ] }, "title" : "Gene expression profiling of Tsp1 deficient rat aortic smooth muscle cells with mechanical stretch", "dateAssigned" : "2019-05-24T00:00:00.000-05:00", "summary" : "The extracellular matrix (ECM) initiates mechanical cues and transduces intracellular signaling through matrix-cell interactions. The nature of cues and how they coordinate with a mechanical microenvironment are not fully understood. We identified the matricellular protein,thrombospondin-1 (Tsp1, also called Thbs1),as a mediator of matrix mechanotransduction that acts via integrin αvβ1 to establish focal adhesions and promotes nuclear shuttling of Yes-associated protein (YAP) in response to cyclic stretch. Thbs1-mediatedYAP activation depends on the small GTPase Rap2 and Hippo pathway, and is not influenced by altered actin fibers. Hence, to gain insight into the molecular mechanisms underlying the Tsp1-mediated matrix mechanotransduction, we performed a comprehensive analysis of gene expression changes in Tsp1deficiant SMCs with mechanical stretch using RNA sequencing (RNA-Seq).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32321834" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131774" }, "primaryId" : "GEO:GSE131774", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131774" } ] }, "title" : "IL4 improves white matter repair after stroke", "dateAssigned" : "2019-05-25T00:00:00.000-05:00", "summary" : "The repair of white matter damage is of paramount importance for functional recovery after brain injuries.We report that interleukin-4 (IL-4) promotes oligodendrocyte regeneration and remyelination. IL-4 receptor expression was detected in a variety of glial cells after ischemic brain injury, including oligodendrocyte lineage cells. IL-4 deficiency in knockout mice resulted in greater deterioration of white matter over 14 days after stroke. Consistent with these findings, intranasal delivery of IL-4 nanoparticles after stroke improved white matter integrity and attenuated long-term sensorimotor and cognitive deficits in wild-type mice, as revealed by histological immunostaining, electron microscopy, diffusion tensor imaging, and electrophysiology. The selective effect of IL-4 on remyelination was verified in an ex vivo organotypic model of demyelination. By leveraging primary oligodendrocyte progenitor cells (OPCs), microglia-depleted mice, and conditional OPC-specific PPARγ knockout mice, we discovered a direct salutary effect of IL-4 on oligodendrocyte differentiation that was mediated by the PPARγ axis. Our findings reveal a new regenerative role of IL-4 in the CNS, which lies beyond its known immunoregulatory functions on microglia/macrophages or peripheral lymphocytes. Therefore, intranasal IL-4 delivery may represent a novel therapeutic strategy to improve white matter integrity in stroke and other brain injuries.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31226122" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131884" }, "primaryId" : "GEO:GSE131884", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131884" } ] }, "title" : "Calcaneal tendon plasticity following gastrocnemius muscle injury in rat", "dateAssigned" : "2019-05-29T00:00:00.000-05:00", "summary" : "We investigated calcaneal tendon extracellular matrix (ECM) remodeling after gastrocnemius muscle injury using a rat model. Wistar rats were randomly divided into four groups: control group (C; animals that were not exposed to muscle injury) and harvested at different time points post gastrocnemius muscle injury (3, 14 and 28 days) for gene expression analysis. qRT-PCR was performed using TaqMan Universal PCR Master Mix system (Applied Biosystems, CA, USA - Cat. 4304437).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31551799" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131975" }, "primaryId" : "GEO:GSE131975", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE131975" } ] }, "title" : "Effect of dietary protein on gut gene expression in rat", "dateAssigned" : "2019-05-30T00:00:00.000-05:00", "summary" : "A total of 49.88 Gb high quality reads of 6 samples (n=3) were obtained. The result of sample distance indicated that the cecal gene expression profiles of rats fed with diets composed of casein and chicken protein were clearly separated into two clusters. The variation of samples in casein protein fed group was higher than that in chicken protein fed group. There were 2524 differential expressed genes between the two groups, of which 871 genes were up regulated in chicken protein diet group compared with casein diet group.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132094" }, "primaryId" : "GEO:GSE132094", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132094" } ] }, "title" : "Postweaning iron deficiency in rats alters reelin expression in the nucleus accumbens", "dateAssigned" : "2019-06-03T00:00:00.000-05:00", "summary" : "Background: Epidemiological research indicates that iron deficiency (ID) in infancy correlates with long-term cognitive impairment and behavioral disturbances, despite therapy. However, the mechanisms underlying these effects are unknown. Objective: We investigated how ID affected postweaning behavior and monoamine concentration in rat brains to determine whether ID during the juvenile period affected gene expression and synapse formation in the prefrontal cortex (PFC) and nucleus accumbens (NAcc). Methods: Fischer344/Jcl male rats aged 21–39 days were fed low-iron diets (0.35 mg/kg iron; ID group) or standard AIN-93 G diets (3.5 mg/kg iron; control group). The locomotor activity of male offspring was evaluated by the open field and elevated plus maze tests at ages 8 and 12 weeks. Monoamine concentrations in the PFC, NAcc, caudate-putamen, ventral midbrain, dorsal midbrain, and pons were analyzed. Comprehensive gene expression analysis was performed in the PFC and NAcc at age 13 weeks. Finally, we investigated synaptic density in the PFC and NAcc by synaptophysin immunostaining. Results: Behavioral tests revealed significant interactions between age and iron consumption for the total distance traveled and the distance traveled in the peripheral area (p < 0.05), indicating that ID during the juvenile period affected hyperactivity and that this persisted to adulthood. At age 13 weeks, the ID group had increased levels of both dopamine and the metabolites of dopamine and serotonin in the NAcc. Comprehensive gene expression analysis and immunostaining showed decreased Reelin gene expression (adjusted p < 0.01) and significantly increased spine density in the NAcc in the ID group compared with the control group (p < 0.01). Conclusions: ID during the postweaning juvenile period led to long-term hyperactivity, monoamine disturbance in the brain, and downregulation of Reelin expression in the NAcc despite complete iron repletion. Epigenetic modification of Reelin genes may be involved in synaptic plasticity in the NAcc.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31599944" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132224" }, "primaryId" : "GEO:GSE132224", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132224" } ] }, "title" : "Cell Type- and Sex-Dependent Transcriptome Profiles of Rat Anterior Pituitary Cells", "dateAssigned" : "2019-06-05T00:00:00.000-05:00", "summary" : "Understanding of physiology and pathology of an organ composed of variety of cell populations depends critically on genome-wide information on each cell type. Here, we report single-cell transcriptome profiling of over 6800 freshly dispersed anterior pituitary cells from postpubertal male and female rats. Six pituitary-specific cell types were identified based on known marker genes and characterized: folliculostellate cells and hormone producing corticotrophs, gonadotrophs, thyrotrophs, somatotrophs, and lactotrophs. Also identified were endothelial and blood cells from the pituitary capillary network. The expression of numerous developmental and neuroendocrine marker genes in both folliculostellate and hormone producing cells supports that they have a common origin. For several genes, the validity of transcriptome analysis was confirmed by qRT-PCR and single cell immunocytochemistry. Folliculostellate cells exhibit impressive transcriptome diversity, indicating their major roles in production of endogenous ligands and detoxification enzymes, and organization of extracellular matrix. Transcriptome profiles of hormone producing cells also indicate contributions toward those functions, while also clearly demonstrating their endocrine function. This survey highlights many novel genetic markers contributing to pituitary cell type identity, sexual dimorphism, and function and points to relationships between hormone producing and folliculostellate cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31620083" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132375" }, "primaryId" : "GEO:GSE132375", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132375" } ] }, "title" : "Systems modeling of developmental vascular toxicity", "dateAssigned" : "2019-06-07T00:00:00.000-05:00", "summary" : "More than 80,000 chemicals in commerce present a challenge for hazard assessments that toxicity testing in the 21st century strives to address through high-throughput screening (HTS) assays. Assessing chemical effects on human development adds an additional layer of complexity to the screening, with a need to capture complex and dynamic events essential for proper embryo-fetal development. HTS data from ToxCast/Tox21 informs systems toxicology models, which incorporate molecular targets and biological pathways into mechanistic models describing the effects of chemicals on human cells, 3D organotypic culture models, and small model organisms. Adverse Outcome Pathways (AOPs) provide a useful framework for integrating the evidence derived from these in silico and in vitro systems to inform chemical hazard characterization. To illustrate this formulation, we have built an AOP for developmental toxicity through a mode of action linked to embryonic vascular disruption (Aop43). Here, we review the model for quantitative prediction of developmental vascular toxicity from ToxCast HTS data and compare the HTS results to functional vascular development assays in complex cell systems, virtual tissues, and small model organisms. ToxCast HTS predictions from several published and unpublished assays covering different aspects of the angiogenic cycle were generated for a test set of 38 chemicals representing a range of putative vascular disrupting compounds (pVDCs). Results boost confidence in the capacity to predict adverse developmental outcomes from HTS in vitro data and model computational dynamics for in silico reconstruction of developmental systems biology. Finally, we demonstrate the integration of the AOP and developmental systems toxicology to investigate the unique modes of action of two angiogenesis inhibitors.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132409" }, "primaryId" : "GEO:GSE132409", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132409" } ] }, "title" : "Transcriptome of adult rat hepatocytes with different ploidy statuses", "dateAssigned" : "2019-06-08T00:00:00.000-05:00", "summary" : "To investigate whether rat adult hepatocytes would exhibit different characteristics dependent on their ploidy statuses, we compared the transcriptome profile of 2c, 4c and 8c hepatocytes by mRNA microarray.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31493546" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132417" }, "primaryId" : "GEO:GSE132417", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132417" } ] }, "title" : "Dietary Effects on T Cell Methylomes and Functional Inhibition of DNA Methyltransferase Attenuates Salt-Sensitive Hypertension and Renal Damage in Dahl SS Rat", "dateAssigned" : "2019-06-09T00:00:00.000-05:00", "summary" : "The Dahl salt-sensitive (SS) rat is an established model of hypertension and renal damage that is accompanied with an activation of the immune system in the response to a high salt diet. Investigations into the effects of sodium-independent and –dependent components of the diet were shown to affect the disease phenotype with Dahl SS/JrHsdMcwi (SS/MCW) rats maintained on a purified diet (AIN-76A) presenting with a more severe phenotype relative to the grain-fed Dahl SS/JrHsdMcwiCrl rat (SS/CRL). Recently, T cells isolated from the kidneys of the two strains unveiled that transcriptomic and functional differences may contribute to the susceptibility of hypertension and renal damage. Since contributions of the immune system, environment and diet are documented to alter this phenotype, this present study examined the epigenetic profile of T cells isolated from the periphery and the kidney from these strains. In response to high salt challenge, the methylome of T cells isolated from the kidney of SS/MCW exhibit significantly more differentially methylated regions with a preference for hypermethylation compared to the SS/CRL kidney T cells. Circulating T cells exhibited similar methylation profiles between the strains. Utilizing transcriptomic data from T cells isolated from the same animals upon which the DNA methylation analysis was performed, a predominant negative correlation was observed between gene expression and DNA methylation in all groups. Lastly, inhibition of DNA methyltransferases blunted salt-induced hypertension and renal damage in the SS/MCW rats providing a functional role for methylation. The study demonstrated the influence of epigenetic modifications to immune cell function, highlighting the need for further investigations.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132437" }, "primaryId" : "GEO:GSE132437", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132437" } ] }, "title" : "Molecular consequences of fetal alcohol exposure on amniotic exosomal miRNAs with functional implications for stem cell potency and differentiation", "dateAssigned" : "2019-06-10T00:00:00.000-05:00", "summary" : "Alcohol (ethanol, EtOH) consumption during pregnancy can result in fetal alcohol spectrum disorders (FASDs), which are characterized by prenatal and postnatal growth restriction and craniofacial dysmorphology. The specific mechanisms by which alcohol mediates these injuries have yet to be determined. Cell-derived extracellular vesicles, including exosomes and microvesicles containing several species of RNAs (exRNAs), have recently emerged as a mechanism of cell-to-cell communication. However, EtOH’s effects on the biogenesis and function of non-coding exRNAs during fetal development have not been explored. Therefore, we studied the effects of maternal EtOH exposure on the composition of exRNAs in the amniotic fluid (AF) using a rat fetal alcohol exposure (FAE) model. Timed pregnant Sprague Dawley rats received 0 or 2.5 g/kg of 20% EtOH by oral gavage on embryonic days 5, 8, 10, 12 and 15. Through RNA-Seq analysis we identified and verified AF exosomal miRNAs with differential expression levels specifically associated with maternal EtOH exposure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132459" }, "primaryId" : "GEO:GSE132459", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132459" } ] }, "title" : "Single cell qRT-PCR (scPCR) for rat hepatocytes and biliary epithelial cell (BEC)-enriched non-parenchymal cells (NPCs).", "dateAssigned" : "2019-06-10T00:00:00.000-05:00", "summary" : "Using FACS-sorted adult rat hepatocytes with distinct DNA contents (2c and 4c), we compared the expression levels of a 47 gene panel. As non-hepatic control samples, BEC-enriched NPCs were also used for the same scPCR experiment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31493546" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132491" }, "primaryId" : "GEO:GSE132491", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132491" } ] }, "title" : "Spinal cord stimulation prevents paclitaxel-induced mechanical and cold hypersensitivity and modulates spinal gene expression in rats", "dateAssigned" : "2019-06-10T00:00:00.000-05:00", "summary" : "Introduction: Paclitaxel-induced peripheral neuropathy (PIPN) is a common dose-limiting side effect of this cancer treatment drug. Spinal cord stimulation (SCS) has demonstrated efficacy for attenuating some neuropathic pain conditions. Objective: We aim to examine the inhibitory effect of SCS for the development of PIPN pain in rats. Methods: We examined whether traditional SCS administered during paclitaxel treatment attenuates PIPN-related pain behavior. After SCS, we carried out RNA-seq of the lumbar spinal cord to examine which genes are differentially expressed after PIPN with and without SCS. Results: Compared to rats treated with paclitaxel alone (n=7) or sham SCS (n=6), SCS treatment (n= 11) significantly inhibited the development of paclitaxel-induced mechanical and cold hypersensitivity, without altering open-field exploratory behavior. RNA-seq showed that SCS induced upregulation of 836 genes and downregulation of 230 genes in the spinal cord of paclitaxel-treated rats (n=3), as compared to sham SCS (n=5). SCS upregulated immune responses in paclitaxel-treated rats, including transcription of astrocyte- and microglial-related genes, but repressed transcription of multiple gene networks associated with synaptic plasticity, neuron projection development, g-aminobutyric acid reuptake, and long-term potentiation. Conclusion: Our findings suggest that traditional SCS may attenuate the development of pain-related behaviors in PIPN, partially by causing aggregate inhibition of synaptic plasticity through up- and down-regulation of gene networks in the spinal cord.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31875188" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132515" }, "primaryId" : "GEO:GSE132515", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132515" } ] }, "title" : "Acetyl-CoA production by specific metabolites promotes cardiac repair after myocardial infarction via mediating histone acetylation", "dateAssigned" : "2019-06-11T00:00:00.000-05:00", "summary" : "We examined the gene expression profile in rat hearts at 24 hours after ischemic reperfusion with/out treatment of sodium octanoate (8C).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34939931" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132815" }, "primaryId" : "GEO:GSE132815", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132815" } ] }, "title" : "Application of toxicogenomics for the risk assessment of the food contaminant acetamide", "dateAssigned" : "2019-06-17T00:00:00.000-05:00", "summary" : "Acetamide (CAS 60-35-5) is detected in common foods including milk, eggs, beef, and roasted coffee beans. Chronic rodent bioassays using high doses (≥1000 mg/kg/day) suggest acetamide is a group 2B possible human carcinogen due to the induction of liver tumors. Weight-of-evidence indicates acetamide is not genotoxic, and therefore a threshold response is expected. We used a toxicogenomics approach in Wistar rats gavaged daily for 7 and 28 days to determine the benchmark dose (BMD), and investigate its mode of action from differential gene expression. Two exposure experiements were carried out in succsession. An initial dose range finding experiment used male Wistar rats gavaged daily for 7 days at 0, 30, 100, 300 and 1000 mg/kd/day. A second experiment used both male and female Wistar rats exposed for 7 and 28 days to 0, 300,500,750,1000 and 1500 mg/kg/day. No treatment related changes in terminal body weight, clinical chemistry, or histopathology were observed at doses of 30, 100, or 300 mkd. At 1000 mkd, the dose reported to elicit carcinogenesis, liver weights decreased 1.3-fold with the presence of single cell necrosis, hepatocyte vacuolization, and increased mitotic activity consistent with a 4.2 fold increase in the cell proliferation index. Accordingly, plasma ALT and AST were increased 2.0- and 2.2-fold, respectively. RNA-Seq analysis identified 1 differentially expressed gene at 300 mkd, and 2,685 at 1000 mkd (|fold-change| ≥ 1.5 and FDR ≤ 0.05). Down-regulated genes were associated with lipid metabolism while up-regulated genes included cell signaling, immune response, and cell cycle functions. Collectively, these results revealed a no-observable adverse effect level (NOAEL) and no-observed-transcriptional effect level (NOTEL) at 300 mkd, warranting further investigation at doses between 300 and 1000 mkd to identify the benchmark dose (BMD). Functional enrichment indicates perturbation of cell cycle and lipid metabolism, though a more refined dose-response evaluation will be needed to demonstrate dose-dependent effects related to the MOA of acetamide. Funding by the Bill and Melinda Gates Foundation (OPP1142801).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31881176" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132816" }, "primaryId" : "GEO:GSE132816", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132816" } ] }, "title" : "In vivo evaluation of the 94 GHz-chronic exposure effect on Hairless rat skin gene expression [C1]", "dateAssigned" : "2019-06-17T00:00:00.000-05:00", "summary" : "Millimeter waves are new broadband frequencies that start to be used in several applications such as future wireless communications, medical, and also non-lethal weapons (the 94-GHz band in Active Denial Systems). However, low information are available on their potential effects on human. These frequencies belong to radiofrequency and they have the property to be stopped by the first layer of the skin. Therefore our studies have aimed to evaluate 94 GHz effects on skin cells whole gene expression. Chronic long term 94 GHz MMW exposures were performed on two rat populations constituted by 17 young animals and 14 adult ones. Each group of animals were equally split in Exposed and Sham exposed subgroup. This two independent exposure experiments were conducted during 5 months, with rats exposed 3 h per day, 3 days per week, to an incident power density of 10 mW/cm², which correspond to twice the ICNIRP limit of exposure for professional. At the end of the experiment, skin explant were taken and RNA were extracted. Then, the modification of the whole gene expression were analyzed with gene expression microarray. Without modification of the animal’s temperature, long term chronic 94 GHz-MMW exposure did not significantly modify the rat’s skin gene expression on both young and adult rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32126188" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132817" }, "primaryId" : "GEO:GSE132817", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE132817" } ] }, "title" : "In vivo evaluation of the 94 GHz-chronic exposure effect on Hairless rat skin gene expression [C2]", "dateAssigned" : "2019-06-17T00:00:00.000-05:00", "summary" : "Millimeter waves are new broadband frequencies that start to be used in several applications such as future wireless communications, medical, and also non-lethal weapons (the 94-GHz band in Active Denial Systems). However, low information are available on their potential effects on human. These frequencies belong to radiofrequency and they have the property to be stopped by the first layer of the skin. Therefore our studies have aimed to evaluate 94 GHz effects on skin cells whole gene expression. Chronic long term 94 GHz MMW exposures were performed on two rat populations constituted by 17 young animals and 14 adult ones. Each group of animals were equally split in Exposed and Sham exposed subgroup. This two independent exposure experiments were conducted during 5 months, with rats exposed 3 h per day, 3 days per week, to an incident power density of 10 mW/cm², which correspond to twice the ICNIRP limit of exposure for professional. At the end of the experiment, skin explant were taken and RNA were extracted. Then, the modification of the whole gene expression were analyzed with gene expression microarray. Without modification of the animal’s temperature, long term chronic 94 GHz-MMW exposure did not significantly modify the rat’s skin gene expression on both young and adult rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32126188" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133093" }, "primaryId" : "GEO:GSE133093", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133093" } ] }, "title" : "Brainstem control of transcription after spinal cord injury (SCI)", "dateAssigned" : "2019-06-20T00:00:00.000-05:00", "summary" : "The spinal cord after injury shows altered transcription in numerous genes. We tested in a pilot study whether the nucleus raphé magnus, a descending serotonergic brainstem region whose stimulation improves recovery after incomplete spinal cord injury, can influence these transcriptional changes. Rats received 2 hours of low-frequency electrical stimulation in the raphé magnus three days after an impact contusion at segment T8. Comparison groups lacked injuries or activated stimulators or both. Immediately following stimulation, spinal cords were extracted, their RNA transcriptome sequenced, and differential gene expression quantified. Confirming many previous studies, injury primarily increased inflammatory and immune transcripts and decreased those related to lipid and cholesterol synthesis and neuronal signaling. Stimulation plus injury, contrasted with injury alone, caused significant changes in 43 transcripts (39 increases, 4 decreases), all protein-coding. Injury itself decreased only four of these 43 transcripts, all reversed by stimulation, and increased none of them. The non-specific 5-HT7 receptor antagonist pimozide reversed 25 of the 43 changes. Stimulation in intact rats principally caused decreases in transcripts related to oxidative phosphorylation, none of which were altered by stimulation in injury. Gene ontology (biological process) annotations comparing stimulation with either no stimulation or pimozide treatment in injured rats highlighted defense responses to lipopolysaccharides and microorganisms, and also erythrocyte development and oxygen transport (possibly yielding cellular oxidant detoxification). Connectivity maps of human orthologous genes generated in the CLUE database of perturbagen-response transcriptional signatures showed that drug classes whose effects in injured rats most closely resembled stimulation without pimozide include peroxisome proliferator-activated receptor agonists and angiotensin receptor blockers, which are reportedly beneficial in spinal cord injury. Thus, the initial transcriptional response of injured spinal cord to raphé magnus stimulation is upregulation of genes that in various ways are mostly protective, some probably located in recently arrived myeloid cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31803022" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133157" }, "primaryId" : "GEO:GSE133157", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133157" } ] }, "title" : "Differential Expression profiles of tRNA-Derived Small RNAs in Rats After Traumatic Spinal Cord Injury", "dateAssigned" : "2019-06-21T00:00:00.000-05:00", "summary" : "The goals of this study are to screen differential expression profiles of tRNA-Derived small RNAs (tsRNAs) in rats after traumatic spinal cord injury (SCI) using next-generation sequencing and qRT-PCR.As a result, in rat spinal cord 1 day after contusion, totally 297 tsRNAs differentially expressed were identified. 155 tsRNAs were significantly differentially expressed: 91 were significantly up-regulated, while 64 were significantly down-regulated after SCI (folding change>1.5; P<0.05).Next, four tsRNAs were selected to be verified by qRT-PCR. Taken together,this study explored, for the first time, the significant alteration of tsRNA expression profiles after traumatic SCI in rats and offered deep insights into many possible treatment targets of SCI by regulating tsRNAs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31998075" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133223" }, "primaryId" : "GEO:GSE133223", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133223" } ] }, "title" : "Inhibitory effects of Fusobacterium nucleatum on osteogenic differentiation of osteoblasts and its molecular mechanism", "dateAssigned" : "2019-06-24T00:00:00.000-05:00", "summary" : "Background: F.nucleatum is one of the important pathogens of periodontitis, and the main symptom of periodontitis is alveolar bone loss. The study of F.nucleatum in alveolar bone loss caused by periodontitis is still very insufficient. In this study, the biological behavior of osteoblasts stimulated by F.nucleatum was studied to elucidate the mechanism of bone loss in periodontitis. Methods:A primary rat calvarial osteoblast culture model was established and invaded repeatedly with F.nucleatum (ATCC 25586). Transcriptome analysis at multiple time points(days 1, 3, 7, 14, 21 and 28) was applied to identify gene expression changes in osteoblasts stimulated by F.nucleatum. Cell-counting and EDU-labeling assay were used to analyze the effects of F.nucleatum on the cell proliferation. Flow cytometry and enzyme linked immunosorbent assay (ELISA) was used to analysis the cell apoptosis, cell cycle and secreted inflammatory cytokines changes. ALP activity testing, Alizarin red mineralized nodules staining and calcium content assays, qPCR and western blot were carried on to evaluate the osteogenic differentiation and mineralization of osteoblasts. Results: Cytology experiments and RNA-seq analysis showed that F.nucleatum could inhibit cell proliferation, promote cell apoptosis, block cell cycle of osteoblasts and promote inflammatory cytokines production in a dose- and time-dependent manner. Besides, F. nucleatum could significantly inhibited osteoblasts differentiation and mineralization via a series inhibition of the differentiation regulatory genes and proteins. Whole-transcriptome analysis identified a total of 235 transcripts that were differentially expressed in all six time-points, most of which were inflammatory-related genes. The genes, Ccl2, Ccl20, Csf1, Cx3cl1, Cxcl1, Cxcl3, Il6, Birc3, Map3k8, Nos2, Nfkb2, Tnfrsf1b and Vcam1, played core roles in a PPI network and interacted closely with other ones in the infection. In addition, 133 osteogenesis-related DEGs were time-serially dynamically changed in a short time-series expression miner (STEM) analysis, which were enriched in multiple cancer-related pathways. The core dynamic DEGs (Mnda, Cyp1b1, Comp, Phex, Mmp3, Tnfrsf1b, Fbln5 and Nfkb2) had been reported to be closely related to the development and metastasis in tumor and cancer progress. This study is the first to evaluate the long-term interaction of F. nucleatum on osteoblasts, which might increase the risk of cell carcinogenesis of normal osteoblasts, and provides new insight into the pathogenesis of bacterial-induced bone destruction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33042984" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133293" }, "primaryId" : "GEO:GSE133293", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133293" } ] }, "title" : "Ozone exposure differentially changed global gene expression at brainstem and hypothalamus in healthy (SHAM) and adrenalectomized rats", "dateAssigned" : "2019-06-25T00:00:00.000-05:00", "summary" : "Ozone exposure in SHAM rats resulted in increases and decreases in expression of hundreds of genes in brainstem and hypothalamus relative to air-exposed SHAM rats (303 and 568 genes, respectively). Adrenalectomy in air-exposed rats resulted in few significant transcriptional differences in the brainstem and hypothalamus (~20 genes per tissue). Differentially expressed genes from ozone exposure were enriched for pathways involving hedgehog signaling, responses to alpha-interferon, hypoxia, and mTORC1, among others. Gene changes in both brain areas were analogous to those altered by corticosteroids and L-dopa, suggesting a role for endogenous glucocorticoids and catecholamines. AD completely prevented this ozone-induced transcriptional response. These findings show that short-term ozone inhalation promotes a shift in brainstem and hypothalamic gene expression that is dependent on the presence of circulating adrenal-derived stress hormones.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133330" }, "primaryId" : "GEO:GSE133330", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133330" } ] }, "title" : "Gene expression fingerprinting of ameloblasts shows changes in the endocytosis/cytoskeleton interface across stages.", "dateAssigned" : "2019-06-26T00:00:00.000-05:00", "summary" : "We used RNA-seq to identify differentially expressed genes across ameloblast stages in rats. We found expression patterns of enamel matrix proteins, ion channels and transporters, and endocytosis regulators such as clathrin to match those found in previous experimental studies on ameloblasts. We hypothesized that ameloblasts change their endocytotic pathways as they progress from stage and stage, and we sought to identify novel patterns in expression of genes at the endocytosis/cytoskeleton interface. We found that maturation ameloblasts preferentially express synaptojanin 1 and intersectin 2 and secretory ameloblasts preferentially express Numb protein and amphiphysin. We also uncovered differential alternative splicing of ECI genes across ameloblast populations. In pointing to endocytotic genes hitherto unexplored in ameloblasts that also regulate cell morphology, this bioinformatics study suggests a mechanism by which cervical loop, secretory, and maturation ameloblasts switch modes of endocytosis in order to express genes that better suit the distinct morphology of each cell stage.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133402" }, "primaryId" : "GEO:GSE133402", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133402" } ] }, "title" : "Transcriptomic profiles reveal differences between the right and left ventricle (RV and LV) in both normoxia and hypoxia", "dateAssigned" : "2019-06-27T00:00:00.000-05:00", "summary" : "We performed RNA-seq to analyze gene expression in rat cardiac tissue from the left and right ventricle for animals in a) normoxia and b) exposed to hypoxia (10% O2) for 2 weeks", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31960631" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133508" }, "primaryId" : "GEO:GSE133508", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133508" } ] }, "title" : "Gene Expression Profiling of Oligodendrocyte Precursor Cells Conditioned with Interferon gamma", "dateAssigned" : "2019-06-28T00:00:00.000-05:00", "summary" : "Interferon Gamma suppresses genes associated with OPC differentiation and induces genes associated with antigen presentation", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31467299" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133563" }, "primaryId" : "GEO:GSE133563", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133563" } ] }, "title" : "Transcriptional profiling of the rat retina after optic nerve crush uncovers sustained activation of the complement cascade and Delta-Notch signaling pathways", "dateAssigned" : "2019-07-01T00:00:00.000-05:00", "summary" : "Glaucoma is a multifactorial neurodegenerative disease, characterized by degeneration of the neurons known as retinal ganglion cells (RGCs). Although distinct in vivo animal models have been used to investigate the mechanisms of both RGC degeneration and reorganization of the retina, there has been little progress in developing efficient strategies for neuroprotection in glaucoma. In the present study, we used transcriptomic profiles of Lister Hooded rats’ retinas 2 weeks after optic nerve crush (ONC) and applied systems biology approaches to better understand the molecular mechanisms by which ONC induced the remodeling of the retinal tissue. We calculated the relative expression variability scored as a statistical measure of the variability of transcript abundance in our datasets and found higher variability after ONC. Also, gene expression stability was used as a score of transcription control and we found a reduction in the number of very stably expressed genes from 336 to 124. Enrichment analysis showed that Complement cascade and Notch signaling pathway were the main affected pathways after ONC. In order to deepen our studies on these two pathways, we performed coordination analysis of genes within each pathway and with the entire transcriptome. ONC increased the number of synergistically coordinated pairs of genes and increased the number of similar profiles. This study goes beyond the regulation of individual gene expression showing striking changes in the control of expression by Complement cascade and Notch signaling functional pathways important for RGC degeneration and remodeling of the retinal tissue two weeks after ONC.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133602" }, "primaryId" : "GEO:GSE133602", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133602" } ] }, "title" : "Circular RNA expression profile in the spinal cord of morphine tolerated rats and screen of putative key circRNAs", "dateAssigned" : "2019-07-01T00:00:00.000-05:00", "summary" : "Microarray analysis for circRNA expression in the spinal cord was conducted and compared between 4 morphine tolerated rats and 4 normal rats", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133696" }, "primaryId" : "GEO:GSE133696", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133696" } ] }, "title" : "Digitoxin Inhibits Epithelial-to-Mesenchymal-Transition in Hereditary Castration Resistant Prostate Cancer", "dateAssigned" : "2019-07-02T00:00:00.000-05:00", "summary" : "We have previously reported that the cardenolide drug digitoxin blocks TNFα/NFκB-driven proinflammatory signaling. We therefore hypothesized that digitoxin might break the collaborative process between NFκB and TGFβ by also inhibiting expression of TGFBR2. We therefore tested whether TGFβ-driven EMT and resulting metastases would be suppressed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31428571" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133716" }, "primaryId" : "GEO:GSE133716", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133716" } ] }, "title" : "Phenotypic and Functional Characteristics of Human Schwann Cells as Revealed by Cell-Based Assays and RNA-SEQ", "dateAssigned" : "2019-07-02T00:00:00.000-05:00", "summary" : "In this study we show the inherent differences between human and rat Schwann cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:29327207" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133717" }, "primaryId" : "GEO:GSE133717", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133717" } ] }, "title" : "Development of 2D organotypic rat liver co-culture models for assessing hepatotoxicant modes of action", "dateAssigned" : "2019-07-02T00:00:00.000-05:00", "summary" : "In both the regulatory and commercial arenas, the goal is to move away from time consuming, costly in-life rodent studies and towards safety assessment strategies that rely on testing species-relevant cells in vitro. The liver has been a major focus of these efforts, yet there are currently no in vitro alternatives for hepatotoxicity testing accepted by regulators, and the assays that do exist typically utilize hepatocyte monolayer culture. While hepatocytes have been the primary component of in vitro hepatotoxicity assay development, the non-parenchymal cells (NPCs) (i.e., hepatic stellate cells, Kupffer cells, and liver sinusoidal endothelial cells) also play a critical role in the progression of liver pathologies. The goal of this study was to develop an organotypic co-culture system that could read out the various mechanisms of action observed in vivo, as well as maintain metabolic capability and extended viability to allow for repeat dosing. We developed a two-dimensional 96-well plate-based co-culture system that includes primary rat hepatocytes, stellate, Kupffer, and endothelial cells that supports hepatocyte viability and phenotype stability for up to eight days. Importantly, markers of hepatocyte differentiation and polarity are maintained in co-culture, but hepatocyte monocultures with no other cell types lose phenotypic markers after prolonged culture. This co-culture model was leveraged to assess the effects of known hepatotoxic stimuli, and the co-culture model resulted in responses that were more representative of the in vivo phenotypes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133744" }, "primaryId" : "GEO:GSE133744", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133744" } ] }, "title" : "Expression Profile Analysis of Rat Motoneurons During Myelination", "dateAssigned" : "2019-07-02T00:00:00.000-05:00", "summary" : "To identify the core components of the myelination process, we adopted a microarray analysis approach combined with laser capture microdissection of spinal motoneurons (MNs) during the myelinogenic phase of development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32647008" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133747" }, "primaryId" : "GEO:GSE133747", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133747" } ] }, "title" : "Single-cell connectomic analysis of adult mammalian lungs", "dateAssigned" : "2019-07-02T00:00:00.000-05:00", "summary" : "Single-cell RNA sequencing (scRNAseq) has made it possible to analyze complex organs such as the lung with unprecedented resolution. We have leveraged these techniques to identify conserved patterns of cell-cell cross-talk in adult mammalian lungs, analyzing mouse, rat, pig and human pulmonary tissues. Following clustering and histological registration, we mapped putative ligand-receptor interactions within and between cell types and assessed the significance of these interactions. Our findings demonstrate specific, stereotyped functional roles for each cell type in the distal lung which emerge as top candidates for the regulation of tissue phenotype.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31840053" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133750" }, "primaryId" : "GEO:GSE133750", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133750" } ] }, "title" : "Transcriptomes in the Sciatic Nerves of Lewis Rats with Experimental Autoimmune Neuritis", "dateAssigned" : "2019-07-03T00:00:00.000-05:00", "summary" : "Guillain-Barré syndrome (GBS) is characterized by acute immune-mediated peripheral neuropathy, which may result in rapidly progressive paralysis and fatal respiratory failure. As the underlying pathological mechanisms of GBS are unclear, we surveyed the transcriptome of rats with experimental autoimmune neuritis (EAN), a model of GBS. Briefly, sciatic nerves on both sides were collected from 8–10-week-old Lewis rats during early (10 days post-induction), peak (19 days), and late neuritis (30 days). Total RNA was sequenced to identify differentially expressed genes. Compared to control rats without induced neuritis, 33 genes were differentially expressed in the early phase (14 upregulated and 19 downregulated), with an adjusted P-value < 0.05 and |log2 fold-change| > 1, as were 137 genes in the peak phase (126 upregulated and 11 downregulated) and 60 genes in the late phase (58 upregulated and 2 downregulated). Eleven of these genes were common to all stages, suggesting their crucial roles throughout the disease course. Analysis of protein-protein interactions revealed Fos, Ccl2, Itgax and C3 as node genes at different stages. Functional analysis of differentially expressed genes identified biological processes and pathways that are activated as neuritis progresses. This is the first genome-wide gene expression study of peripheral nerves in experimental autoimmune neuritis model. Dynamic gene expression and significantly altered biological functions were detected in different phases of the disease, increasing our understanding of the molecular mechanisms underlying EAN and highlighting potential targets for its diagnosis and treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31344254" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133787" }, "primaryId" : "GEO:GSE133787", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133787" } ] }, "title" : "Genome-wide alteration of 5-hydroxymethylcytosine in hypoxic-ischemic neonatal rat model of cerebral palsy", "dateAssigned" : "2019-07-03T00:00:00.000-05:00", "summary" : "Our results revealed that hypoxic-ischemic brain injury decreased the overall 5hmC abundance in rat temporal cortex, and these results suggest that 5hmC modifications are involved in the cerebral palsy pathogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31551709" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133843" }, "primaryId" : "GEO:GSE133843", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133843" } ] }, "title" : "A novel model for chronic rejection in vascularized composite allotransplantation identifies CXCL9-11 as potential biomarkers", "dateAssigned" : "2019-07-05T00:00:00.000-05:00", "summary" : "Global mRNA expression profiling of transplanted rat hindlimbs (muscle and skin) were collected using Agilent rat whole genome array (Agilent-028282 Whole Rat Genome Microarray 4x44K v3). Hind limb transplantation between Fischer344 (donor) and Lewis (recipient) rats were performed. Isogenic transplantations served as controls. Administration of irregular immunosuppression induced chronic rejection. At the endpoint (post-operativ day 100), hind limbs presented clinicial, histomorphological and genetic changes, known to be highly suspicious for chronic rejection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32589662" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133886" }, "primaryId" : "GEO:GSE133886", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133886" } ] }, "title" : "Niche stiffness underlies the aging of CNS progenitor cells.", "dateAssigned" : "2019-07-05T00:00:00.000-05:00", "summary" : "Next generation sequencing of OPCs grown on stiff and soft hydrogels", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31413369" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133904" }, "primaryId" : "GEO:GSE133904", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133904" } ] }, "title" : "The Right Ventricular Fibroblast Secretome Drives Cardiomyocyte Dedifferentiation", "dateAssigned" : "2019-07-06T00:00:00.000-05:00", "summary" : "Conclusions: These data suggest that paracrine factor(s) released by Cfib from the PH calf signal a phenotypic transformation in a population of cardiomyocytes that likely contributes to RV dysfunction. Therapies targeting this process, such as inhibition of periostin, have the potential to prevent RV dysfunction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31374110" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133917" }, "primaryId" : "GEO:GSE133917", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133917" } ] }, "title" : "The NMDA receptor subunit GluN3A regulates a program of synaptic activity-induced and MEF2C-dependent transcription", "dateAssigned" : "2019-07-07T00:00:00.000-05:00", "summary" : "N-methyl-D-aspartate type glutamate receptors (NMDARs) are key mediators of synaptic activity-regulated gene transcription in neurons, both during development and in the adult brain. Developmental differences in the GluN2 subunit composition of NMDARs determines whether NMDARs activate the transcription factor CREB. However, whether the developmentally-regulated GluN3A subunit also modulates NMDAR-induced transcription was unknown. Here we show that knocking down GluN3A in rat hippocampal neurons promotes the inducible transcription of a subset of NMDAR-sensitive genes. This enhancement is mediated by the accumulation of phosphorylated p38 MAP kinase in the nucleus, which drives the activation of the transcription factor MEF2C and promotes the transcription of a subset of synaptic activity-induced genes including Bdnf and Arc. Our evidence that GluN3A negatively regulates MEF2C-dependent transcription reveals a novel mechanism by which NMDAR subunit composition confers specificity on the program of synaptic activity-regulated gene transcription in developing neurons.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32393578" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133951" }, "primaryId" : "GEO:GSE133951", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE133951" } ] }, "title" : "Functional specification of CCK+ interneurons by alternative isoforms of Kv4.3 auxiliary subunits", "dateAssigned" : "2019-07-08T00:00:00.000-05:00", "summary" : "CCK-expressing interneurons (CCK+INs) are crucial for controlling hippocampal activity. We found two firing phenotypes of CCK+INs in rat CA3 area; either possessing a previously undetected membrane potential-dependent firing or regular firing phenotype, due to different low-voltage-activated potassium currents. These different excitability properties destine the two types for distinct functions, because the former is essentially silenced during realistic 8-15 Hz oscillations. The general excitability, morphology and gene-profiles of the two types were surprisingly similar. Even the expression of Kv4.3 channels were comparable, despite evidences showing that Kv4.3-mediated currents underlie the distinct firing properties. Instead, the firing phenotypes were correlated with the presence of distinct isoforms of Kv4 auxiliary subunits (KChIP1 vs. KChIP4e and DPP6S). Our results reveal the underlying mechanisms of two previously unknown types of CCK+INs and demonstrate that alternative splicing of few genes, which may be viewed as a minor event in the cells’ whole transcriptome, can underlie distinct cell-type identity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134070" }, "primaryId" : "GEO:GSE134070", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134070" } ] }, "title" : "Gene expression alternations in the offspring rat intestine from sitagliptin-treated dams", "dateAssigned" : "2019-07-10T00:00:00.000-05:00", "summary" : "More and more evidence shows that maternal overnutrition may increase the risk of diabetes in offspring. This study aimed to find out whether maternal early sitagliptin intervention improves glucose intolerance through gut target in offspring.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33240638" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134071" }, "primaryId" : "GEO:GSE134071", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134071" } ] }, "title" : "Gene expression alternations in Shenqi Jiangtang Granule-treated rats kidney", "dateAssigned" : "2019-07-10T00:00:00.000-05:00", "summary" : "Diabetic nephropathy (DN) is a major microvascular complication of diabetes. In addition to moderating hyperglycemia, Shenqi Jiangtang Granule (SJG) had a beneficial effect on kidney function in a clinical trial. However, the mechanism involved remains unclear. This study was conducted to identify the underlying molecular mechanisms. A diabetic rat model was generated by using a high-fat diet and streptozotocin (STZ) injection. Then, rats were given SJG at dosages of 800 mg/kg/d by gavage for 8 weeks.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31827549" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134072" }, "primaryId" : "GEO:GSE134072", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134072" } ] }, "title" : "Gene expression alternations in Qishen Yiqi Dripping Pill-treated rats kidney", "dateAssigned" : "2019-07-10T00:00:00.000-05:00", "summary" : "Diabetic nephropathy (DN) is a severe microvascular complication of diabetes. Qishen Yiqi Dripping Pill (QYDP) has been reported to be a renal protective drug. However, the mechanisms remain not certain. This study was performed to investigate the mechanisms of the extract. In this study, Sprague Dawley SD rats were fed with a high-fat diet, and injected with streptozotocin (STZ) to generate a diabetic model. Diabetic rats were administered QYDP.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33679423" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134107" }, "primaryId" : "GEO:GSE134107", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134107" } ] }, "title" : "Tolerance to cocaine-induced motor effects in rats: transcriptomic regulations in the ventral striatum", "dateAssigned" : "2019-07-10T00:00:00.000-05:00", "summary" : "Comparison of gene expression in the dorsal striatum of rats after chronic binge or acute binge cocaine injections or saline treatment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33159041" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134149" }, "primaryId" : "GEO:GSE134149", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134149" } ] }, "title" : "Genome-wide analysis of liver gene expression in prenatally undernourished male rat offspring under high-fat diet", "dateAssigned" : "2019-07-11T00:00:00.000-05:00", "summary" : "Based on the developmental origin of health of disease hypothesis, we previously showed that prenatal 70% maternal food restriction (FR30) predisposes the offspring to development of pathologies in adulthood. In the present study, we focused on the liver gene expression profile of standard and high fat (HF)-fed FR30 adult offspring.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134154" }, "primaryId" : "GEO:GSE134154", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134154" } ] }, "title" : "Tolerance to cocaine-induced motor effects in rats: transcriptomic regulations in the dorsal striatum", "dateAssigned" : "2019-07-11T00:00:00.000-05:00", "summary" : "Comparison of gene expression in the dorsal striatum of rats after chronic binge or acute binge cocaine injections or saline treatment", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33159041" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134203" }, "primaryId" : "GEO:GSE134203", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134203" } ] }, "title" : "Genomic decoding of neuronal depolarization by stimulus-specific NPAS4 heterodimers, RNA sequencing", "dateAssigned" : "2019-07-12T00:00:00.000-05:00", "summary" : "Cells regulate gene expression in response to salient external stimuli. In neurons, depolarization leads to the expression of inducible transcription factors (ITFs) that direct subsequent gene regulation. Depolarization encodes both a neuron’s action potential (AP) output and synaptic inputs, via excitatory postsynaptic potentials (EPSPs). However, it is unclear if distinct types of electrical activity can be transformed by an ITF into distinct modes of genomic regulation. Here, we show that APs and EPSPs in mouse hippocampal neurons trigger two spatially segregated and molecularly distinct induction mechanisms that lead to the expression of the ITF NPAS4. These two pathways culminate with the formation of stimulus-specific NPAS4 heterodimers that exhibit distinct DNA binding patterns. Thus, NPAS4 differentially communicates increases in a neuron’s spiking output and synaptic inputs to the nucleus, enabling gene regulation to be tailored to the type of depolarizing activity along the somato-dendritic axis of a neuron.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134272" }, "primaryId" : "GEO:GSE134272", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134272" } ] }, "title" : "Gene expression changes in rat islets with glucolipotoxic conditions with or without protective compound", "dateAssigned" : "2019-07-15T00:00:00.000-05:00", "summary" : "To determine which GLT-regulated genes might be affected by compound D, we performed an RNA-sequencing analysis of rat islets treated ex-vivo with or without GLT and compound D for 3 hours and 24 hours. Compound E (related inactive compound) was used to account for non-specific scaffold effects.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134309" }, "primaryId" : "GEO:GSE134309", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134309" } ] }, "title" : "RNA-Seq data from cortex and hippocampus (post novel object recognition test) of rats in a vagus nerve stimulation study", "dateAssigned" : "2019-07-15T00:00:00.000-05:00", "summary" : "Vagus nerve stimulation (VNS) has been shown to enhance learning and memory, yet the mechanisms behind these enhancements are unknown. We show that VNS altered the hippocampal, cortical, and blood epigenetic transcriptomes in male Sprague Dawley rats whether or not the rats performed a novelty preference behavioral task. In the hippocampus, novelty preference correlated with decreased histone deacetylase 11 (HDAC11), a transcriptional repressor enriched in CA1 cells important for memory consolidation. In the cortex, the immediate early gene (IEG) ARC was increased in VNS rats and correlated with transcription of plasticity genes and epigenetic regulators, including HDAC3. For rats performing the novelty preference task, ARC correlated with performance. Surprisingly, VNS did not significantly reduce transcription of cortical or hippocampal proinflammatory cytokines. However, TNFRSF11B (osteoprotegerin) correlated with novelty preference as well as plasticity, stress–response signaling, and epigenetic regulation in both hippocampus and cortex. Together, our findings provide the first evidence that VNS induces widespread changes in the cognitive epigenetic landscape and specifically affects epigenetic modulators associated with novelty preference, stress–response signaling, memory consolidation, and cortical neural remodeling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30804093" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134340" }, "primaryId" : "GEO:GSE134340", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134340" } ] }, "title" : "microRNAs from rat muscle derived stem cells treated with lipid factors", "dateAssigned" : "2019-07-16T00:00:00.000-05:00", "summary" : "This is to test whether exposure to lipids has an effect, particularly a damaging effect, on stem cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31430893" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134362" }, "primaryId" : "GEO:GSE134362", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134362" } ] }, "title" : "Changes in rat sperm DNA methylation induced by age and by perinatal exposure to brominated flame retardant flame retardants 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47)", "dateAssigned" : "2019-07-16T00:00:00.000-05:00", "summary" : "Advanced paternal age at fertilization has been suggested to be a risk factor for neurodevelopmental, psychiatric and other disorders in offspring. One emerging hypothesis suggests that altered offspring phenotype is linked with age-related accumulation of epigenetic changes in the sperm of fathers. Given that paternal age is increasing in the developed world, understanding aging-related epigenetic changes in sperm is needed as well as environmental factors that modify such changes. In this study, we characterize age-dependent changes in sperm DNA methylation profiles between young pubertal (postnatal day (PNDs) 65) and mature (PND120) Wistar rats. We also analyze these changes in rats exposed perinatally to 0.2 mg/kg of ubiquitous environmental xenobiotic 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47). Reduced representation bisulfite sequencing (RRBS) libraries were prepared from caudal epididymal sperm DNA and differentially methylated regions (DMRs; ≥ 10x coverage depth, ≥ 3 CpGs per cluster, ≥ 5% methylation change, q < 0.05) were identified via MethPipe package. We identified 21 and 9 exposure-related DMRs in sperm collected on PND65 and PND120, respectively. Two DMRs overlapped between the two time-points. This is the first study to demonstrate that environmentally-relevant perinatal exposure to PBDE results in long-lasting changes in sperm DNA methylation. In control animals, 5,319 age-dependent DMRs were identified, with 99.3% DMRs hypermethylated in mature animals compared to young pubertal rats. These age-related DMRs were enriched for functional categories essential for embryonic development, such as pattern specification, forebrain and sensory organ development, and the Wnt pathway. In BDE-47 exposed rats, sperm DNA methylation was higher in young pubertal and lower in mature animals when compared to controls, which resulted in a significant attenuation in the number of age-dependent DMRs (N = 189) identified in the exposed group. In conclusion, our results indicate that the natural aging process has profound effects on sperm methylation levels and this effect may be modified by environmental exposures. Moreover, our results further support the role of sperm DNA methylation as a likely mechanism by which advanced paternal age is associated with adverse offspring health and development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134569" }, "primaryId" : "GEO:GSE134569", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134569" } ] }, "title" : "In vitro transcriptomic responses to thioacetamide-S-oxide exposure in Sprague-Dawley rat primary hepatocytes, renal tube epithelial, and cardiomyocytes", "dateAssigned" : "2019-07-19T00:00:00.000-05:00", "summary" : "In this study we tested the ability to predict organ injury endpoints from in vitro transcriptomics responses at early time points (9 and 24 hours) after to thioacetamide-S-oxide treatment, the toxic metabolite of thioacetamide. Thioacetamide, an organosulfur compound, have been extensively used in animal studies as a hepatotoxin and carcinogen for its ability to cause acute liver damage.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31850077" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134699" }, "primaryId" : "GEO:GSE134699", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134699" } ] }, "title" : "A circular RNA generated from an intron of the insulin gene controls insulin secretion", "dateAssigned" : "2019-07-23T00:00:00.000-05:00", "summary" : "Fine-tuning of insulin release from pancreatic β-cells is essential to maintain blood glucose homeostasis. Here, we report that insulin secretion is regulated by a circular RNA containing the lariat sequence of the second intron of the insulin gene. Silencing of this intronic circular RNA in pancreatic islets leads to a decrease in the expression of key components of the secretory machinery of β-cells, resulting in impaired glucose- or KCl-induced insulin release and calcium signaling. The effect of the circular RNA is exerted at the transcriptional level and involves an interaction with the RNA-binding protein TAR DNA-binding protein 43 kDa (TDP-43). The level of this circularized intron is reduced in the islets of rodent diabetes models and of type 2 diabetic patients, possibly explaining their impaired secretory capacity. The study of this and other circular RNAs helps understanding β-cell dysfunction under diabetes conditions, and the etiology of this common metabolic disorder.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33154349" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134705" }, "primaryId" : "GEO:GSE134705", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134705" } ] }, "title" : "Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program (scRNA-seq)", "dateAssigned" : "2019-07-23T00:00:00.000-05:00", "summary" : "Here we characterize microglia transcriptional program across ten species spanning more than 450 million years of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human, including ligands and receptors associated with interactions between glia and neurons. In most species, microglia show a single dominant transcriptional state, while humans express significant microglia heterogeneity. In addition, we observed notable differences in complement, phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders, including Alzheimer’s and Parkinson’s disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia-based therapies in humans.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134706" }, "primaryId" : "GEO:GSE134706", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134706" } ] }, "title" : "Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program (bulk RNA-seq)", "dateAssigned" : "2019-07-23T00:00:00.000-05:00", "summary" : "Here we characterize microglia transcriptional program across ten species spanning more than 450 million years of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human, including ligands and receptors associated with interactions between glia and neurons. In most species, microglia show a single dominant transcriptional state, while humans express significant microglia heterogeneity. In addition, we observed notable differences in complement, phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders, including Alzheimer’s and Parkinson’s disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia-based therapies in humans.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134715" }, "primaryId" : "GEO:GSE134715", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134715" } ] }, "title" : "Rat (Wistar) Liver CDAA Diet 4-8-12 Weeks Ensembl84 (BIBC)", "dateAssigned" : "2019-07-23T00:00:00.000-05:00", "summary" : "Nonalcoholic steatohepatitis (NASH) is a major cause of liver fibrosis with increasing prevalence worldwide. Currently there are no approved drugs available. The development of new therapies is difficult as diagnosis and staging requires biopsies. Consequently, predictive plasma biomarkers would be useful for drug development. Here we present a multi-omics approach to characterize the molecular pathophysiology and to identify new plasma biomarkers in a choline-deficient L-amino acid-defined diet rat NASH model. We analyzed liver samples by RNA-Seq and proteomics, revealing disease relevant signatures and a high correlation between mRNA and protein changes. Comparison to human data showed an overlap of inflammatory, metabolic, and developmental pathways.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31992752" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134765" }, "primaryId" : "GEO:GSE134765", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134765" } ] }, "title" : "Transcriptome analysis of freshly isolated young and aged rat oligodendrocyte progenitor cells (OPCs)", "dateAssigned" : "2019-07-24T00:00:00.000-05:00", "summary" : "The age-related failure to regenerate lost oligodendrocytes from oligodendrocyte progenitor cells (OPCs) is associated with irreversible neurodegeneration in multiple sclerosis. Consequently, regenerative therapies for chronic demyelinating diseases remain a long sought after but elusive goal. Here we show that adult OPCs lose their inherent differentiation potential with increasing age. Moreover, aged OPCs do not remain responsive to pro-differentiation signals, posing significant constraints on the effectiveness of remyelination therapies based on the enhancement of OPC differentiation. We show that this reduced regenerative capacity is associated with hallmarks of cellular ageing, including reduced metabolic function and increased DNA damage. We find that fasting or treatment with metformin can reverse these changes and restore the regenerative capacity of aged OPCs, improving remyelination in aged animals following white matter injury. Importantly, aged OPCs treated with metformin regain their responsiveness to pro-differentiation factors, suggesting a potential for synergistic effects of rejuvenation and pro-differentiation therapies. Our findings have direct implications for understanding oligodendrocyte regeneration failure with ageing and how it might be reversed therapeutically.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31585093" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134799" }, "primaryId" : "GEO:GSE134799", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134799" } ] }, "title" : "ChIP assay in adult ventricular cardiomyocytes", "dateAssigned" : "2019-07-24T00:00:00.000-05:00", "summary" : "ChIP assay was performed to study the genomic location of SRF myocytes cistrome in adult ventricular cardiomyocytes. The myocytes were stimulated by phenylephrine (PE) combined with adenoviral overexpression of SRF serine-103 mutants.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32933333" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134800" }, "primaryId" : "GEO:GSE134800", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134800" } ] }, "title" : "PRO-seq assay in adult ventricular cardiomyocytes", "dateAssigned" : "2019-07-24T00:00:00.000-05:00", "summary" : "PRO-seq assay was performed for the quantitative detection of nascent pre-mRNA transcripts induced by phenylephrine (PE) and adenoviral overexpression of SRF serine-103 mutants in adult ventricular cardiomyocytes", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32933333" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134804" }, "primaryId" : "GEO:GSE134804", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134804" } ] }, "title" : "Pan-ampk activation improves renal function in a rat model of progressive diabetic nephropathy", "dateAssigned" : "2019-07-24T00:00:00.000-05:00", "summary" : "Chronic kidney disease (CKD) remains a tremendous and growing burden on the healthcare system and new therapies are needed to prevent or slow disease progression. Metabolic dysregulation and mitochondrial dysfunction are important features of acute and chronic tissue injury across species, and human genetics and preclinical data suggest that the master metabolic regulator 5'-adenosine monophosphate activated protein kinase (AMPK) may be an effective therapeutic target for CKD. Merck has recently disclosed a pan-AMPK activator MK-8722 which was shown to have beneficial effects on metabolic parameters in preclinical models. In this study we investigate the effects of MK-8722 in a progressive model of diabetic nephropathy to determine whether activation of AMPK would be of therapeutic benefit. We find that MK-8722 administration in a therapeutic paradigm is profoundly reno-protective. We provide evidence that the therapeutic effects may be mediated by modulation of renal mitochondrial quality control as well as by attenuating fibrotic and lipotoxic mechanisms in kidney cells. These data further validate the concept that targeting metabolic dysregulation in CKD could be a potential therapeutic approach.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31300612" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134824" }, "primaryId" : "GEO:GSE134824", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134824" } ] }, "title" : "Genome-wide analysis of long noncoding RNAs and mRNAs associated with contrast-induced acute kidney injury", "dateAssigned" : "2019-07-25T00:00:00.000-05:00", "summary" : "Conclusions:These prefound findings provide the first evidence of lncRNA in the development of CI-AKI.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134935" }, "primaryId" : "GEO:GSE134935", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134935" } ] }, "title" : "Cannabinoid exposure in adolescence reprograms the PFC’s molecular response to cocaine", "dateAssigned" : "2019-07-26T00:00:00.000-05:00", "summary" : "There are still no neurobiological data on whether prior cannabinoid exposure modifies the brain’s molecular response to cocaine. We investigated epigenomics, transcriptomics to characterize molecular changes in subcellular PFC compartments, including nucleus, cytoplasm and synaptosomes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134963" }, "primaryId" : "GEO:GSE134963", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134963" } ] }, "title" : "4 Week Post Partical Pancreatectomy", "dateAssigned" : "2019-07-26T00:00:00.000-05:00", "summary" : "There are two groups of rats, 1) Post 90% Partial Pancreatectomy (PPX) and the Sham Group.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134966" }, "primaryId" : "GEO:GSE134966", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE134966" } ] }, "title" : "10 Week Post Partical Pancreatectomy", "dateAssigned" : "2019-07-26T00:00:00.000-05:00", "summary" : "There are two groups of rats, Post 90% Partial Pancreatectomy (PPX) and the Sham group.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135000" }, "primaryId" : "GEO:GSE135000", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135000" } ] }, "title" : "Expression data from Sprague Dawley rat lenses cultured for 4 days - addition of various inhibitors", "dateAssigned" : "2019-07-29T00:00:00.000-05:00", "summary" : "We created a rat sugar cataract model and examined the effects of various inhibitors on lens clouding. Lenses were removed from 6-week-old SD rats and cultured in M199 medium containing 30 mM galactose.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31882756" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135061" }, "primaryId" : "GEO:GSE135061", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135061" } ] }, "title" : "The aryl hydrocarbon receptor regulates nucleolar activity and protein synthesis in MYC-expressing cells", "dateAssigned" : "2019-07-29T00:00:00.000-05:00", "summary" : "MYC enhances protein synthesis by regulating genes involved in ribosome biogenesis and protein translation. Here, we show that MYC-induced protein translation is mediated by the transcription factor aryl hydrocarbon receptor (AHR), which is induced by MYC in colonic cells. AHR promotes protein synthesis by activating the transcription of genes required for ribosome biogenesis and protein translation, including OGFOD1 and NOLC1. Using surface sensing of translation (SUnSET) to measure global protein translation, we found that silencing AHR or its targets diminishes protein synthesis. Therefore, targeting AHR or its downstream pathways could provide a novel approach to limit biomass production in MYC-driven tumors.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30254109" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135073" }, "primaryId" : "GEO:GSE135073", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135073" } ] }, "title" : "Changes in axonal and somatic transcriptomes in response to Pum2 knockdown", "dateAssigned" : "2019-07-29T00:00:00.000-05:00", "summary" : "We report that knockdown of Pum2 results in an increase of PBE containing mRNAs in axons, without changing mRNA levels in the cell bodies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31606248" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135080" }, "primaryId" : "GEO:GSE135080", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135080" } ] }, "title" : "Novel drug-like RAR-Beta agonist induces BRCA1 to prevent neuropathic pain", "dateAssigned" : "2019-07-30T00:00:00.000-05:00", "summary" : "Neuropathic pain (NP) is associated with profound gene expression alterations within the nociceptive system. DNA mechanisms, such as epigenetic remodelling and repair pathways have been implicated in NP. Here we have used a rat model of peripheral nerve injury to study the effect of a novel RARβ-agonist, C286, currently under clinical research, in NP. A four week treatment initiated two days after the injury normalised pain sensation. Genome-wide and pathway enrichment analysis showed that multiple mechanisms persistently altered in the spinal cord were restored to preinjury levels by the agonist. Concomitant upregulation of DNA repair proteins, ATM and BRCA1, the latter being required for C286 mediated pain modulation, suggest that early DNA repair may be important to prevent phenotypic epigenetic imprints in NP. Thus, C286 is a promising drug candidate for neuropathic pain and DNA repair mechanisms may be useful therapeutic targets to explore.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31726373" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135172" }, "primaryId" : "GEO:GSE135172", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135172" } ] }, "title" : "The role of stretch, tachycardia and sodium-calcium exchanger in induction of early cardiac remodeling", "dateAssigned" : "2019-07-31T00:00:00.000-05:00", "summary" : "Neonatal rat ventricular cardiomyocytes (NRVCM) were subjected to mechanical stress and high freqency elecrical stimulation to study genes regulated during the early phase of trigger induced cardiac remodeling. Inhibition of the sodium calcium exchanger was used in an attempt to supress the early remodeling process and gain insight into the pathological signaling pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32573098" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135388" }, "primaryId" : "GEO:GSE135388", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135388" } ] }, "title" : "Germline development in rat revealed by visualization and deletion of Prdm14", "dateAssigned" : "2019-08-05T00:00:00.000-05:00", "summary" : "Primordial germ cells (PGCs), the founder cells of the germline, are specified in pre-gastrulating embryos in mammals, and subsequently migrate towards gonads to mature into functional gametes. Here, we investigated PGC development in rats, by genetically modifying Prdm14, a unique marker and a critical PGC transcriptional regulator. We trace PGC development in rats, for the first time, from specification until sex determination stage in fetal gonads using Prdm14 H2BVenus knock-in rats. We uncover that Prdm14’s crucial role in PGC specification is conserved between rat and mice, by analyzing Prdm14 deficient rat embryos. Notably, loss of Prdm14 completely abrogates the PGC program: failure in maintenance and/or activation of germ cell markers and pluripotency genes. Finally, we profile the transcriptome of the postimplantation epiblast and all PGC stages in rat, to reveal enrichment of distinct gene sets at each transition point, thereby providing an accurate transcriptional time-line for rat PGC development. Thus, the novel genetically modified rats and data sets obtained in this study will advance our knowledge on conserved vs species-specific features for germline development in mammals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135441" }, "primaryId" : "GEO:GSE135441", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135441" } ] }, "title" : "Transcriptomes of Major Proximal-Tubule Cell-Culture Models", "dateAssigned" : "2019-08-06T00:00:00.000-05:00", "summary" : "Results and conclusion: Transcripts expressed in cell lines showed variable match to transcripts selectively expressed in native proximal tubule. Opossum kidney (OK) cells displayed the highest percentage match (45%) with pig kidney cells (LLC-PK1) close behind (39%). Much lower percentage matches were seen for various human lines including HK-2 cells (26%) and lines from rodent kidneys (18-23%).An online resource (https://esbl.nhlbi.nih.gov/JBrowse/KCT/) has been created for interrogation of the data.No cell line closely matched the transcriptome of native proximal tubule cells. However, some of the lines tested are suitable for the study of particular metabolic and transport processes seen in the proximal tubule.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33122286" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135538" }, "primaryId" : "GEO:GSE135538", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135538" } ] }, "title" : "mRNA sequencing of clinical-grade neural stem cells derived from human ES cells", "dateAssigned" : "2019-08-07T00:00:00.000-05:00", "summary" : "We report the transcriptome profile of human neural stem cells derived from ES cells. Cells were transplanted into rodent models, and mRNA transcripts from the chimeric graft tissue were bioinformatically split according to species of origin.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31740836" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135611" }, "primaryId" : "GEO:GSE135611", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135611" } ] }, "title" : "TDP-43 knockdown in primary rat astrocytes", "dateAssigned" : "2019-08-08T00:00:00.000-05:00", "summary" : "TDP-43 is an RNA binding protein involved in amyotrophic lateral sclerosis and other neurodegenerative diseases. The purpose of this study was to determine if loss of TDP-43 function leads to accumulation of repetitive element transcripts, double-stranded RNA (dsRNA) and innate immune activation that may be involved in disease pathology. TDP-43 was knocked down in primary rat astrocytes via siRNA, cells were treated with/without ATP (an immune modulator), and polyA RNA-seq was performed to profile gene expression. Immunoprecipitation/RNA-seq was also performed using a dsRNA-specific antibody to identify potential dsRNAs resulting from TDP-43 knockdown.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31229690" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135700" }, "primaryId" : "GEO:GSE135700", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135700" } ] }, "title" : "Regular exercise potentiates energetically expensive hepatic de novo lipogenesis during early weight regain", "dateAssigned" : "2019-08-11T00:00:00.000-05:00", "summary" : "Obese rats were calorically restricted with (EX) or without (SED) treadmill exercise (1 h/day, 6 days/wk, 15 m/min) to induce and maintain weight loss. After 6 weeks of WLM, subsets of WLM-SED and WLM-EX rats were allowed ad libitum access to food for 1 day to promote relapse (REL). An energy gap-matched group of sedentary, relapsing rats (REL-GM) were provided a diet matched to the positive energy imbalance of the REL-EX rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31553623" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135709" }, "primaryId" : "GEO:GSE135709", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135709" } ] }, "title" : "RNA-seq analysis for mRNA expression difference between male and female cultured oligodendrocyte precursor cells", "dateAssigned" : "2019-08-12T00:00:00.000-05:00", "summary" : "The susceptibility to neurological and psychiatric disorders reveals sex-specific differences. Several studies have reported sex-related differences in the structure and function of human brains. Oligodendrocyte precursor cells (OPCs) regulate the neuronal system in various ways and play crucial roles in brain homeostasis besides their well-known role as a reservoir for mature oligodendrocytes. Here, we revealed transcriptomic differences in OPCs isolated from male and female neonatal rat brains.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32563975" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135822" }, "primaryId" : "GEO:GSE135822", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135822" } ] }, "title" : "Hypolipidemic effects of Zexie Decoction on the lipid profile in hyperlipidemia rats by RNA-sequencing", "dateAssigned" : "2019-08-14T00:00:00.000-05:00", "summary" : "RNA sequencing and transcriptome analysis were performed collaboratively, including analysis of differentially expressed genes (DEGs), GO functions and KEGG pathway analysis. The results showed that 1981 (1370 upregulated and 611 downregulated) DEGs were identified in the HFD group compared to those in the CON group. 474 DEGs (350 upregulated and 124 downregulated) were detected in the ZXD group compared to those in the HFD group. Furthermore, GO analysis revealed that DEGs were mainly involved in the following functions: developmental process, response to external stimulus, ion transport, alcohol binding and plasma membrane part. Pathway analysis suggested that these DEGs were significantly enriched in bile secretion, malaria, cell adhesion molecules, retinol metabolism, the sphingolipid signaling pathway, chemical carcinogenesis, and the T cell receptor signaling pathway. In conclusion, our study demonstrated that ZXD alleviated the lipid metabolism disorder caused by hyperlipidemia through multiple mechanisms, which provided vital scientific evidence for further pharmacological studies of ZXD.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135856" }, "primaryId" : "GEO:GSE135856", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135856" } ] }, "title" : "Gene expression levels after TMAO treatment", "dateAssigned" : "2019-08-15T00:00:00.000-05:00", "summary" : "We used microarray to analyze the genes regulated by TMAO treatment in primary rat hepatocytes to further understand the mechanistic view of TMAO action.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31543404" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135931" }, "primaryId" : "GEO:GSE135931", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135931" } ] }, "title" : "Effect of dioxin on hypothalamic mRNAs in maternal rats at postpartum day 7", "dateAssigned" : "2019-08-18T00:00:00.000-05:00", "summary" : "We found that oral administration of TCDD (1 µg/kg) to pregnant rats on gestational day 15 suppressed maternal production of prolactin, a pituitary hormone essential for nursing including milk production, during the lactational stage. To comprehensively investigate genes linked to the lower prolactin expression, we performed a DNA microarray analysis in the hypothalamus, which regulates the pituitary prolactin synthesis, of lactating dam rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135932" }, "primaryId" : "GEO:GSE135932", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE135932" } ] }, "title" : "Effect of dioxin on pituitary mRNAs in maternal rats at postpartum day 7", "dateAssigned" : "2019-08-18T00:00:00.000-05:00", "summary" : "We found that oral administration of TCDD (1 µg/kg) to pregnant rats on gestational day 15 suppressed maternal production of prolactin, a pituitary hormone essential for nursing including milk production, during the lactational stage. To comprehensively investigate genes linked to the lower prolactin expression, we performed a DNA microarray analysis in the pituitary of lactating dam rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136098" }, "primaryId" : "GEO:GSE136098", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136098" } ] }, "title" : "Identification of AIA-related genes", "dateAssigned" : "2019-08-21T00:00:00.000-05:00", "summary" : "To obtain AIA-related genes [the significant differentially expressed genes (DEGs) of AIA model group vs. Normal control group], the microarray analysis was carried out.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136387" }, "primaryId" : "GEO:GSE136387", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136387" } ] }, "title" : "Acclimation to a High Salt Diet is Sex-Dependent", "dateAssigned" : "2019-08-27T00:00:00.000-05:00", "summary" : "We report the relative difference in renal inner medulla transcript abundance between male and female rats,", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136575" }, "primaryId" : "GEO:GSE136575", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136575" } ] }, "title" : "Gene expression in the livers of rats with no infection and at 2 and 4 weeks after Clonorchis sinensis infection", "dateAssigned" : "2019-08-28T00:00:00.000-05:00", "summary" : "We examined gene expression profiles (27028 genes) in the livers of Sprague-Dawley rats with no infection and at 2 and 4 weeks after Clonorchis sinensis infection using Whole Rat Genome Microarray 4x44K v3 (GPL14745, Agilent-028282)", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136643" }, "primaryId" : "GEO:GSE136643", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136643" } ] }, "title" : "The Rac2 GTPase contributes to Cathepsin H-mediated protection against cytokine-induced β-cell apoptosis", "dateAssigned" : "2019-08-29T00:00:00.000-05:00", "summary" : "Microarray analysis identified a total of 63 annotated genes differentially expressed between stable CTSH-overexpressing insulin-secreting INS-1 cells and control cells transfected with an empty vector after treatment with IL-1β and IFNγ for 0, 6 and 16 hours. Permutation test taking all time-points into consideration identified 10 genes differentially expressed between the CTSH-overexpressing cells and the control cells: Elmod1, Fam49a, Gas7, Gna15, Msrb3, Nox1, Ptgs1, Rac2, Scn7a and Ttn. Pathway analysis identified one significant pathway “Inflammation mediated by chemokine and cytokine signaling pathway” with the genes Gna15, Ptgs1 and Rac2. Since Gna15 and Rac2 were upregulated by CTSH overexpression, their expression was knocked down using small interfering RNAs (siRNAs) to evaluate their potential as mediators of the protective effect of CTSH. Knockdown of Rac2 abolished the protective effect of CTSH overexpression on cytokine-induced apoptosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32814070" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136659" }, "primaryId" : "GEO:GSE136659", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136659" } ] }, "title" : "Determination of Sox10-regulated genes in the oligodendroglial precursor cell line OLN93", "dateAssigned" : "2019-08-29T00:00:00.000-05:00", "summary" : "To determine Sox10-regulated genes in the oligodendroglial precursor cell line OLN93, CRISPR/Cas9-mediated genome editing was performed to inactivate Sox10. For CRISPR/Cas9-mediated Sox10 inactivation, two guide sequences (5’-GCTGCGAGCCAGCCCAGGGCC-3’ for clone A and 5’-GTTGCCCAATTCGCCG GGCCC-3’ for clone B) were separately cloned into pX330. Oln93 cells were co-transfected with pEGFP-N1 and the pX330 plasmids that express the respective guide RNA and SpCas9. Transfected GFP-positive cells were enriched by fluorescence activated cell-sorting and seeded at single cell density in 96-well plates. Homogeneously GFP-expressing clones were analysed for loss of Sox10 protein by immunocytochemistry. Clones without Sox10 protein were obtained with both guide RNAs. Sox10 inactivation was confirmed by Sanger sequencing of the Sox10 gene. RNA was isolated from one clone A and one clone B as well as two independent RNA samples of wildtype OLN93 cells and submitted to RNA-seq.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136670" }, "primaryId" : "GEO:GSE136670", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136670" } ] }, "title" : "TBK1 Regulates Regeneration of Pancreatic b-cells", "dateAssigned" : "2019-08-30T00:00:00.000-05:00", "summary" : "b-cell proliferation induction is one of the most tangible therapeutic strategies to restore b-cell mass. However, this approach has proven challenging due to a remarkable resistance of adult human b-cells to proliferation. Here we aim to unravel the role of a non-canonical IkB kinase TBK1 (TANK-binding kinase 1), which is predominantly expressed in b-cells in mammalian islets, in regulating cell cycle progression. Genetic silencing of TBK1 in INS-1 832/13 rat b-cell line promoted proliferation of b-cells. Proteomic and transcriptome analyses further revealed changes of proteins and genes critical for cell growth and proliferation, including upregulation of ribosomal proteins and cell cycle regulators, upon depletion of TBK1. TBK1 overexpression decreased sensitivity of b-cells to the elevation of cAMP levels and reduced proliferation of b-cells in a manner dependent on the activity of phosphodiesterase 3 (PDE3). Importantly, pharmacological inhibition of TBK1 using (E)3-(3-phenylbenzo[c]isoxazol-5-yl) acrylic acid (PIAA) augmented proliferation and function of rat and human embryonic stem cell (hESC)-derived insulin-producing b-cells under basal conditions. Diabetogenic insults further induced TBK1 expression and accordingly, PIAA protected b-cells against cytokine- and streptozotocin-induced diabetogenic challenges and promoted b-cell replication. Furthermore, PIAA increased proliferation of β-cells in normal and type 2 diabetic human islets with elevation in insulin secretion. Altogether, these data unveil novel and essential function of TBK1 as a key cell-autonomous negative regulator of b-cell replication and presenting PIAA as a valid therapeutic strategy for augmenting proliferation and function of b-cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136736" }, "primaryId" : "GEO:GSE136736", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136736" } ] }, "title" : "Maternal Vitamin D deficiency induces transcriptomic changes in newborn rat lungs", "dateAssigned" : "2019-09-02T00:00:00.000-05:00", "summary" : "Vitamin D deficiency during pregnancy is common and is related to several maternal and fetal morbidities. Past studies suggest that vitamin D plays a role in normal lung development and we have shown that vitamin D regulates lung alveolar and vascular growth and preserves lung structure in experimental bronchopulmonary dysplasia (BPD) through improved pro-angiogeneic signaling. In addition, maternal vitamin D deficiency causes abnormal airway, alveolar, and vascular growth, as well as impaired lung function and airway hyper-reactivity in newborn rats. However, the mechanisms responsible for these physiologic effects are unknown. To gain insight into the role that maternal vitamin D status has on fetal lung development we used an unbiased transcriptomic approach to identify pathways altered in the lungs of offspring from vitamin D deficient dams.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32007564" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136737" }, "primaryId" : "GEO:GSE136737", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136737" } ] }, "title" : "Gestational diabetes exposure induces an altered cardiac transcriptome that is associated with impaired cardiac function in the rat offspring", "dateAssigned" : "2019-09-02T00:00:00.000-05:00", "summary" : "Gestational diabetes mellitus (GDM) is the most common complication of pregnancy. Children of mothers with GDM are at an increased risk for the development of cardiometabolic disease later in life, though the mechanisms responsible for this observation are unknown. We propose that an altered cardiac transcriptome, programmed in utero, may be a contributing mechanism to cardiometabolic disease development and hypothesize that the hearts of offspring exposed to GDM will exhibit altered gene expression pathways. The purpose of this project will be to study alterations in the cardiac transcriptome of young adult rat offspring after exposure to GDM to investigate the mechanisms responsible for the developmental origins of cardiovascular disease.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136833" }, "primaryId" : "GEO:GSE136833", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136833" } ] }, "title" : "Effects of lidocaine on the expression of rat spinal cord", "dateAssigned" : "2019-09-04T00:00:00.000-05:00", "summary" : "The aim of gene chip analysis is to screen potential genes involved in lidocaine-induced neurotoxicity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136913" }, "primaryId" : "GEO:GSE136913", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136913" } ] }, "title" : "Transcriptome analysis of CA1 rat hippocampus 1 week after kainate seizure at P7", "dateAssigned" : "2019-09-05T00:00:00.000-05:00", "summary" : "Seizures that occur during early development are associated with adverse neurodevelopmental outcomes. Causation and mechanisms are currently under investigation. Induction of an early life seizure by kainic acid (KA) in immature rats on post-natal day (P) 7 results in behavioral changes in the adult rat that reflect social and intellectual deficits without overt cellular damage. Our previous work also demonstrated increased expression of CA1 hippocampal long-term potentiation (LTP) and reduced desensitization of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid-type ionotropic glutamate receptors (AMPA-R) one week following a kainic acid induced seizure (KA-ELS). Here we used RNA sequencing (RNAseq) of mRNA from dorsal hippocampal CA1 to probe changes in mRNA levels one week following KA-ELS as a means to investigate the mechanisms for these functional changes. Ingenuity pathway analysis (IPA) confirmed our previous results by predicting an up-regulation of the synaptic LTP pathway. Differential gene expression results revealed significant differences in 7 gene isoforms. Additional assessments included AMPA-R splice variants and adenosine deaminase acting on RNA 2 (ADAR2) editing sites as a means to determine the mechanism for reduced AMPA-R desensitization. Splice variant analysis demonstrated that KA-ELS result in a small, but significant decrease in the \"flop\" isoform of Gria3, and editing site analysis revealed significant changes in the editing of a kainate receptor subunit, Grik2, and a serotonin receptor, Htr2c. While these specific changes may not account for altered AMPA-R desensitization, the differences indicate that KA-ELS alters gene expression in the hippocampal CA1 one week after the insult.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32062370" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136945" }, "primaryId" : "GEO:GSE136945", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE136945" } ] }, "title" : "Tobacco smoke exposure exacerbates silica-induced pulmonary toxicity in rats", "dateAssigned" : "2019-09-05T00:00:00.000-05:00", "summary" : "Previous studies have shown that smoking induces oxidative stress and inflammation, known factors that coincide with the development and progression of silicosis. Nevertheless, the precise role of cigarette smoke exposure in silicosis and the underlying mechanisms are not clearly understood. Therefore, the objective of the present study was to determine the effect of smoking, if any, on silica-induced pulmonary response and the underlying mechanisms. Pulmonary toxicity and lung gene expression profiles were determined in male Fischer 344 rats exposed to air, crystalline silica, cigarette smoke or cigarette smoke plus crystalline silica. Silica exposure resulted in significant pulmonary toxicity which was further exacerbated by cigarette smoke exposure in the rats. Significant differences in the gene expression profiles were detected in the lungs of the rats exposed to cigarette smoke, silica or a combination of both compared with the control rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32976597" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137008" }, "primaryId" : "GEO:GSE137008", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137008" } ] }, "title" : "Gene expression profiles in rat alveolar macrophages exposure to multi-walled carbon nanotubes", "dateAssigned" : "2019-09-06T00:00:00.000-05:00", "summary" : "To evaluate the biological effects at the transcriptional level of manufactured nanomaterials, we performed whole genome microarrays of rat alveolar macrophages (NR8383) exposed to multi-walled carbon nanotubes (MWCNTs) with different physicochemical properties.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137094" }, "primaryId" : "GEO:GSE137094", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137094" } ] }, "title" : "Maternal protein restriction changes skeletal muscle metabolism and structural gene expression in aging rats", "dateAssigned" : "2019-09-09T00:00:00.000-05:00", "summary" : "We intended to evaluate the phenotypic characteristics of the muscle microenvironment, involving muscle fiber and extracellular matrix, in skeletal muscle of elderly rats, at 540 days, arising from maternal protein restriction.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137118" }, "primaryId" : "GEO:GSE137118", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137118" } ] }, "title" : "Habenular Tcf7l2 links nicotine addiction to diabetes", "dateAssigned" : "2019-09-09T00:00:00.000-05:00", "summary" : "Nicotine contained in tobacco smoke increases blood glucose levels in humans, and the risk of developing diabetes is dramatically increased in habitual smokers. Little is currently known about how nicotine increases blood glucose levels or the relevance of this action to either the persistence of the smoking habit or the pathophysiology of diabetes in smokers. Here, we show that the diabetes-associated gene Tcf7l2 is highly expressed in the medial habenula (mHb), where it regulates the function of local nicotinic acetylcholine receptors. We find that Tcf7l2 mutant (Tcf7l2mut) rats consume far greater quantities of nicotine than wild-type rats. Similarly, CRISPR-mediated cleavage of wild-type Tcf7l2 in the mHb increases nicotine intake in mice. Polysynaptic tracing identified a connection from the mHb to the pancreas, and nicotine-induced activation of the mHb elevates blood glucose. This effect is mimicked by chemogenetic stimulation of the mHb and blocked by Tcf7l2 knockdown in mHb. A history of nicotine consumption elevates circulating levels of the pancreas-derived hormones glucagon and insulin and precipitates diabetes-like dysregulation of blood glucose homeostasis in wild-type rats, whereas Tcf7l2mut rats are resistant to these actions of nicotine. Our findings suggest that Tcf7l2 regulates the stimulatory actions of nicotine on the habenula-pancreas axis, linkings the addictive properties of nicotine to its diabetes-promoting actions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31619789" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137131" }, "primaryId" : "GEO:GSE137131", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137131" } ] }, "title" : "The novel long noncoding RNA Lnc19959.2 modulating triglyceride metabolism associated genes through interaction with Purb and hnRNPA2B1", "dateAssigned" : "2019-09-09T00:00:00.000-05:00", "summary" : "High triglycerides can lead to atherosclerotic cardiovascular disease. Long noncoding RNAs (lncRNAs) are currently consider to have vital and wide range of biological functions, but the molecular mechanism underlying TG metabolism remains poorly understood. To identify novel lncRNAs differentially expressed in rat liver with hypertriglyceridemia using transcriptome sequencing and elucidated the function role in TG metabolism. In our study, we identified a novel lncRNA, Lnc19959.2, which was highly expression in rat liver with hypertriglyceridemia. Knockdown of lnc19959.2 has profound TG lowering effects in vitro and vivo. Subsequently genome-wide analysis identified that knockdown of Lnc19959.2 caused deregulation of many genes during TG homeostasis. Further mechanism studies reveal that Lnc19959.2 specifically bound to Purb to up-regulate expression of Apoa4, while bound to hnRNPA2B1 to down-regulate the expression of Cpt1a, Tm7sf2 and Gpam, respectively. In the upstream pathway, palmitate acid up-regulated CCAAT/Enhancer-Binding Protein Beta (Cebpb) facilitates its binding to promoter region of Lnc19959.2, which resulted in significant promotion of lnc19959.2 transcriptional activity. Our findings provide novel insights into transcriptional regulation of TG homeostasis by a novel lncRNA. This newly identified lncRNA could be exploited as novel therapeutic targets for hypertriglyceridemia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32302712" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137139" }, "primaryId" : "GEO:GSE137139", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137139" } ] }, "title" : "Vitamin C regulates Schwann cell myelination by promoting DNA demethylation of pro-myelinating genes", "dateAssigned" : "2019-09-09T00:00:00.000-05:00", "summary" : "In this study we show that vitamin C promotes demethylation of DNA and regulates the expression of genes involved in Schwann cell development and function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32219848" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137217" }, "primaryId" : "GEO:GSE137217", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137217" } ] }, "title" : "Imprinting effects of UBE3A loss on synaptic gene networks and Wnt signaling pathways", "dateAssigned" : "2019-09-10T00:00:00.000-05:00", "summary" : "UBE3A encodes a E3 ubiquitin ligase whose loss from the maternal allele causes the neurodevelopmental disorder Angelman syndrome. Previous studies of UBE3A function have not examined full Ube3a deletion in mouse, the complexity of imprinted gene networks in brain, nor the molecular basis of systems-level cognitive dysfunctions in Angelman syndrome. We therefore utilized a systems biology approach to elucidate how UBE3A loss impacts the early postnatal brain in a novel CRISPR/Cas9 engineered rat Angelman model of a complete Ube3a deletion. Strand-specific transcriptome analysis of offspring from maternally or paternally inherited Ube3a deletions revealed the expected parental expression patterns of Ube3a sense and antisense transcripts by postnatal day 2 (P2) in hypothalamus and day 9 (P9) in cortex, compared to wild-type littermates. The dependency of genome-wide effects on parent-of-origin, Ube3a genotype, and time (P2, P9) was investigated through transcriptome (RNA-seq of cortex and hypothalamus) and methylome (whole genome bisulfite sequencing of hypothalamus). Weighted gene co-expression and co-methylation network analyses identified co-regulated networks in maternally inherited Ube3a deletion offspring enriched in postnatal developmental processes including Wnt signaling, synaptic regulation, neuronal and glial functions, epigenetic regulation, ubiquitin, circadian entrainment, and splicing. Furthermore, we showed that loss of the paternal Ube3a antisense transcript resulted in both unique and overlapping dysregulated gene pathways with maternal loss, predominantly at the level of differential methylation. Together, these results provide a holistic examination of the molecular impacts of UBE3A loss in brain, supporting the existence of interactive epigenetic networks between maternal and paternal transcripts at the Ube3a locus.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137252" }, "primaryId" : "GEO:GSE137252", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137252" } ] }, "title" : "The novel long noncoding RNA Lnc19959.2 modulating triglyceride metabolism associated genes through interaction with Purb and hnRNPA2B1 (RNA-seq data set)", "dateAssigned" : "2019-09-11T00:00:00.000-05:00", "summary" : "High triglycerides can lead to atherosclerotic cardiovascular disease. Long noncoding RNAs (lncRNAs) are currently consider to have vital and wide range of biological functions, but the molecular mechanism underlying TG metabolism remains poorly understood. To identify novel lncRNAs differentially expressed in rat liver with hypertriglyceridemia using transcriptome sequencing and elucidated the function role in TG metabolism. In our study, we identified a novel lncRNA, Lnc19959.2, which was highly expression in rat liver with hypertriglyceridemia. Knockdown of lnc19959.2 has profound TG lowering effects in vitro and vivo. Subsequently genome-wide analysis identified that knockdown of Lnc19959.2 caused deregulation of many genes during TG homeostasis. Further mechanism studies reveal that Lnc19959.2 specifically bound to Purb to up-regulate expression of Apoa4, while bound to hnRNPA2B1 to down-regulate the expression of Cpt1a, Tm7sf2 and Gpam, respectively. In the upstream pathway, palmitate acid up-regulated CCAAT/Enhancer-Binding Protein Beta (Cebpb) facilitates its binding to promoter region of Lnc19959.2, which resulted in significant promotion of lnc19959.2 transcriptional activity. Our findings provide novel insights into transcriptional regulation of TG homeostasis by a novel lncRNA. This newly identified lncRNA could be exploited as novel therapeutic targets for hypertriglyceridemia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32302712" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137255" }, "primaryId" : "GEO:GSE137255", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137255" } ] }, "title" : "Gene expression profilings in human embryonic stem cell-derived cardiomyocytes in vivo and in vitro", "dateAssigned" : "2019-09-11T00:00:00.000-05:00", "summary" : "RNA sequencing of human embryonic stem cell-derived cardiomyocytes", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32681032" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137326" }, "primaryId" : "GEO:GSE137326", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137326" } ] }, "title" : "Transcriptional Profiling of Lumbar Spinal Cord in a Rat Model of Bone Cancer Pain", "dateAssigned" : "2019-09-12T00:00:00.000-05:00", "summary" : "Bone cancer pain (BCP), in which the majority is caused by metastasis from other cancer sites, is the most common type of chronic cancer pain. Bone cancer pain is developed accompanied by changes of numerous genes expression, from peripheral to central nervous system, which may account for this dysfunctional nociceptive perception. Although the pivotal role of lncRNA in neuropathic pain are well acknowledged, the involvement of lncRNA in bone cancer pain development are remain to be clarified. Thus, in the present study we performed transcriptome sequencing to explore changes in expression profiles of lncRNA and mRNA to provide a landscape of dysregulated lncRNA and mRNA in spinal cord of bone cancer pain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137379" }, "primaryId" : "GEO:GSE137379", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137379" } ] }, "title" : "Comparison of the modes of action of p-dialkoxy chlorobenzenes in rat primary hepatocytes", "dateAssigned" : "2019-09-12T00:00:00.000-05:00", "summary" : "It is considered that read-across based on only structure similarity has a risk of error on risk assessment. Under this circumstances, considering biological similarity based on adverse outcome pathways (AOPs) using in vitro omics technologies is expected to enhance the accuracy and robustness of conclusions in read-across. However, because of a lack of practical case studies, it is not well discussed key considerations and how to use these technologies for data gap filling. In the present case study, we elucidated and compared the mode of action for structural analogs ; p-dialkoxy chlorobenzenes including 1,4-dichloro-2,5-dimethoxybenzene (DDMB), 2,5-dichloro-1,4-diethoxybenzene (DDEB), 2-chloro-1,4-dimethoxybenzene (CDMB), and 1-chloro-2,5-diethoxybenzene (CDEB) using in vitro omics technologies. To reveal the modes of action, we conducted microarray analysis with rat primary hepatocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32087351" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137473" }, "primaryId" : "GEO:GSE137473", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137473" } ] }, "title" : "A systems approach delivers a functional microRNA catalog and expanded targets for seizure suppression in temporal lobe epilepsy", "dateAssigned" : "2019-09-16T00:00:00.000-05:00", "summary" : "MicroRNAs (miRNAs) are short noncoding RNAs that shape the gene expression landscape, including during the pathogenesis of temporal lobe epilepsy (TLE). In order to provide a full catalog of the miRNA changes that happen during experimental TLE, we sequenced Argonaute 2-loaded miRNAs in the hippocampus of three different animal models at regular intervals between the time of the initial precipitating insult to the establishment of spontaneous recurrent seizures. The commonly upregulated miRNAs were selected for a functional in vivo screen using oligonucleotide inhibitors. This revealed anti-seizure phenotypes upon inhibition of miR-10a-5p, miR-21-5p and miR-142-5p as well as neuroprotection-only effects for inhibition of miR-27a-3p and miR-431-5p. Pathway enrichment analysis on predicted and validated targets of these miRNAs indicated a role for TGFβ signaling in a shared seizure-modifying mechanism. Together, these results identify functional miRNAs in the hippocampus and a pipeline of new targets for seizure control in epilepsy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33584828" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137536" }, "primaryId" : "GEO:GSE137536", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137536" } ] }, "title" : "Adipocyte Epigenetic Alterations and Potential Therapeutic Targets in Transgenerationally Inherited Lean and Obese Phenotypes Following Ancestral Exposure to Environmental Toxicants", "dateAssigned" : "2019-09-16T00:00:00.000-05:00", "summary" : "This study examines the transgenerational adipocyte (fat cell) epigenetic alterations in F3 generation obese and lean rats ancestrally exposed to DDT and atrazine. Adipocytes were isolated from the gonadal fat pad of F3 generation 1-year old rats ancestrally exposed to DDT, atrazine, or vehicle control in order to obtain adipocyte DNA for DNA methylation analysis. Observations indicate that there were differential DNA methylated regions (DMRs) in the adipocytes with the lean or obese phenotypes compared to control normal (non-obese or lean) populations. Interestingly, there were epigenetic changes that were distinct when comparing the lean and obese DMRs between the control and exposure lineage groups. DMR gene associations were identified which included common set of genes previously shown to associate with adipocyte pathology. The comparison of epigenetic alterations indicated that there were substantial overlaps between the different treatment lineage groups for both the lean and obese phenotypes. Novel correlated genes and gene pathways associated with DNA methylation were identified, and may aid in the discovery of potential therapeutic targets for metabolic diseases such as obesity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137562" }, "primaryId" : "GEO:GSE137562", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137562" } ] }, "title" : "Sirena1: The most abundant lncRNA in mouse oocytes brings together post-transcriptional regulations and mitochondrial distribution (rat wild-type GV oocytes)", "dateAssigned" : "2019-09-17T00:00:00.000-05:00", "summary" : "Long non-coding RNAs (lncRNAs) are a large group of rapidly evolving non-coding RNAs. Tens of thousands of lncRNAs were identified but function has been assigned to relatively few. LncRNAs expressed in mouse oocytes have been annotated but their contribution to oocyte development and early development remains unknown. Here, we report evolutionary history and functional analysis of Sirena1, maternal lncRNA that is the most expressed maternal lncRNA and 10th most abundant Pol II transcript in mouse oocytes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137568" }, "primaryId" : "GEO:GSE137568", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137568" } ] }, "title" : "A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response", "dateAssigned" : "2019-09-17T00:00:00.000-05:00", "summary" : "The goal of this experiment was to determine how dopamine receptor activation in medium spiny neurons alters rapid transcriptional programs. To identify genes altered by dopamine, we used a rat primary striatal neuronal culture system in which striatal neurons were removed from the rat brain at embryonic day 18, cultured for 11 days in vitro using standard neuronal conditions, and treated neurons with either vehicle (neurobasal media) or dopamine (at a concentration of 1µM) for 1hr. This dataset contains PolyA+ RNA-seq results from this experiment, in which we identified 100 upregulated genes and 3 downregulated genes after dopamine stimulation using DESeq2 pipelines.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32637607" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137641" }, "primaryId" : "GEO:GSE137641", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137641" } ] }, "title" : "Ancestral folate promotes neuronal regeneration in serial generations of progeny [RNA-seq]", "dateAssigned" : "2019-09-18T00:00:00.000-05:00", "summary" : "Folate supplementation in F0 mating rodents increases regeneration of injured spinal axons in vivo in at least 4 generations of progeny (F1-F4) in the absence of interval folate administration to the progeny. Transmission of the enhanced regeneration phenotype to untreated progeny parallels axonal growth in neuron culture after in vivo folate administration to the F0 ancestors alone, in correlation with transformed patterns of genomic DNA methylation and gene expression in treated lineages. Enhanced axonal regeneration phenotypes are observed with diverse folate preparations and routes of administration, in outbred and inbred rodent strains, in distinct rodent genera, and are reversed in F4-F5 progeny by pretreatment with DNA demethylating agents prior to phenotyping. Uniform transmission of the phenotype to progeny suggests a non-Mendelian mechanism. The capacity of an essential nutritional co-factor to induce a beneficial transgenerational phenotype in untreated offspring carries broad implications for the diagnosis, prevention, and treatment of inborn and acquired disorders.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31919777" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137642" }, "primaryId" : "GEO:GSE137642", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137642" } ] }, "title" : "Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny [MeDIP]", "dateAssigned" : "2019-09-18T00:00:00.000-05:00", "summary" : "Ancestral folate promotes neuronal regeneration in serial generations of progeny, eliciting transgenerational disruptions in DNA methylation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31919777" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137658" }, "primaryId" : "GEO:GSE137658", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137658" } ] }, "title" : "Dopaplex RNA-seq dataset for \"A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response\"", "dateAssigned" : "2019-09-18T00:00:00.000-05:00", "summary" : "This dataset contains whole-genome RNA sequencing results from rat embryonic striatal neuronal cultures and serves as the basis for characterization of multiplexed CRISPR/dCas9 gene activation of 16 genes induced by dopamine receptor activation. The goal of this experiment was to define the transcriptional response to multiplexed CRISPR-based upregulation of 16 dopamine-induced genes (Tent5b, Junb, Prox1, Nr4a2, Nptx1, Gsx1, Gadd45g, Btg2, Fosb, Nr4a1, Egr4, Fos, Sstr2, Gadd45b, Egr3, & Egr2), together termed \"Dopaplex\", as compared to a LacZ control sgRNA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32637607" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137693" }, "primaryId" : "GEO:GSE137693", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137693" } ] }, "title" : "Integrating Enhancer RNA Signatures with Diverse Omics Data identifies characteristics of transcription initiation in pancreatic islets", "dateAssigned" : "2019-09-19T00:00:00.000-05:00", "summary" : "Identifying active regulatory elements and their characteristics is critical to understand gene regulatory mechanisms and subsequently better delineating biological mechanisms of complex diseases and traits. Studies have shown that active enhancers can be transcribed into enhancer RNA (eRNA). We identified actively transcribed elements in human pancreatic islets by performing cap analysis of gene expression (CAGE) across 70 islet samples. We used the self-transcribing active regulatory region sequencing (STARR-seq) assay in a rat pancreatic islet beta cell line to experimentally validate the regulatory activity of the CAGE-identified transcribed elements.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33849996" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137700" }, "primaryId" : "GEO:GSE137700", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137700" } ] }, "title" : "RTD-1 therapeutically normalizes synovial gene signatures in rat autoimmune arthritis and suppresses proinflammatory mediators in RA synovial fibroblasts", "dateAssigned" : "2019-09-19T00:00:00.000-05:00", "summary" : "Rhesus theta defensin-1 (RTD-1), a macrocyclic immunomodulatory host defense peptide from Old World monkeys, is therapeutic in pristane-induced arthritis (PIA) rat model. RNA-sequence (RNA-seq) analysis was used to interrogate the changes in gene expression in PIA rats diseased model. To, study the anti-arthritic mechanisms of systemic RTD-1, the differentially expressed genes between synovial tissues of rats with pristane induced arthritis (PIA) and naïve animals were identified and the effect of RTD-1 treatment for 1, 3 or 5 days was then evaluated. The results indicate a regulation of arthritogenic gene networks in a manner that correlates temporally with clinical resolution of rat PIA.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137712" }, "primaryId" : "GEO:GSE137712", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137712" } ] }, "title" : "The novel long noncoding RNA Lnc19959.2 modulating triglyceride metabolism associated genes through interaction with Purb and hnRNPA2B1 [RNA-seq]", "dateAssigned" : "2019-09-19T00:00:00.000-05:00", "summary" : "High triglycerides can lead to atherosclerotic cardiovascular disease. Long noncoding RNAs (lncRNAs) are currently consider to have vital and wide range of biological functions, but the molecular mechanism underlying TG metabolism remains poorly understood. To identify novel lncRNAs differentially expressed in rat liver with hypertriglyceridemia using transcriptome sequencing and elucidated the function role in TG metabolism. In our study, we identified a novel lncRNA, Lnc19959.2, which was highly expression in rat liver with hypertriglyceridemia. Knockdown of lnc19959.2 has profound TG lowering effects in vitro and vivo. Subsequently genome-wide analysis identified that knockdown of Lnc19959.2 caused deregulation of many genes during TG homeostasis. Further mechanism studies reveal that Lnc19959.2 specifically bound to Purb to up-regulate expression of Apoa4, while bound to hnRNPA2B1 to down-regulate the expression of Cpt1a, Tm7sf2 and Gpam, respectively. In the upstream pathway, palmitate acid up-regulated CCAAT/Enhancer-Binding Protein Beta (Cebpb) facilitates its binding to promoter region of Lnc19959.2, which resulted in significant promotion of lnc19959.2 transcriptional activity. Our findings provide novel insights into transcriptional regulation of TG homeostasis by a novel lncRNA. This newly identified lncRNA could be exploited as novel therapeutic targets for hypertriglyceridemia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32302712" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137733" }, "primaryId" : "GEO:GSE137733", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137733" } ] }, "title" : "Aqp1 overexpression may enhance glioma tumorigenesis by interacting with the transcriptional regulation networks of Foxo4, Maz, and E2F families", "dateAssigned" : "2019-09-19T00:00:00.000-05:00", "summary" : "Gliomas is the most common and aggressive primary brain tumor. The C6 glioma cell line has been widely used for decades as experimental model system for the study of glioblastoma growth and invasion. Recently, aquaporin-1 (Aqp1) is reported to facilitate cell migration and potentially involved in tumor progression. Here we overexpressed Aqp1 in C6 cells to examine its potential role in glioblastoma. We found overexpression of Aqp1 in C6 cells significantly increased cell viability and cell migration. The upregulated genes were enriched for cell mobility and glioblastoma. Transcriptional factor binding analysis indicates the upregulated genes were regulated by FOXO4, MAZ, and E2F TF families, which are known factors involved in cell cycle control and cancer progression. Our study suggests Aqp1 is potentially involved in gliomas formation by interacting with the transcriptional regulation networks of FOXO4, MAZ, and E2F TF families.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137759" }, "primaryId" : "GEO:GSE137759", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137759" } ] }, "title" : "Striatal cultured neurons single-nucleus RNA-seq dataset for \"A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response\"", "dateAssigned" : "2019-09-19T00:00:00.000-05:00", "summary" : "This dataset contains single-nucleus RNA sequencing results from rat embryonic striatal neuronal cultures and serves as the basis for characterization of transcriptional response to dopamine (50µM), the Drd1 agonist SKF-38393 (1µM), and potassium chloride (25mM). The goal of this experiment was to define the transcriptional response to each of these stimulations across distinct cell types in cultured neurons. Single-cell sequencing was carried out on FACS-sorted nuclei isolated from these experiments using the 10X Genomics Chromium single cell sequencing platform.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32637607" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137763" }, "primaryId" : "GEO:GSE137763", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137763" } ] }, "title" : "Adult nucleus accumbens single-nucleus RNA-seq dataset for \"A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response\"", "dateAssigned" : "2019-09-19T00:00:00.000-05:00", "summary" : "This dataset contains single-nucleus RNA sequencing results from adult rat brain (nucleus accumbens) and serves as the basis for characterization of transcriptional response to cocaine (20mg/kg, intraperitoneal injection). The goal of this experiment was to define the transcriptional response to cocaine across distinct cell types in the nucleus accumbens. Single-cell sequencing was carried out on FACS-sorted nuclei isolated from these experiments using the 10X Genomics Chromium single cell sequencing platform.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32637607" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137837" }, "primaryId" : "GEO:GSE137837", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137837" } ] }, "title" : "Altered miRNA expression of cultured dorsal root ganglia neurons at different times of rat", "dateAssigned" : "2019-09-23T00:00:00.000-05:00", "summary" : "To explored the function of miRNAs during the axon regeneration of rat dorsal root ganglia neurons, we utilized miRCURYTM LNA Array (v.18.0) to find out the altered expression of miRNAs in cultured DRG neurons at different times. When we digest the cells from rat DRGs with enzymes, we only get the cell bodies without axons. During the axons re-growth after the neurons planted, it must be amount of gene and miRNAs will changed. However, we still not fully understand which miRNAs and mRNA will changed and the function of these miRNAs and mRNAs. In addition, this cell model could mimic the regeration of sciatic nerve after injure in vivo, which is still a challenge in clinical.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33683649" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137838" }, "primaryId" : "GEO:GSE137838", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137838" } ] }, "title" : "Altered mRNA expression of cultured dorsal root ganglia neurons at different times of rat", "dateAssigned" : "2019-09-23T00:00:00.000-05:00", "summary" : "To explored the altered genes during the axon regeneration of rat dorsal root ganglia neurons, we utilized Gene Expression Array to find out the altered expression of genes in cultured DRG neurons at different times. When we digest the cells from rat DRGs with enzymes, we only get the cell bodies of neurons without axons. During the axons re-growth after the neurons planted, it must be amount of genes expression will changed. However, we still not fully understand which genes will changed and the function of these genes. In addition, this cell model could mimic the regeration of sciatic nerve after injure in vivo, which is still a challenge in clinical.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33683649" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137869" }, "primaryId" : "GEO:GSE137869", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137869" } ] }, "title" : "Caloric restriction reprograms the single-cell transcriptional landscape of Rattus norvegicus aging", "dateAssigned" : "2019-09-23T00:00:00.000-05:00", "summary" : "Aging causes a functional decline in tissues throughout the body that may be delayed by caloric restriction (CR). However, the cellular profiles and signatures of aging, as well as those ameliorated by CR, remain unclear. Here, we built comprehensive single-cell and single-nucleus transcriptomic atlases across various rat tissues undergoing aging and CR. CR attenuated aging-related changes in cell type composition, gene expression, and core transcriptional regulatory networks. Immune cells were increased during aging, and CR favorably reversed the aging-disturbed immune ecosystem. Computational prediction revealed that the abnormal cell-cell communication patterns observed during aging, including the excessive proinflammatory ligand-receptor interplay, were reversed by CR. Our work provides multi-tissue single-cell transcriptional landscapes associated with aging and CR in a mammal, enhances our understanding of the robustness of CR as a geroprotective intervention, and uncovers how metabolic intervention can act upon the immune system to modify the process of aging.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32109414" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137963" }, "primaryId" : "GEO:GSE137963", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137963" } ] }, "title" : "Developmental Origins of Transgenerational Sperm Histone Retention Following Ancestral Exposures", "dateAssigned" : "2019-09-25T00:00:00.000-05:00", "summary" : "This study was designed to investigate the developmental origins of the transgenerational differential histone retention sites (called DHRs) during gametogenesis of the sperm. Vinclozolin and DDT were independently used to promote the epigenetic transgenerational inheritance of these DHRs. Male control, DDT lineage and vinclozolin lineage F3 generation rats were used to isolate round spermatids, caput epididymal spermatozoa, and caudal sperm. The DHRs between the control versus DDT lineage or vinclozolin lineage were determined in these three developmental stages. DHRs and a reproducible core of histone H3 retention sites were observed using an H3 chromatin immunoprecipitation (ChIP-Seq) analysis in the germ cell populations. The chromosomal locations and genomic features of the DHRs were also analyzed. A cascade of epigenetic histone retention site alterations was found to be initiated in or prior to the round spermatids that is further altered during epididymal sperm maturation. Observations show that in addition to alterations in sperm DNA methylation previously identified, the induction of differential histone retention sites (DHRs) in the later stages of spermatogenesis also occurs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137988" }, "primaryId" : "GEO:GSE137988", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE137988" } ] }, "title" : "Inhibition of the Dead Box RNA Helicase 3 prevents HIV-1 Tat and cocaine-induced neurotoxicity by targeting microglia activation", "dateAssigned" : "2019-09-25T00:00:00.000-05:00", "summary" : "We have investigated the protective effect of DDX3 inhibitor RK33 on toxic damage done by combined TAT and cocaine.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31802418" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138071" }, "primaryId" : "GEO:GSE138071", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138071" } ] }, "title" : "Integrative proteomics of primary hepatocytes during dedifferentiation", "dateAssigned" : "2019-09-26T00:00:00.000-05:00", "summary" : "To understand the relationship between protein expression and mRNA translation during primary hepatocytes dedifferentiation, we have employed transcriptome microarrayas a discovery platform. Rat primary hepatocytes were isolated by the method of two-step enzymes perfusion and then cultured on mono-layer in vitro. Samples at 0h( just after perfusion, before planking) , 6h, 12h ,24h and 48h were collected. Integrative analysis of transcriptome and whole cell proteomics (WCP) leaded us to realize the poor correlation of them. This discovery made us realize that targeting mRNA was far from enough in illustrating this process. It would provide new insights from the aspects of post-translational modifications(PTMs).Post-translational modifications play important role in numorous biological and pathological process, but a few reports are related to primary hepatocytes dedifferentiation process, and there is still no integrative proteomics analysis in this field yet. In this study, we perform ubiquitinome phosphorylated proteome, whole cell proteome and transcriptome simultaneously during the five different time points of dedifferentiation in vitro quantified over 6000 modified sites mapping to over 2000 proteins. And comprehensive analysis of these datasets provides novel insight in this field.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138117" }, "primaryId" : "GEO:GSE138117", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138117" } ] }, "title" : "CTCF-dependent chromatin architecture and SUZ12/PRC2 complex recruitment are required for peripheral myelination and repair", "dateAssigned" : "2019-09-27T00:00:00.000-05:00", "summary" : "Chromatin organization is critical for cell growth, differentiation, and disease development, however, its functions in peripheral myelination and myelin repair remain elusive. Here we observed a global diminution of chromatin accessibility during Schwann cell differentiation and demonstrated that the chromatin organizer CCCTC-binding factor (CTCF) is critical for Schwann cell myelination and myelin regeneration after nerve injury. Inhibition of Ctcf or its deletion blocked Schwann cell differentiation at the pre-myelinating stage, whereas overexpression of CTCF promoted the myelination program. CTCF establishes the chromatin interaction loop between promoters and regulatory elements to promote expression of key pro-myelinogenic factors such as EGR2. In addition, CTCF interacts with SUZ12, a component of polycomb-repressive-complex 2, to repress expression of immature Schwann cell-associated regulators including HES1, RSPO2, and CALCA. Together, our findings reveal the dual role of CTCF-dependent chromatin organization in promoting myelinogenic programs and recruiting chromatin-repressive complexes to block differentiation inhibitors to control peripheral myelination and myelin repair.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32807777" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138275" }, "primaryId" : "GEO:GSE138275", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138275" } ] }, "title" : "Inflammatory Stimuli Trigger Genome-Wide Shifts in Gene Expression, Increased Androgen Production and Proliferation in Rat Theca-Interstitial Cells", "dateAssigned" : "2019-10-01T00:00:00.000-05:00", "summary" : "The goals of this study are to compare the in vitro theca-interstitial cell transcriptome profile (RNAseq) between cells cultured with pro-inflammatory IL-1ß or LPS and control media.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138317" }, "primaryId" : "GEO:GSE138317", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138317" } ] }, "title" : "Transcriptome analysis of common and diverged circulating miRNAs between arterial and venous during aging", "dateAssigned" : "2019-10-02T00:00:00.000-05:00", "summary" : "Conclusion: This study screened and analyzed the differential differential-expressed miRNA profiles in arterial and venous plasma under aging conditions, suggesting the importance of origin of candidate circulating miRNA biomarkers upon the certain scenario and its potential regulatory rule.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138454" }, "primaryId" : "GEO:GSE138454", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138454" } ] }, "title" : "Impact of inflammation on hepatic subcellular energetics in anesthetized rats", "dateAssigned" : "2019-10-04T00:00:00.000-05:00", "summary" : "Rats anesthetized with the two anesthetics i.e. isoflurane and propofol respond differently to inflammation initiated by cecal ligation and puncture.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33392215" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138472" }, "primaryId" : "GEO:GSE138472", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138472" } ] }, "title" : "MicroRNA-7a overexpression in VMH restores the sympathoadrenal response to hypoglycemia", "dateAssigned" : "2019-10-06T00:00:00.000-05:00", "summary" : "It is proposed that the impaired sympathoadrenal response to hypoglycemia induced by recurrent insulin-induced hypoglycemia (RH) is an adaptive phenomenon induced by specific changes in microRNA expression in the ventromedial hypothalamus (VMH). To test this hypothesis, genome-wide microRNAomic profiling of the VMH by RNA-sequencing was performed in control and RH treated rats. Differential expression analysis identified microRNA-7a-5p and microRNA-665 as potential mediators of this phenomenon. To further test this hypothesis, experiments were conducted consisting of targeted lentiviral-mediated overexpression of microRNA-7a-5p and downregulation of microRNA-665 in the VMH. Hyperinsulinemic hypoglycemic clamp experiments demonstrated that targeted overexpression of microRNA-7a-5p (but not downregulation of microRNA-665) in the VMH of RH rats restored the epinephrine response to hypoglycemia. This restored response to hypoglycemia was associated with a restoration of GABAA receptor gene expression. Finally, a direct interaction of microRNA-7a-5p with 3’-UTR of GABAA receptor α1-subunit (Gabra1) gene was demonstrated in a luciferase assay. These findings indicate that 1) the impaired sympathoadrenal response induced by RH is associated with changes in VMH microRNA expression, and 2) microRNA-7a-5p, possibly via direct downregulation of GABA receptor gene expression, may serve as a mediator of the altered sympathoadrenal response to hypoglycemia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31619588" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138482" }, "primaryId" : "GEO:GSE138482", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138482" } ] }, "title" : "Effect of DMHF (2,5-dimethyl-4-hydroxy-3(2H)-furanone) inhalation on gene expression in Rat brain", "dateAssigned" : "2019-10-07T00:00:00.000-05:00", "summary" : "Results: The inhalation of DMHF increased the dietary intake of rats during the feeding period. However, body weight gain was suppressed after six weeks of feeding. A DNA microarray analysis showed that DMHF altered gene expression associated with feeding behavior and neurotransmission in the rat brain. Conclusion: DMHF inhalation promotes appetite and changes gene expression in rats. Furthermore, phenotypic changes may regulate neurotransmission and appetite at the mRNA level in addition to controlling the autonomic nervous system.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32232993" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138540" }, "primaryId" : "GEO:GSE138540", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138540" } ] }, "title" : "Transcriptional analysis of tendons from rat", "dateAssigned" : "2019-10-07T00:00:00.000-05:00", "summary" : "We report RNA sequencing data from the Achilles, patellar, supraspinatus, and forepaw flexor tendons of adult male rats in the Sprague-Dawley", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138624" }, "primaryId" : "GEO:GSE138624", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138624" } ] }, "title" : "Evaluation of global gene expression in regenerate tissues during Masquelet treatment", "dateAssigned" : "2019-10-09T00:00:00.000-05:00", "summary" : "We present RNAseq data obtained from tissues harvested directly from rat segmental osteotomies managed using the Masquelet induced membrane technique or left empty.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32233004" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138637" }, "primaryId" : "GEO:GSE138637", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138637" } ] }, "title" : "Genome wide analysis of thoracic spinal cord at 5 days after T9 hemisection injury.", "dateAssigned" : "2019-10-09T00:00:00.000-05:00", "summary" : "The goal of this study is to elucidate the influence of hemisection injury at thoracic spinal cord (T9) and epidural electrical spinal stimulation (L2-S1) on transcriptome of injured thoracic spinal cord. mRNA profiles of spinal cord at 5 days-post injury with or without epidural electrical spinal stimulation (L2-S1) and before injury were generated. Our study represents the detailed analysis of transcriptomes of injured spinal cord with biologic replicates, generated by RNA-seq technology.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138666" }, "primaryId" : "GEO:GSE138666", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138666" } ] }, "title" : "TSPO ameliorated the liver fibrosis in non-alcoholic fatty liver disease mice", "dateAssigned" : "2019-10-09T00:00:00.000-05:00", "summary" : "The 18-kDa translocator protein TSPO is a conserved ubiquitous high affinity cholesterol binding protein localized in the outer mitochondrial membrane. It plays a critical role in the segregation and transport of cholesterol from the outer to the inner mitochondrial membrane in steroidogenic cells. Imaging studies in humans, using specific TSPO ligands, showed that TSPO is highly expressed and accurately mirrors the histological picture of non-alcoholic fatty liver disease (NAFLD)/nonalcoholic steatohepatitis (NASH). However, the functions of TSPO in simple steatosis (SS) and NASH are unknown. In the present study, we examined the TSPO functions with in vivo NAFLD model. To induce NASH in vivo, we fed the WT and TSPO KO rat with MCD (methionine-choline deficient) diet. Loss of TSPO ameliorated the liver fibrosis through down regulation of bile acid synthesis by reduction of CYP7A1 and CYP27A1 and increase of farnesoid X receptor (FXR).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34013171" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138694" }, "primaryId" : "GEO:GSE138694", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138694" } ] }, "title" : "Effect of maternal dioxin exposure on pituitary mRNAs in fetal rats at gestational day 18", "dateAssigned" : "2019-10-10T00:00:00.000-05:00", "summary" : "We found that oral administration of TCDD (1 µg/kg) to pregnant rats on gestational day 15 suppressed pituitary syntheisis of growth hormone during the last fetal stage. We performed a DNA microarray analysis to identify the genes linked to the attenuated expression of GH, using the male and female fetal pituitary at GD18 when the reduced expression of GH started to occur because of TCDD.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138744" }, "primaryId" : "GEO:GSE138744", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138744" } ] }, "title" : "Microarray was used to detect the expression of lncRNAs and mRNAs in INS-1 cells treated with GLP-1RA Geniposide for 24 hours.", "dateAssigned" : "2019-10-11T00:00:00.000-05:00", "summary" : "Studies have shown that long noncoding RNAs (lncRNAs) can be widely involved in various physiological and pathological processes. In recent years, there have been many studies on GLP-1 receptor agonists (GLP-1RA) regulating islet β cells function and mass of type 2 diabetes (T2DM) patients. However, the function of lncRNAs in this process have not been fully elucidated. In this study, lncRNA microarray was used to identify the differently expressed (DE) lncRNAs and mRNAs in β cells exposed to Geniposide, which is a GLP-1RA. 308 lncRNAs and 128 mRNAs were detected with a set filter fold change≥1.5 and P-value<0.05. Gene Ontology and KEGG pathway analysis were performed to assess the underlying functions of DE mRNAs. Co-expression network of DE lncRNAs and mRNAs was constructed based on Pearson coefficient of expression level. And hub mRNAs were selected through String database and Cytoscape plugin Cytohubba. Additionally, a ceRNA network was constructed among the co-expressed lncRNAs and hub mRNAs. This study reveals key mRNAs involved in the regulation of GLP-1RA on β cells function and mass. More importantly, screening out lncRNAs that play an importance regulatory role in this process. This original research could provide valuable information for the further investigation between lncRNAs and GLP-AR in the protection of β cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32994866" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138770" }, "primaryId" : "GEO:GSE138770", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138770" } ] }, "title" : "Neonatal injury increases gut permeability by epigenetically suppressing E-cadherin in adulthood", "dateAssigned" : "2019-10-11T00:00:00.000-05:00", "summary" : "Epithelial cell juntion integrity is thought to play an important role in the pathogenesis of inflammatory bowel disease (IBD). Early life stressors are suspected to impact epithelial barrier function later in life. We postulated that based on our previous findings that early life exposure to an inflammatory event could lead to epigegenetic changes mediating an exagerated response to a second inflammatory insult as an adult. In addition, we hypothesized that this increased inflammatory response could be mediated by alterations in miRNA expression impacting essential junction protein E-cadherin.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31889022" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138966" }, "primaryId" : "GEO:GSE138966", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE138966" } ] }, "title" : "Long non-coding RNA and mRNA transcriptomic profiles after ischemia-reperfusion injury in rat spinal cord.", "dateAssigned" : "2019-10-16T00:00:00.000-05:00", "summary" : "With the aim of exploring expression profiles and biological functions of long non-coding RNA (lncRNA) and mRNAs after ischemia-reperfusion injury (SCII), differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) in rat spinal cords were identified following SCII through high-throughput RNA sequencing. In total, 1455 lncRNAs and 6707 mRNAs were observed to be differentially expressed (FC ≥1.5 and P <0.05) after SCII, including 761 up-regulated and 694 down-regulated lncRNAs and, 3772 up-regulated and 2935 down-regulated mRNAs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139080" }, "primaryId" : "GEO:GSE139080", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139080" } ] }, "title" : "NMDA receptor positive allosteric modulator induced genome wide gene expression changes in neuronal cultures", "dateAssigned" : "2019-10-18T00:00:00.000-05:00", "summary" : "To investigate genome-wide gene expression changes induced by an NMDA receptor positive allosteric modulator in neuronal cultures using next-generation sequencing", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139098" }, "primaryId" : "GEO:GSE139098", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139098" } ] }, "title" : "Transcriptional Profiling of Adult Male Rat Liver and Testis following 14 Day Myclobutanil Exposure", "dateAssigned" : "2019-10-18T00:00:00.000-05:00", "summary" : "We report the RNAseq-based transcriptome profiles of adult male rat liver and testis following 14 day exposure to myclobutanil. A treatment-related change in mRNA levels were observed in both liver and testis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32268158" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139106" }, "primaryId" : "GEO:GSE139106", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139106" } ] }, "title" : "Genomic profiles of tremolite-induced malignant peritoneal mesotheliomas developed in rats", "dateAssigned" : "2019-10-18T00:00:00.000-05:00", "summary" : "Intraperitoneal injection of tremolite initiates mesothelial injury and chronic inflammation that causes the development of malignant mesothelioma (MM). We performed high-resolution comparative genomic hybridization to identify characteristics in the genomic profiles of tremolite-induced MMs in rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32080953" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139147" }, "primaryId" : "GEO:GSE139147", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139147" } ] }, "title" : "BRIN-BD11 pancreatic beta cell mRNA profile upon treatment with Class1 HDAC inhibitor MS-275", "dateAssigned" : "2019-10-21T00:00:00.000-05:00", "summary" : "Inference: Gene ontology reveals that the upregulated pathways upon MS-275 treatment include endocytosis, cAMP signaling, insulin secretion, Wnt signaling PI3K-Akt signaling and thermogenesis while the downregulated genes include histone modification, chromosome organization and cell cycle regulation. The study represents first detailed mRNA profiling of BRIN-BD11 pancreatic beta cell in context of modulation of expression upon treatment with Class1 HDAC inhibitor MS-275.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139220" }, "primaryId" : "GEO:GSE139220", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139220" } ] }, "title" : "Expression data from sevoflurane anesthesia treated rat", "dateAssigned" : "2019-10-21T00:00:00.000-05:00", "summary" : "We explored the expression and regulation pattern profiles of lncRNAs in the hippocampus of aged rats after sevoflurane anesthesia with microarrays.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33354572" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139276" }, "primaryId" : "GEO:GSE139276", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139276" } ] }, "title" : "RNAseq analysis of retinal microglia during early diabetes", "dateAssigned" : "2019-10-23T00:00:00.000-05:00", "summary" : "We report the use of RNAseq to identify gene changes in isolated retinal microglia after 4 weeks of STZ-induced diabetes. At this early time point in diabetes induction, single retinal cell suspensions were sorted via FACS using a Cd11b-FITC conjugate. RNA was isolated and preamplified using the SMARTSeq v4 low RNA input kit. After library preparation a 50bp single end read was performed at a depth of 19-34 million reads per sample using the Illumina HiSeq. Constructs were mapped to the rat genome and differential expression calculated between the STZ-treated and control groups.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34903661" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139308" }, "primaryId" : "GEO:GSE139308", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139308" } ] }, "title" : "Low dose bisphenol A gene signature and endometrial cancer", "dateAssigned" : "2019-10-23T00:00:00.000-05:00", "summary" : "We found rats exposed to 250ug/kg/day BPA (BPA250) showed abnormal transition in estrous cycle at postnatal (PND) 90 whereas 25ug/kg/day BPA (BPA25) and BPA250 in 1-year-old rats showed prolonged estrus phase, suggesting that BPA25 and BPA250 may act like high dose EE2 (EE2-05) in disrupting normal estrous cycling. To dissect the underlying molecular mechanism, we performed RNA-sequencing on 1-year-old samples and found that both BPA25 and BPA250 groups shared similar gene signature. Pathway analysis suggested that 710 unique genes from both groups were associated with estradiol and also linked to female cancer as suggested by disease prediction analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33296240" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139318" }, "primaryId" : "GEO:GSE139318", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139318" } ] }, "title" : "Autologous adipose-derived cells transiently moderate inflammation and fibrogenesis in early renal ischemia reperfusion injury", "dateAssigned" : "2019-10-24T00:00:00.000-05:00", "summary" : "Adipose-derived regenerative cell (ADRC) heterogeneity and functionality in renal ischemia reperfusion injury", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139321" }, "primaryId" : "GEO:GSE139321", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139321" } ] }, "title" : "Schwann Cell Tn5Prime", "dateAssigned" : "2019-10-24T00:00:00.000-05:00", "summary" : "Here we provide sequencing data derived from our efforts to identify SOX10-regulated promoters in Schwann cells genome-wide. We assess the activity of SOX10-bound promoters using Tn5Prime to identify and quantify transcription start sites in adult peripheral nerve, in differentiating primary Schwann cells, and upon ablation of SOX10 in vitro. Tn5Prime libraries were prepared essentially as described by Cole and colleagues (NAR, 2018). Analyses focused on transcription start sites associated with H3K4me3 and SOX10 ChIP-Seq peaks from sciatic nerve (ChIP-Seq data derived from previously published datasets).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32770939" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139383" }, "primaryId" : "GEO:GSE139383", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139383" } ] }, "title" : "Expression data from rat vocal fold at different periods after vocal fold injury", "dateAssigned" : "2019-10-25T00:00:00.000-05:00", "summary" : "Vocal cord healing is a dynamic process, and many genes and proteins are involved, which play varying roles at different regeneration stages after injury. Previous studies have shown that inflammatory responses occur at the early stage of vocal cord injury, where the fibroblasts proliferate exuberantly with intensive secretion and deposition of ECM. These activities reach the peak at 3-7 days and their intensity begins to decline 15 days later. A study based on the dermal system has shown that ECM remodeling during the repair of injury can last for several months. However, few studies have been conducted as to the dynamic changes of gene expressions and signaling pathway during the healing process of vocal cord injury. Plotting these changes will facilitate the understanding about the physiological changes during healing and the identification of key time points and target genes in fibrosis formation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139438" }, "primaryId" : "GEO:GSE139438", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139438" } ] }, "title" : "Microarray Analysis of Striatal Tissue derived RNA isolated from Chronic Levodopa (L-DOPA) treated Parkinsonian and Dyskinetic (LID) Rats as compared to Parkinsonian Disease (PD) Control Rats", "dateAssigned" : "2019-10-27T00:00:00.000-05:00", "summary" : "as compared to Control Rats with Prakinson's disease by performing differential gene expression and pathway analyses.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139446" }, "primaryId" : "GEO:GSE139446", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139446" } ] }, "title" : "Body temperature-dependent microRNA expression analysis in rats", "dateAssigned" : "2019-10-28T00:00:00.000-05:00", "summary" : "We made rat models of mild, moderate and severe hypothermia, and performed body temperature-dependent microRNA expression analysis in illiopsoas muscle.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32963265" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139447" }, "primaryId" : "GEO:GSE139447", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139447" } ] }, "title" : "LncRNA and mRNA Sequencing Analysis of Left Testis in Experimental Varicocele Rats Treated with Morinda officinalis Polysaccharide", "dateAssigned" : "2019-10-28T00:00:00.000-05:00", "summary" : "Conclusions: Our study try to offer a indication for novel diagnose marker and therapeutic method, as well as provide feasible research orientations for further study.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34466146" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139532" }, "primaryId" : "GEO:GSE139532", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139532" } ] }, "title" : "miRNA microarray in the synovial tissue 14 days after anterior cruciate ligament transection (ACLT)", "dateAssigned" : "2019-10-29T00:00:00.000-05:00", "summary" : "To investigate changes in miRNA expression in the synovial tissue, miRNA microarray was performed at day 14 after ACLT and revealed that several miRNA expressions were changed more than 1.5-fold. We chose to analyze the role of miR-21 in joint pain after ACLT because it had the highest signal intensity among the increased miRNAs. Quantitative PCR confirmed that miR-21 expression in synovial tissue was significantly increased 14 days after ACLT.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31841992" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139561" }, "primaryId" : "GEO:GSE139561", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139561" } ] }, "title" : "Pressure overload greatly promotes neonatal right ventricular cardiomyocyte proliferation - a new model for heart regeneration study", "dateAssigned" : "2019-10-29T00:00:00.000-05:00", "summary" : "Conclusions: Pressure overload profoundly promotes RVCM proliferation in the neonatal stage both in rats and human beings, activated a regeneration-specific gene program, and may offer a better alternative animal model for heart regeneration research..", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32475201" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139660" }, "primaryId" : "GEO:GSE139660", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139660" } ] }, "title" : "Adipose Mesenchymal Cells-Derived Extracellular Vesicles Alleviate DOCA-salt-Induced Hypertension by Promoting Cardio-Renal Protection", "dateAssigned" : "2019-10-31T00:00:00.000-05:00", "summary" : "By applying miRNA microarray profile of the kidney of DOCA-salt rats, we identified a selective miRNA signature associated with epithelial-mesenchymal transition (EMT)", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139672" }, "primaryId" : "GEO:GSE139672", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139672" } ] }, "title" : "Expression data from IEC6 cells after treatment with Na2S3", "dateAssigned" : "2019-10-31T00:00:00.000-05:00", "summary" : "In this dataset, we include the expression data obtained from IEC6 cells after treatment with Na2S3. We confirmed that IEC6 cells expressed Kruppel-like transcription factor 4 (KLF4). Results provide insight into the effect of Na2S3 on MAP kinase pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32522929" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139953" }, "primaryId" : "GEO:GSE139953", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139953" } ] }, "title" : "Cerebellar Interpositus Nucleus Transcriptome Following Early-Life Limited Bedding Stress in P70 Male and Female Rats", "dateAssigned" : "2019-11-05T00:00:00.000-06:00", "summary" : "Purpose: This particular experiment is part of a broader study on the effects of early-life stress on the cerebellar endocannabinoid system. Early-life stress is a major developmental risk factor. Though studies are now considering the endogenous cannabinoid system, which is highly intertwied with the stress-response, as a moderator of these effects, studies have been largely focused on cerebral effects. Cerebellum is vulnerable to stress during early development and is dense with cannabinoid receptors, making it an important target for stress effects. Moreover, relatively little is known about sex-specific effects in cerebellum. Methods: Limited bedding, a naturalistic rodent model of early-life stress, was performed at postnatal days 2-9. Following, rats were reared normally and adult (postnatal day 70) cerebellar interpositus nucleus mRNA was assessed. Results: Transcriptomics for cerebellar interpositus nucleus revealed substantial sex effects, with minimal effects of stress. Specifically, expression of 25% of the genes evaluated significantly differed by sex alone. Interestingly, in the non-stressed groups, there were significant sex differences in Cnr1, cannabinoid receptor 1. Conclusion: We show robust sex-specific transcriptomics effects in cerebellar interpositus, perhaps suggesting a role for this system in sexual differentiation of the brain. Other regions of cerebellum should be evaluated.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32350298" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139994" }, "primaryId" : "GEO:GSE139994", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE139994" } ] }, "title" : "Molecular analyses of antifibrotic effect of BK channel activatior on rat livers in fibrosis", "dateAssigned" : "2019-11-06T00:00:00.000-06:00", "summary" : "Liver fibrosis is a high-morbidity and high-mortality chronic disease throughout the world without any satisfying treatment Large-conductance Ca2+- and voltage-activated K+ (Slo1, BK) channels are widely expressed in human body and important for numerous physiological processes. Previous studies have shown that BK channels are expressed in HSCs of patients with liver fibrosis and they are involved in contraction/relaxation of the HSCs To investigate the molecular mechanism of antifibrotic effect of BK channel opener rottlerin using in vivo fibrosis models. transcriptomic analyses of differential expression genes in livers from rats of vehicle, CCl4 and CCl4 combined with rottlerin treatment were for discrimination. The RNA samples were extracted from three samples of each group for microarray profiling and performed in Affymetrix Rats Genome 230 2.0 arrays for gene expression profiling analysis, which contained 31 042 probe sets. The biotinylated cRNA targets were hybridized with the microarray. After hybridization, arrays were stained in the Fluidics Station 450 and scanned on the Affymetrix Scanner 3000. The microarray experiments were performed by following the protocol of Affymetrix Inc at Shanghai Biotechnology Corporation. Under the criteria fold change > 1.5 or < 0.67, we obtained 10672 differential expressed genes (DEGs) between CCl4 and CCl4 combined with rottlerin treatment group, and the data was applied to further analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140087" }, "primaryId" : "GEO:GSE140087", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140087" } ] }, "title" : "Impact of acute noise trauma on the gene expression profile of the hippocampus", "dateAssigned" : "2019-11-07T00:00:00.000-06:00", "summary" : "To investigate the early changes in the hippocampus following noise-induced hearing loss, the gene expression profile of the hippocampus was evaluated using microarray analyses immediately after exposure to intense noise stimuli.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140146" }, "primaryId" : "GEO:GSE140146", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140146" } ] }, "title" : "Transcriptomic Modifications in Developmental Cardiopulmonary Adaptations to Chronic Hypoxia Using a Murine Model of Simulated High Altitude Exposure", "dateAssigned" : "2019-11-08T00:00:00.000-06:00", "summary" : "Mechanisms driving adaptive developmental responses to chronic high altitude (HA) exposure are incompletely known. We developed a novel rat model mimicking the human condition of cardiopulmonary adaptation to HA starting at conception and spanning the in utero and early life timeframe. We assessed lung growth and cardiopulmonary structure and function, and performed transcriptome analyses to identify mechanisms facilitating developmental adaptations to chronic hypoxia. To generate the model, breeding pairs of Sprague-Dawley rats were exposed to hypobaric hypoxia (equivalent to 9,000 feet elevation). Mating, pregnancy and delivery occurred in hypoxic conditions. Six weeks postpartum, structural and functional data were collected in the offspring. RNAseq was performed on right ventricle (RV) and lung tissue. Age-matched breeding pairs and offspring under room air (RA) conditions served as controls. Hypoxic rats exhibited significantly lower body weights and higher hematocrit levels, alveolar volumes, pulmonary diffusion capacities, RV mass, RV systolic pressure as well as increased pulmonary artery remodeling. RNAseq revealed multiple differentially expressed genes in lungs and RVs from hypoxic rats. While there was considerable similarity between hypoxic lungs and RVs compared to RA controls, several upstream regulators unique to lung or RV were identified. We noted a pattern of immune down-regulation and regulation patterns of immune and hormonal mediators similar to the genome from patients with pulmonary arterial hypertension. In summary, we developed a novel murine model of chronic hypoxia exposure that demonstrates functional and structural phenotypes similar to human adaptation. We identified transcriptomic alterations that suggest potential mechanisms for adaptation to chronic HA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32639867" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140162" }, "primaryId" : "GEO:GSE140162", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140162" } ] }, "title" : "RNA-sequencing of lidocaine treatment on rat dorsal root ganglion neurons", "dateAssigned" : "2019-11-08T00:00:00.000-06:00", "summary" : "We conducted RNA-sequencing of lidocaine hydrochloride in treating rat dorsal root ganglion neurons to detect lidocaine’s effect of transcriptome profiling changes compared with control.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140190" }, "primaryId" : "GEO:GSE140190", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140190" } ] }, "title" : "Abrogation of esophageal carcinoma development by miR-31 genetic knockout", "dateAssigned" : "2019-11-11T00:00:00.000-06:00", "summary" : "Transcriptomics analyses in these Zn-deficient rats revealed the molecular basis of ESCC abrogation by miR-31 knockout: Egln3, a negative regulator of NF-FB, was shown to be a direct miR-31 target; miR-31 inhibition/deletion resulted in suppression of miR-31-associated-EGLN3-NF-KB controlled inflammatory pathways.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32123074" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140287" }, "primaryId" : "GEO:GSE140287", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140287" } ] }, "title" : "Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: RNA-Seq Data from Generation F43", "dateAssigned" : "2019-11-12T00:00:00.000-06:00", "summary" : "The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans. This dataset was part of a larger RNA-Sequencing study examining gene expression in the bHR/bLR hippocampus, a region critical for emotional regulation. The original study compared repeated injections of either antidepressant medication (fluoxetine or desipramine) or vehicle (VEH=1:1 saline and water) solution in bHR and bLR rats (14 days of intraperitoneal injections - P78-P92, 1 per day) under either standard laboratory housing conditions or chronic variable stress. This upload includes only the data from the control subjects: generation F43 adult male bHR VEH rats and bLR VEH rats housed in standard conditions (n=5/group). Prior to sacrifice, at age P92, the rats underwent social interaction testing after 15 minutes of exposure to an anxiogenic environment (the elevated plus maze). The results from the social interaction testing are provided here along with the gene expression data.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32762937" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140298" }, "primaryId" : "GEO:GSE140298", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140298" } ] }, "title" : "Sex Differences in the Effects of Prenatal Bisphenol A Exposure on Genes Associated with Autism Spectrum Disorder in the Hippocampus", "dateAssigned" : "2019-11-13T00:00:00.000-06:00", "summary" : "In this study, we investigated the prenatal effects of bisphenol-A (BPA) exposure on transcriptome profiles in the hippocampus of the rat offspring. Transcriptome profiling by RNA-seq analysis of hippocampi isolated from neonatal pups prenatally exposed to BPA was conducted and revealed a list of differentially expressed genes (DEGs) associated with ASD. Among the DEGs, several ASD candidate genes, including Auts2 and Foxp2, were dysregulated and showed sex differences in response to BPA exposure. The interactome and pathway analyses of DEGs revealed significant associations between the DEGs in males and neurological functions/disorders associated with ASD. The findings from this study indicate that prenatal BPA exposure alters the expression of ASD-linked genes in the hippocampus and suggest that maternal BPA exposure may increase ASD susceptibility by dysregulating genes associated with neurological functions known to be negatively impacted in ASD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30816183" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140368" }, "primaryId" : "GEO:GSE140368", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140368" } ] }, "title" : "Expression analysis of microRNA in malignant peritoneal mesothelioma induced by intraperitoneal injections of iron saccarate in rats", "dateAssigned" : "2019-11-14T00:00:00.000-06:00", "summary" : "Iron plays an important role in oxidative tissue damage and subsequent carcinogenesis. Iron deposition in the peritoneum causes neoplastic changes. Here we used microRNA (miR) microarrays in a rat model by repeated intraperitoneal injections of ferric saccharate. miR microarray revealed the miR-199/214 as a distinctive feature of sarcomatoid mesothelioma.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32248600" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140392" }, "primaryId" : "GEO:GSE140392", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140392" } ] }, "title" : "Genome regulation by long noncoding RNAs during amelogenesis", "dateAssigned" : "2019-11-14T00:00:00.000-06:00", "summary" : "We conducted the genome-wide lncRNA and mRNA expression profiling using RNA samples extracted from rat incisor enamel organs, so as to refine the number of predicted gene targets for lncRNA regulators.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140420" }, "primaryId" : "GEO:GSE140420", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140420" } ] }, "title" : "Hippocampal Subregion Transcriptomic Profiles Associated with Age-Related Changes in Spatial Pattern Separation", "dateAssigned" : "2019-11-14T00:00:00.000-06:00", "summary" : "Previous studies of age-related transcriptional changes indicate that cognitive impairments are associated with differentially expressed genes DEGs linked to defined neural systems; however, studies that examine multiple regions of the hippocampus fail to find major links between behavior and transcription in the dentate gyrus DG. The DG is implicated in pattern separation PS and exhibits multiple age-related changes that may affect PS performance. We hypothesize that an age-related decline in PS performance is associated with distinct changes in transcriptional profile, most strongly within the DG compared to other hippocampal subregions. We used a water maze beacon discrimination task to characterize PS in young 5 mo and middle-age 12 mo male F344 rats, followed by a spatial reference memory test. Middle-age rats showed consistent deficits in discriminating two identical beacons compared to young. Reference memory was not different between these two age groups. Interestingly, with increasing spatial overlap between the cues, older animals appeared to compensate for impaired PS performance though greater reliance on spatial reference memory. mRNA sequencing of hippocampal subregions DG, CA1, and CA3 indicated that the DG of middle-age rats expressed more genes correlated with PS performance. In contrast, reliance on a spatial reference memory was associated with differential expression of genes in regions CA1 and CA3. These results indicate that the beacon task is sensitive to PS impairment as early as middle-age, and distinct gene profiles are observed in neural circuits that underlie different strategies used to solve the task.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32376783" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140524" }, "primaryId" : "GEO:GSE140524", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140524" } ] }, "title" : "Mitochondrial Dysfunction Induces Epigenetic Dysregulation by H3K27 Hyperacetylation to Perturb Active Enhancers in Parkinson’s Disease Models", "dateAssigned" : "2019-11-18T00:00:00.000-06:00", "summary" : "We aim to explore the predominant mitochondrial dysfunctions in PD, with a focus on how altering the histone code contributes to PD pathogenesis. We employ a multidisciplinary approach to convincingly demonstrate that neurotoxicant exposure- and genetic mutation-driven mitochondrial dysfunction share a common mechanism of epigenetic dysregulation. Under both scenarios, lysine 27 acetylation of likely variant H3.2 (H3.2K27ac) increased in dopaminergic neuronal models of PD, thereby opening that region to active enhancer activity via H3K27 hyperacetylation. These vulnerable epigenomic loci represent potential transcription factor motifs for PD pathogenesis. Our results reveal an exciting axis of ‘exposure/mutation-mitochondrial dysfunction-metabolism-H3K27ac-transcriptome’ for PD pathogenesis. Collectively, the novel mechanistic insights presented here interlinks mitochondrial dysfunction to epigenetic transcriptional regulation in dopaminergic degeneration as well as offer potential new epigenetic intervention strategies for PD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34494552" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140594" }, "primaryId" : "GEO:GSE140594", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140594" } ] }, "title" : "Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: Illumina Microarray Data from Generation F15", "dateAssigned" : "2019-11-18T00:00:00.000-06:00", "summary" : "The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans. This Illumina (RatRef-12v1 Beadchip) microarray study examined gene expression in the hippocampus in generation F15 male bHR rats and bLR rats at age postnatal day 14 (P14, n=6 per group).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32762937" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140595" }, "primaryId" : "GEO:GSE140595", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140595" } ] }, "title" : "Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: Affymetrix Microarray Data from Generation F15", "dateAssigned" : "2019-11-18T00:00:00.000-06:00", "summary" : "The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans. This Affymetrix (Rat Expression Set 230 A) microarray study examined gene expression in the hippocampus in generation F15 male bHR rats and bLR rats at age postnatal day 14 (P14, n=6 per group).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32762937" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140596" }, "primaryId" : "GEO:GSE140596", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140596" } ] }, "title" : "Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: Affymetrix Microarray Data from Generation F4", "dateAssigned" : "2019-11-18T00:00:00.000-06:00", "summary" : "The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans. This Affymetrix (Rat Expression Set 230 A) microarray study examined gene expression in the hippocampus in generation F4 adult male bHR rats and bLR rats (n=6 per group).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32762937" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140597" }, "primaryId" : "GEO:GSE140597", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140597" } ] }, "title" : "Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: RNA-Seq Data from Generation F29", "dateAssigned" : "2019-11-18T00:00:00.000-06:00", "summary" : "The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans. This RNA-sequencing study examined gene expression in the hippocampus, a region critical for emotional regulation, in generation F29 male bHR rats and bLR rats from two ages: P14 and adulthood (n=2/group).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32762937" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140598" }, "primaryId" : "GEO:GSE140598", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140598" } ] }, "title" : "Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: RNA-Seq Data from Generation F37", "dateAssigned" : "2019-11-18T00:00:00.000-06:00", "summary" : "The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans. This RNA-sequencing study examined gene expression in the hippocampus, a region critical for emotional regulation, in generation F37 adult male bHR rats and bLR rats (n=6/group), as well as in rats that showed an intermediate locomotor response to a novel field (“bred Intermediate Responder” or bIR rats, n=6), which were obtained by cross-breeding F37 bHR and bLR rats. Prior to sacrifice, the animals experienced behavioral testing. Locomotor response to a novel environment was assessed between age P50–75 as part of our selective breeding paradigm. We also measured anxiety-like behavior in adulthood (bHR/bLR: P160-P167; bIR: P65-75) using the percent time spent in the open arms of an Elevated Plus Maze (EPM; 5 min test). These behavioral testing results are provided here along with the gene expression data.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32762937" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140601" }, "primaryId" : "GEO:GSE140601", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140601" } ] }, "title" : "Cisplatin-induced rat model of kidney injury: physiological, functional, histological and gene expression profile evaluations", "dateAssigned" : "2019-11-18T00:00:00.000-06:00", "summary" : "Cisplatin is a chemotherapeutic drug used for the treatment of solid tumors and hematological malignancies and it is considered as a gold standard therapy in oncology. Its nephrotoxic effect has been largely investigated in vivo but a comprehensive overview that illustrates the effect of cisplatin not only in kidney but also on the entire organism at the same time is still missing. Here we established a stable model of cisplatin-induced acute renal injury in immune competent Sprague Dawley (SD) rats and described the systemic effects of the aforementioned drug. A broad panel of plasma and urine parameters was checked, the histology of different organs was evaluated and the assessment of renal function was measured by using an innovative transcutaneous device. Additionally gene expression profiling with RNAseq technology was performed. Changes in renal injury markers, such as plasma creatinine and urea and urinary albumin, were detected already 2 days after cisplatin administration. Renal function was seriously compromised and so the cytoarchitecture of the kidney. Inflammation was found in liver, lungs and heart. Gene expression profiling of renal tissue revealed 6333 significant differentially expressed genes, 49 pathways and 14 miRNAs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140629" }, "primaryId" : "GEO:GSE140629", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140629" } ] }, "title" : "Identification of therapeutic targets for treatment of intermittent claudication that mimic the effects of exercise", "dateAssigned" : "2019-11-18T00:00:00.000-06:00", "summary" : "Exercise is considered as the most efficacious intervention for improving walking capacity in patients with intermittent claudication (IC). Despite its benefits, the underlying mechanisms inducing this effect remain unclear. To elucidate the local mechanisms in skeletal muscle, we previously developed an electrical stimulating (ES) model which caused skeletal muscle contraction mimicking exercise. ES showed the improvement in walking ability in rat IC model. In this study, we compared gene expressions among hindlimb ischemia (Isch) group, Isch + exercise group, and Isch + ES group in rat using GeneChip analysis and real-time PCR. By extracting genes which were similarly altered in both exercise and ES groups compared with Isch group, we revealed candidate genes that might be involved in improvement of walking ability.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140685" }, "primaryId" : "GEO:GSE140685", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140685" } ] }, "title" : "Differential effect of repeated lipopolysaccharide treatment and aging on hippocampal function and biomarkers of hippocampal senescence", "dateAssigned" : "2019-11-19T00:00:00.000-06:00", "summary" : "Aging is associated with low-grade chronic systemic inflammation. Elevated peripheral serum cytokines and chemokines contribute to age-related diseases and correlate with cognitive decline. This study compared the effects of repeated lipopolysaccharide (LPS) treatment in young rats to age-related changes in hippocampal-dependent cognition, synaptic transmission, and transcription. Young (5-7 months) Fischer 344 X Brown Norway hybrid rats were injected intraperitoneally once a week for 6-7 weeks with either LPS (1 mg/kg) or vehicle. Older (14-16 months) rats received a similar injection schedule of vehicle. Older-vehicle animals and young-LPS rats exhibited impaired retention of spatial memory. Examination of the transcriptome of the CA1 and the dentate gyrus indicated that older-vehicle and young-LPS animals exhibited an increase in immune response genes. In contrast to aging, young-LPS animals exhibited an increased expression of genes related to the synapse. Even though young-LPS animals increased the expression of synaptic genes, LPS treatment reduced hippocampal CA3-CA1 total synaptic response and N-methyl-D-aspartate receptor (NMDAR)-mediated component of the synaptic response. Interestingly, the decrease in NMDAR function was not redox-sensitive. This study demonstrates that repeated exposure to LPS has long-term effects on hippocampal synaptic transmission and memory; however, young animals exhibited transcriptional recovery after LPS treatment. Recovery likely results from the acute nature of repeated LPS injections, relative to chronic systemic inflammation observed during aging.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140691" }, "primaryId" : "GEO:GSE140691", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE140691" } ] }, "title" : "Gene expression of Skeletal muscle in Tacrolimus-Induced Post-transplantation Diabetes Mellitus model", "dateAssigned" : "2019-11-19T00:00:00.000-06:00", "summary" : "Post-transplantation diabetes mellitus (PTDM) is a known complication of transplantation which affected the prognosis. Tacrolimus (Tac, or FK506) is a widely used immunosuppressant, has been reported as a risk factor for PTDM and further develops complications in heart and skeletal muscle , while the mechanism is still largely unknown. The gene expression of rat muscles of control group and Tac induced PTDM group were analyzed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141073" }, "primaryId" : "GEO:GSE141073", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141073" } ] }, "title" : "Inherent Motor Impulsivity Associates with Specific Gene Targets in the Rat Medial Prefrontal Cortex", "dateAssigned" : "2019-11-26T00:00:00.000-06:00", "summary" : "The present study profiled the complete set of mRNA expressed from genes (transcriptome) in the medial prefrontal cortex of male, outbred rats stably expressing high (HI) or low (LI) motor impulsivity identified in the 1-choice serial reaction time (1-CSRT) task.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32240784" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141090" }, "primaryId" : "GEO:GSE141090", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141090" } ] }, "title" : "The expression landscape of hepatocarcinogeneis in a rat model", "dateAssigned" : "2019-11-26T00:00:00.000-06:00", "summary" : "Hepatocellular carcinoma (HCC) initiation is characterized by the sequential stepwise accumulation of molecular alterations. However, the earliest events during the dynamic temporal trend of hepatocarcinogenesis are still unknown. Using a diethylnitrosamine (DEN)-induced rat HCC model, we report a comprehensive transcriptomic landscape of liver tissues at the stages of hepatitis, cirrhosis, and HCC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33163943" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141166" }, "primaryId" : "GEO:GSE141166", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141166" } ] }, "title" : "Downstream targets of uc.323-mediated cardiomyocyte hypertrophy", "dateAssigned" : "2019-11-29T00:00:00.000-06:00", "summary" : "To further characterize the downstream targets of uc.323, we performed global microarray analysis after knockdown of uc.323 in cardiomyocytes to gain broad insight into uc.323-mediated transcriptome changes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141242" }, "primaryId" : "GEO:GSE141242", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141242" } ] }, "title" : "Expression data from 18-month old rats", "dateAssigned" : "2019-12-02T00:00:00.000-06:00", "summary" : "We used microarrays to detail the global programme of gene expression in rats after sevoflurane anesthesia and identified distinct classes of changed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141628" }, "primaryId" : "GEO:GSE141628", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141628" } ] }, "title" : "Predicting Changes in Renal Metabolism after Compound Exposure with a Genome-Scale Metabolic Model", "dateAssigned" : "2019-12-08T00:00:00.000-06:00", "summary" : "The kidneys are metabolically active organs that are important for several physiological tasks such as the secretion of soluble wastes into urine. Other functions of the kidneys include synthesizing glucose and oxidizing fatty acids for energy in fasting (non-fed) conditions. Once damaged, the metabolic capability of the kidneys becomes altered. Here, we define metabolic tasks in a computational modeling framework to capture kidney function in an update to the iRno network reconstruction of rat metabolism using literature-based evidence. To demonstrate the utility of iRno for predicting kidney function, we exposed primary rat renal proximal tubule epithelial cells to five compounds with varying levels of nephrotoxicity (acetaminophen, carbon tetrachloride, gentamicin, 2,3,7,8-tetrachlorodibenzodioxin, and trichloroethylene for six and twenty-four hours), and collected transcriptomics and metabolomics data to measure the metabolic effects of compound exposure. We observed changes in fatty acid metabolism and amino acid metabolism, consistent with changes in existing markers of kidney function such as Lcn2 (lipocalin), Clu (clusterin), and the carnitine transporter Octn2 (solute carrier family 22, member 5). The iRno metabolic network reconstruction was able to predict alterations in these same pathways after integrating transcriptomics data, and was able to distinguish between select compound-specific effects on the proximal tubule epithelial cells. Genome-scale metabolic network reconstructions with coupled omics data can be used to predict changes in metabolism to provide a step towards identifying novel biomarkers of kidney function and dysfunction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33387578" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141650" }, "primaryId" : "GEO:GSE141650", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141650" } ] }, "title" : "Fibrosis growth factor 23 is a promoting factor for cardiac fibrosis in the presence of transforming growth factor-β1", "dateAssigned" : "2019-12-09T00:00:00.000-06:00", "summary" : "We used microarrays to elucidate the fibrosis initiating master factor using heart samples obtained from PAB or sham-operated rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141699" }, "primaryId" : "GEO:GSE141699", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141699" } ] }, "title" : "Transcriptional Alterations of Genes Related to Fertility Decline in Male rats Induced by Chronic Sleep Restriction", "dateAssigned" : "2019-12-09T00:00:00.000-06:00", "summary" : "The adverse effects of sleep disorders on male fertility are increasingly concerning. In this study, a rat model of chronic sleep restriction (CSR) was established using the modified multiplatform method. The effects of CSR on the fertility of male rats were evaluated first based on sexual behavior. Serum hormones, including testosterone (T), prolactin (PRL), luteinizing hormone (LH) and follicle-stimulating hormone (FSH), and sperm parameters (concentration, viability, motility, deformation rate) were measured, and testicular histology was analysed by hematoxylin and eosin staining. The transcriptional differences between CSR rats and control rats were detected by RNA sequencing (RNA-Seq), and DNA methylation was then detected by bisulfite sequencing. After the differently expressed genes of CSR rats were sequenced and screened, some representative up- and down-regulated genes were randomly sampled to verify the sequencing results by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). Finally, functional annotations were completed, including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomic (KEGG) pathway analyses. The results showed that the sexual behavior of CSR rats did not change when compared with control group rats. The sperm concentration, viability and motility of the CSR rats decreased significantly, while the sperm malformation rate increased significantly. In the KEGG pathway analysis database, some specific differentially expressed genes were screened, which are involved in metabolic pathways, inflammation-related pathways, the renin-angiotensin system, etc. However, the aforesaid differentially expressed genes in the testes were not related to their DNA methylation status. CSR could significantly reduce the fertility of male rats, and one of its mechanisms occurs by altering gene expression in the testes, which has nothing to do with their DNA methylation. It was suggested that CSR could cause male infertility by significantly altering the testicular transcriptome.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141815" }, "primaryId" : "GEO:GSE141815", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141815" } ] }, "title" : "MiRNA-mRNA expression profiles and functional network after injection of botulinum toxin type A into submandibular gland [miRNA-Seq]", "dateAssigned" : "2019-12-11T00:00:00.000-06:00", "summary" : "Key words: miRNA-mRNA, BTXA, submandibular gland", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141819" }, "primaryId" : "GEO:GSE141819", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141819" } ] }, "title" : "MiRNA-mRNA expression profiles and functional network after injection of botulinum toxin type A into submandibular gland [microarray]", "dateAssigned" : "2019-12-11T00:00:00.000-06:00", "summary" : "Key words: miRNA-mRNA, BTXA, submandibular gland", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141827" }, "primaryId" : "GEO:GSE141827", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141827" } ] }, "title" : "Genome-wide atlas of promoters expression reveals contribution of transcribed regulatory elements to genetic control of disuse-mediated atrophy of skeletal muscles", "dateAssigned" : "2019-12-11T00:00:00.000-06:00", "summary" : "Here we report genome wide estimation of expression profiles at promoter level in Soleus and EDL muscles in rat hindlimbs under unloading conditions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34203013" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141859" }, "primaryId" : "GEO:GSE141859", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141859" } ] }, "title" : "RNA-sequencing reveals transcriptional signature of pathological remodeling in the diaphragm of rats after myocardial infarction", "dateAssigned" : "2019-12-11T00:00:00.000-06:00", "summary" : "Conclusions: Our study represents the first detailed analysis of diaphragm transcriptomes post-myocardial infarction generated by RNA-Seq technology.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141981" }, "primaryId" : "GEO:GSE141981", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE141981" } ] }, "title" : "Expression data from EMT-derived NRK-52E cells before and after the AMPKα2 knockdown", "dateAssigned" : "2019-12-13T00:00:00.000-06:00", "summary" : "TGF-β1 was used to induce epithelial-mesenchymal transition(EMT) in normal rat renal tubular epithelial (NRK-52E) cells. Gene microarray was used to analyze differential gene expression in EMT-derived NRK-52E cells before and after the AMPKα2 knockout", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142087" }, "primaryId" : "GEO:GSE142087", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142087" } ] }, "title" : "Hippocampus miRNA profiles in chronic cerebral-hypoperfusion rats", "dateAssigned" : "2019-12-16T00:00:00.000-06:00", "summary" : "Chronic cerebral hypoperfusion (CCH) is a well-known risk factor for vascular dementia and other neurodegenerative disease, for which there are currently no effective medications available. MicroRNA (miRNA) are noncoding RNAS mediating post-translational silencing of genes, and has been extensively studied for their involvement in neurodegenerative disease. However, little is known about their roles in vascular dementia (VaD). In this work, a bilateral common carotid arteries occlusion (2-VO) surgery in rats was employed to induced CCH related cognitive dysfunction. Four months later, the hippocampi were dissected from 2-VO and sham operated rats for high-throughput profiling of miRNAs. Twelve differentially expressed miRNAs were identified according to a cutoff of |log2(Fold Change)|≥1 and p＜0.05. GO analysis of target genes revealed that the most relevant biological processes included the regulatory region nucleic acid binding, histone acetyltransferase binding, organic acid transmembrane transporter activity, L-amino acid transmembrane transporter activity. The cellular structure mainly included histone deacetylation complexes, endosomes, Golgi membranes, etc. And the involved molecular processes mainly included axon development, organ morphogenesis, macromolecular modification, regulation of neuron projection development, neuron development. This study provides a framework for understanding the alternations in hippocampus miRNA profiles underwent hypoxia insult.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142118" }, "primaryId" : "GEO:GSE142118", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142118" } ] }, "title" : "Next Generation Sequencing of Wild Type and CMG2-/- Rat Lung Transcriptomes", "dateAssigned" : "2019-12-16T00:00:00.000-06:00", "summary" : "Conclusion Our work identifies a novel role for CMG2 in systemic-to-pulmonary shunt induced PAH based on the findings that CMG2 deficiency could exacerbate systemic-to- pulmonary shunt induced vascular remodeling in the development of PAH. CMG2 may be a potential target for CHD-PAH treatment.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142364" }, "primaryId" : "GEO:GSE142364", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142364" } ] }, "title" : "Transcriptome profiling of neonatal rat ventricular cardiomyocytes overexpressing NFYa or NFE2L1", "dateAssigned" : "2019-12-19T00:00:00.000-06:00", "summary" : "The adult mammalian heart is incapable of regeneration following injury. In contrast, the neonatal mouse heart has a transient ability to regenerate, however the molecular mechanism that mediates this regenerative response is not fully understood. Here, by single-nucleus RNA sequencing we map the transcriptome landscape of cardiomyocytes in neonatal mouse hearts at healthy, regenerative, and remodeling conditions. We show that an immature cardiomyocyte population enters cell-cycle in response to injury. Absence of this cardiomyocyte population overtime is associated with the loss of the ability of the heart to regenerate. We show a defined injury response in these cardiomyocytes, including activation of transcription factors NFYa and NFE2L1, which play proliferative and protective roles, respectively. We further show that overexpression of these two factors in vivo promotes heart regeneration. Thus, these findings refined our understanding of cellular basis of neonatal heart regeneration and reveal dynamic transcriptome landscape of cardiomyocytes in response to injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32220304" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142436" }, "primaryId" : "GEO:GSE142436", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142436" } ] }, "title" : "RNA-seq analysis of angiotensin II-induced myocardial fibrosis in rats treated with and without sodium butyrate", "dateAssigned" : "2019-12-20T00:00:00.000-06:00", "summary" : "Analysis of sodium butyrate（NaBu） on angiotensin II（Ang II-induced cardiac fibrosis at gene expression level. The hypothesis tested in the present study was that NaBu influence the balance of gene expression of Ang II-induce cardiac fibrosis. Results provide important information of the response of NaBu to cardiac fibrosis, such as specific genes, up- or down-regulated specific cardiac cellular functions.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142446" }, "primaryId" : "GEO:GSE142446", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142446" } ] }, "title" : "Role of high fat diet on silica-induced lung toxicity in rats", "dateAssigned" : "2019-12-20T00:00:00.000-06:00", "summary" : "From an occupational standpoint, exposure to silica can have devastating consequences. An estimated 2.3 million workers in the U.S. are exposed to dust containing crystalline silica, annually. In addition, of the 140 million people over the age of 20, employed in the U.S., 30% are obese. If and how diet-induced obesity modifies silica-induced pulmonary toxicity is unknown. Therefore, the objective of this study was to determine the effect of diet-induced obesity, if any, on silica induced pulmonary toxicity. Rats (Fischer 344, male) were fed either a regular-fat diet (RFD; 18% kcal as fat) (Envigo, Indianapolis, IN) or a high-fat diet (HFD; 60% kcal as fat) (Envigo, Indianapolis, IN) and exposed by whole-body inhalation to either air or crystalline silica (15 mg/m3, 6 hours/day, 5 days). At designated post-exposure time intervals (1, 3, 6, and 9 months), pulmonary toxicity was determined. Silica inhalation resulted in pulmonary toxicity, which progressed across all post-exposure time points, as evidenced by enhanced neutrophil infiltration, increased LDH levels, enhanced oxidant production, and increased inflammatory cytokine levels. The incidence and severity of silica-induced lung pathology was similar between the two diet groups up to 6 months post-exposure. However, by 9 months post-exposure, silica-induced pathology tended to be slightly more severe in animals fed an RFD compared to those fed an HFD. Lung gene expression profiles were then determined in the rats euthanized at the 3- and 9-month post-silica exposure time intervals by RNA sequencing to identify transcript differences between the two timepoints.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142476" }, "primaryId" : "GEO:GSE142476", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142476" } ] }, "title" : "The role of Lhx4 and Bsx homeobox genes in the rat adult pineal gland", "dateAssigned" : "2019-12-20T00:00:00.000-06:00", "summary" : "Homeobox genes generally encode transcription factors involved in regulating developmental processes. In the pineal gland, a brain structure devoted to nocturnal melatonin synthesis, a number of homeobox genes are also expressed postnatally; among these are the LIM homeobox 4 gene (Lhx4) and the brain‐specific homeobox gene (Bsx). As part of a larger study, we used of siRNA technology to knock down Lhx4 or Bsx expression in cultured adult rat pinealocytes. For RNAseq, nine barcoded libraries were pooled and sequenced on one Flow Cell of a HiSeq2500 (Illumina) in Rapid Run Mode yielding a total of 410 million 2∙x 100‐bp read‐pairs (average reads per sample: 45.6∙106 ± 3.3∙106 SEM). Analysis of control and siRNA‐treated pinealocytes revealed downstream target genes and insights into the role these homeobox genes play in the adult pineal gland. The two processed data file present siLhx4 vs siNT, or siBsx vs siNT.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142478" }, "primaryId" : "GEO:GSE142478", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142478" } ] }, "title" : "Sex- and region-specific transcriptomic differences in brainstem and cervical spinal cord microglia in rat offspring exposed to gestational intermittent hypoxia ", "dateAssigned" : "2019-12-20T00:00:00.000-06:00", "summary" : "We analyzed gene expression via RNA-sequencing in medulla and C3-C6 cervical spinal cord microglia isolated from young adult rats exposed to gestational intermittent normoxia or gestational intermittent hypoxia", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32661056" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142541" }, "primaryId" : "GEO:GSE142541", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142541" } ] }, "title" : "Redefining the heterogeneity of peripheral nerve cells in health and autoimmunity", "dateAssigned" : "2019-12-23T00:00:00.000-06:00", "summary" : "Peripheral nerves contain axons and their enwrapping glia cells named Schwann cells (SC) that are either myelinating or non-myelinating (nmSC). Our understanding of other cells in the peripheral nervous system (PNS) remains limited. Here, we provide an unbiased single-cell transcriptomic characterization of the non-diseased rodent PNS. We identified and independently confirmed novel markers of previously underappreciated nmSC and nerve-associated fibroblasts. We also found and characterized two distinct populations of nerve-resident homeostatic myeloid cells that transcriptionally differed from central nervous system microglia. In a model of chronic autoimmune neuritis, homeostatic myeloid cells were outnumbered by infiltrating lymphocytes which modulated the local cell-cell interactome and induced a specific transcriptional response in glia cells. This response was partially shared between the peripheral and central nervous system glia identifying common immunological features across different parts of the nervous system. Our study thus identifies novel subtypes and cell-type markers of PNS cells and a partially conserved autoimmunity module induced in glia cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32295886" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142617" }, "primaryId" : "GEO:GSE142617", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142617" } ] }, "title" : "RNA-sequencing Reveals Altered Gene Expression in the Ventromedial Hypothalamus Following Predator Odor Exposure", "dateAssigned" : "2019-12-26T00:00:00.000-06:00", "summary" : "It is unknown how the VMH regulates skeletal muscle metabolism and predator threat responses, or potential interactions between these. Because skeletal muscle has a great capacity for increasing energy expenditure and is rapidly activated by PO, understanding how the VMH regulates this process could uncover novel targets for obesity treatments. Due to lack of investigation, we sought to provide a foundation for mechanistic exploration. We report transcriptome-wide alterations of the VMH following PO exposure. Our results uncovered novel functional relationships among genes that can now be probed to better understand the dual processing role of the VMH in skeletal muscle metabolism and predator-threat responses.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142785" }, "primaryId" : "GEO:GSE142785", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE142785" } ] }, "title" : "RNA Sequencing Facilitates Quantitative Analysis of Schwann cells Transcriptomes", "dateAssigned" : "2019-12-31T00:00:00.000-06:00", "summary" : "Our study is the first to detect and analyze mRNAs, lncRNAs and miRNAs changes in Schwann cells from STZ-treated rats with DPN and reveal the novel interactions between dysregulated RNAs and the pathogenesis of DPN. Our data show that dysregulated RNAs have complicated interactions between them and play critical roles in regulating functions of SCs involved in the pathogenesis of DPN", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143168" }, "primaryId" : "GEO:GSE143168", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143168" } ] }, "title" : "microRNA expression profiles in myocardium of diet-induced obesity rat", "dateAssigned" : "2020-01-06T00:00:00.000-06:00", "summary" : "Diet induced obesity in rat was associated with myocardial dysfunction, hypertension and fibrosis. This study aimed to explore microRNA expression profiles in diet obesity-induced rat myocardium. Wistar rats were feed normal chow or high-fat diet for 20 weeks. After that, cardiac function was evaluated by echocardiography. Left ventricular myocardium was harvest to assess the extent of hypertension and fibrosis, meanwile, the left ventricular microRNA expression was analyzed using Agilent Rat miRNA microarray. Significant cardiac dysfunction, hypertension and fibrosis were found in diet-induced obesity rats as compared with normal diet rats. rno-miR-141-3p and rno-miR-144-3p were also significantly increased in myocardium of diet-induced obesity rat. These findings suggest that specific miRNA differences may contribute to the alteration in cardiac function, hypertension and fibrosis which responses to diet-induced obesity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143289" }, "primaryId" : "GEO:GSE143289", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143289" } ] }, "title" : "Expression data from Vehicle, MP and MP+CSE_Bu treated SD rats", "dateAssigned" : "2020-01-08T00:00:00.000-06:00", "summary" : "We used microarray to detail the effect of MP and MP+CSE_Bu on gene expression in SD rats and identified various classes of genes that are either upregulated or down-regulated.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143327" }, "primaryId" : "GEO:GSE143327", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143327" } ] }, "title" : "Genome-wide transcriptome and alternative splicing changes in pregnant rat uterine arteries", "dateAssigned" : "2020-01-08T00:00:00.000-06:00", "summary" : "In the current study, we have focused on a whole genome transcriptome and alternative splicing in utrine artery from pregnant and non pregnant Sprague Dawley rats .", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32197362" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143368" }, "primaryId" : "GEO:GSE143368", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143368" } ] }, "title" : "Transgenerational epigenetic and transcriptomic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure in rat [array]", "dateAssigned" : "2020-01-09T00:00:00.000-06:00", "summary" : "In rats, direct exposure to TCDD causes myriad toxicities. Exposed rats experience hepatotoxicity, wasting syndrome and immune suppression, amongst others. “Inherited exposure”, as occurs in the F3 generation of directly exposed F0 animals, has also been shown to cause toxicity: both male and female F3 rats demonstrate an increased incidence of adult onset disease, females also display reproductive abnormalities and increased incidence of ovarian diseases while males show increased incidence of kidney disease and an altered sperm epigenome. Here, we explore the hepatic transcriptomic profile of male and female F3 Sprague-Dawley rats bred through the paternal germ line from F0 dams exposed to a single dose of TCDD (0, 30, 100, 300 or 1000 ng/kg body weight) by oral gavage. We hypothesize that RNA transcripts with altered abundance in livers of unexposed F3 progeny of treated F0 Sprague-Dawley rats may result from epigenetic modifications to the genome. Female F3 rats demonstrated more TCDD-mediated hepatic transcriptomic changes than males, with differences primarily in the lowest dose group.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143440" }, "primaryId" : "GEO:GSE143440", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143440" } ] }, "title" : "Urinary phosphate-containing nanoparticle contributes to inflammation and kidney injury in salt-sensitive hypertension", "dateAssigned" : "2020-01-10T00:00:00.000-06:00", "summary" : "Although disturbed phosphate metabolism frequently accompanies chronic kidney disease, it is unclear whether it contributes to the progression of renal dysfunction. Here, we show that urinary phosphate-containing nanoparticles promote kidney injury in salt-sensitive hypertension. Remarkably, four weeks of high salt loading resulted in a 2.5-fold increase in urinary phosphate excretion in Dahl salt-sensitive rats on a normal phosphorus diet. Inhibition of intestinal phosphate absorption using sucroferric oxyhydroxide (SF) in this model suppressed phosphaturia, attenuating glomerulosclerosis and tubulointerstitial injury without significantly affecting serum phosphate, blood pressure, or urinary sodium levels. In the kidney, macrophage infiltration and inflammatory cytokine induction were ameliorated by SF. Additionally, macrophage infiltration but not myofibril hypertrophy was alleviated in the heart. In vitro, phosphate loading to proximal tubule cells significantly increased inflammatory cytokine Ccl2, which was abolished by the removal of phosphate-containing nanoparticles but not by the knockdown of phosphate transporter Slc34a1. Finally, transcriptome analysis revealed a potential role of complement C1q in renal inflammation associated with disturbed phosphate metabolism. These data demonstrate that increased phosphaturia promotes inflammation and renal injury from an early stage of salt-sensitive hypertension, and suggest the need for interventions against subclinical phosphate accumulation to improve the prognosis of hypertensive kidney disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33060834" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143555" }, "primaryId" : "GEO:GSE143555", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143555" } ] }, "title" : "RNA sequencing of laser captured hippocampal deep and superficial CA1 subfields in epilepsy", "dateAssigned" : "2020-01-13T00:00:00.000-06:00", "summary" : "We profiled total mRNA of laser captured microdissected hippocampal deep and superficial CA1 subfields from adult male (45-50 days) Wistar rats (Rattus norvegicus) (180-200g) subjected to kainic acid-induced status epilepticus (chronic epileptic phase) and control animals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34107264" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143745" }, "primaryId" : "GEO:GSE143745", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143745" } ] }, "title" : "Transcriptional characterization of cardiac tissue of rat pups with pulmonary banding", "dateAssigned" : "2020-01-15T00:00:00.000-06:00", "summary" : "Expression analysis of cardiac tissue of rat pups with and without pulmonary banding", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143751" }, "primaryId" : "GEO:GSE143751", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143751" } ] }, "title" : "Exploration of small RNA biomarkers for testicular injury in the serum exosomes of rats", "dateAssigned" : "2020-01-15T00:00:00.000-06:00", "summary" : "Testicular injury is often observed in drug development. Serum hormones are usually used as non-invasive biomarkers for testicular injury; however, their sensitivity is low. Therefore, it is difficult to monitor testicular injury in pre-clinical and clinical drug developments. In recent years, molecules in body fluid exosomes are attracting attention as disease biomarkers such as cancer. In this study, small RNAs in serum exosomes were analyzed for identifying non-invasive biomarkers of testicular injury in rats, which are mainly used in a pre-clinical drug development. Testicular injury models in rats were prepared by a single oral administration of 2000 mg/kg ethylene glycol monomethyl ether in which spermatocytes degeneration and sertoli cells vacuolation were observed, or 400 mg/kg carbendazim in which sertoli cells vacuolation and seminiferous tubules dilation were observed. Serum exosome small RNA-seq was performed in these models. The analysis identified 3 small RNAs that fluctuated in common between the models, and miR-423-5p and miR-128-3p were selected as candidate markers. For qPCR validation of the candidates, testicular injury models were further prepared by a single oral administration of 60 mg/kg 1,3-dinitrobenzene or 500 mg/kg nitrofurazone in which spermatocytes degeneration and sertoli cells vacuolation were observed. In qPCR analysis, the selected two miRNAs in exosomes were upregulated in the all models except for 1,3-dinitrobenzene model in which severe hemolysis was observed. On the other hand, the miRNAs in serum did not significantly change in the any models. In conclusion, we identified miR-423-5p and miR-128-3p in serum exosome as non-invasive biomarkers for testicular injury in rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143876" }, "primaryId" : "GEO:GSE143876", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143876" } ] }, "title" : "Gene expression analysis after miR-125a-3p over-expression in oligodendrocyte precursor cells (OPCs)", "dateAssigned" : "2020-01-17T00:00:00.000-06:00", "summary" : "MiR-125a-3p over-expression in OPCs impairs their differentiation into fully mature oligodendrocytes. We performed a whole microarray profiling to identify new miR-125a-3p direct targets and altered signaling pathways responsible for its the detrimental effect on oligodendrocyte maturation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32163190" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143883" }, "primaryId" : "GEO:GSE143883", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143883" } ] }, "title" : "Transgenerational epigenetic and transcriptomic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure in rat [Bisulfite-Seq]", "dateAssigned" : "2020-01-17T00:00:00.000-06:00", "summary" : "In rats, direct exposure to TCDD causes myriad toxicities. Exposed rats experience hepatotoxicity, wasting syndrome and immune suppression, amongst others. “Inherited exposure”, as occurs in the F3 generation of directly exposed F0 animals, has also been shown to cause toxicity: both male and female F3 rats demonstrate an increased incidence of adult onset disease while males show increased incidence of kidney disease and an altered sperm epigenome. Here, we employ bisulfite-sequencing to explore the methylation profile of male F3 Sprague-Dawley rats bred through the paternal germ line from F0 dams exposed to a single dose of TCDD (0 or 1000 ng/kg body weight) by oral gavage. We identified multiple significant differentially methylated regions (DMRs) affecting receptor genes, including multiple olfactory receptors, as well as Egfr and Mc5r, typically with increased methylation among the TCDD-exposed lineage relative to control lineage.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143895" }, "primaryId" : "GEO:GSE143895", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143895" } ] }, "title" : "GPR160 de-orphanization reveals critical roles in neuropathic pain in rodents", "dateAssigned" : "2020-01-17T00:00:00.000-06:00", "summary" : "Treating neuropathic pain is challenging and novel non-opioid based medicines are needed. Using unbiased receptomics, transcriptomic analyses, immunofluorescence and in situ hybridization, expression of the orphan GPCR (oGPCR) GPR160 increased in the rodent dorsal horn of the spinal cord (DH-SC) following traumatic nerve injury. Genetic and immunopharmacological approaches demonstrated that GPR160 inhibition in the spinal cord prevented and reversed neuropathic pain in male and female rodents without altering normal pain response. GPR160 inhibition in the spinal cord attenuated sensory processing in the thalamus, a key relay in the sensory discriminative pathways of pain. We also identified cocaine- and amphetamine-regulated transcript peptide (CARTp) as a GPR160 ligand. Inhibiting endogenous CARTp signaling in spinal cord attenuated neuropathic pain, whereas exogenous intrathecal (i.th.) CARTp evoked painful hypersensitivity through GPR160-dependent ERK and cAMP response element-binding protein (CREB). Our findings de-orphanize GPR160, identify it as a determinant of neuropathic pain and potential therapeutic target, and provide insights to its signaling pathways. CARTp is involved in many diseases including depression, reward and addiction, de-orphanization of GPR160 is a major step forward understanding the role of CARTp signaling in health and disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31999650" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143920" }, "primaryId" : "GEO:GSE143920", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143920" } ] }, "title" : "Characterization of rat ILCs reveals ILC2 as the dominant intestinal subset", "dateAssigned" : "2020-01-19T00:00:00.000-06:00", "summary" : "Innate lymphoid cells (ILCs) are tissue-resident lymphocytes that lack antigen-specific receptors and exhibit innate effector functions such as cytokine production that play an important role in immediate responses to pathogens especially at mucosal sites. Mouse and human ILC subsets have been extensively characterized in various tissues and in blood. In this study, we present the first characterization of ILCs and ILC subsets in rat gut and secondary lymphoid organs. ScRNAseq and flow cytometric data shows that phenotype and function of rat ILC subsets are conserved similar to human and mouse ILCs. However, contrary to human and mouse, our study unexpectedly revealed that ILC2 and not ILC3 was by far the dominant ILC subset in the rat intestinal lamina propria. ILC2 predominance in the gut was independent of rat strain, sex or housing facility. In contrast, ILC3 were the main ILC subset in mesenteric lymph nodes and Peyer patches, in which strain-dependent differences in ILC frequencies were also observed. In conclusion, our study demonstrates that in spite of highly conserved phenotype and function between mice, rat and humans, the distribution of ILC subsets in the intestinal mucosa is species-dependent, likely in response to both genetic and environmental factors.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143935" }, "primaryId" : "GEO:GSE143935", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE143935" } ] }, "title" : "miRNA expression profiling in thephysiological cardiac hypertrophy of rats", "dateAssigned" : "2020-01-20T00:00:00.000-06:00", "summary" : "Using the highly sensitive miRNA array, we screened 220 microRNAs abundant in physiological left ventricular hypertrophy (LVH) and we explored the functions of these miRNAs in the cardiac tissue by Gene Ontology and Kyoto Encyclopedia of Genes annotation. miRNAs showed a high score in the pathway enriched in autophagy. Moreover, the expression levels of miR-26b-5p, miR-204-5p, and miR-497-3p showed an obvious increase in rat hearts. Adenovirus-mediated overexpression of miR-26b-5p, miR-204-5p, and miR-497-3p markedly attenuated IGF-1-induced hypertrophy in H9C2 cells by suppressing autophagy. Furthermore, miR-26b-5p, miR-204-5p, and miR-497-3p attenuated autophagy in H9C2 cells through targeting ULK1, LC3B and Beclin 1, respectively. Taken together, our results demonstrate that swimming exercise induced physiological LVH, at least in part, by modulating the microRNA–autophagy axis, and that miR-26b-5p, miR-204-5p, and miR-497-3p may help distinguish physiological and pathological LVH.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144027" }, "primaryId" : "GEO:GSE144027", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144027" } ] }, "title" : "Single-cell sequencing of the Wistar and SHR stellate ganglia", "dateAssigned" : "2020-01-21T00:00:00.000-06:00", "summary" : "We report 10x Genomics based single-cell sequencing of the dissociated Wistar and Spontaneously Hypertensive Rat (SHR) stellate ganglia at 5-6 weeks of age.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35784866" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144147" }, "primaryId" : "GEO:GSE144147", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144147" } ] }, "title" : "A Balance Between Intermediate Filaments and Microtubules Maintains Nuclear Architecture in the Cardiomyocyte", "dateAssigned" : "2020-01-23T00:00:00.000-06:00", "summary" : "In this manuscript we reported a unique role for desmin in the maintence of nuclear morphology. We performed this LaminB chip-seq to determine if there was a change in LAD organization with desmin KD.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144207" }, "primaryId" : "GEO:GSE144207", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144207" } ] }, "title" : "1H NMR metabolomic and transcriptomic analyses reveal urinary metabolites as biomarker candidates in response to protein undernutrition in adult rats", "dateAssigned" : "2020-01-24T00:00:00.000-06:00", "summary" : "1H NMR metabolomics was performed on urine samples weekly and on plasma and liver samples collected at week 4 from these animals, to identify metabolites that respond to protein undernutrition. To further investigate metabolites which were fluctuated in response to protein undernutrition in terms of metabolic enzymes, hepatic mRNA microarray and quantitative PCR analyses were also performed at week 4.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144219" }, "primaryId" : "GEO:GSE144219", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144219" } ] }, "title" : "Rx-TGx: Toxicogenomic Study Of Pharmaceuticals Using RNA-Seq", "dateAssigned" : "2020-01-24T00:00:00.000-06:00", "summary" : "The robust transcriptional plasticity of liver mediated through xenobiotic receptors underlies its ability to respond rapidly and effectively to diverse chemical stressors. Thus, drug-induced gene expression changes in liver serve not only as biomarkers of liver injury, but also as mechanistic sentinels of adaptation in metabolism, detoxification and tissue protection from chemicals. Modern RNA sequencing methods offer an unmatched opportunity to quantitatively monitor these processes in parallel and to contextualize the spectrum of dose-dependent stress, adaptation, protection and injury responses induced in liver by drug treatments. Using this approach, we profiled the transcriptional changes in rat liver following daily oral administration of 95 different compounds, many of which are known to be associated with clinical risk for drug induced liver injury (DILI) by diverse mechanisms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32119089" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144261" }, "primaryId" : "GEO:GSE144261", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144261" } ] }, "title" : "Comprehensive Expression Analysis of mRNA and microRNA for Investigation of Compensatory Mechanisms in the Rat Kidney after Unilateral Nephrectomy (Male_miRNA)", "dateAssigned" : "2020-01-26T00:00:00.000-06:00", "summary" : "Compensation is a physiological response that occurs during chemical exposure to maintain homeostasis. Because compensatory responses are not usually considered adverse effects, it is important to understand compensatory mechanisms for chemical risk assessment. Although the kidney is a major target organ for toxicity, there is controversy over whether hyperplasia or hypertrophy contributes to the compensatory mechanism, and there is limited information to apply for chemical risk assessment. In the current study, compensatory mechanisms of the kidney were investigated in a unilateral nephrectomy (UNx) model using adult male and female rats. In residual kidneys of male and female rats after UNx, 5-bromo-2'-deoxyuridine-labeling indices and mRNA expression of cell cycle-related genes were increased, although there were no fluctuations in mRNA expression of transforming growth factor-β1, which contributes to hypertrophy in renal tubules. Pathway analysis using mRNA expression data from a cDNA microarray revealed that canonical pathways related to cell proliferation were mainly activated and that forkhead box M1 (FOXM1) was an upstream regulator of compensatory cell proliferation in residual kidneys of male and female rats. cDNA microarray for microRNAs (miRNAs) demonstrated that 9 miRNAs were downregulated in residual kidneys, and mRNA/miRNA integrated analysis indicated that miRNAs were associated with the expression of factors downstream of FOXM1. Overall, these results suggested that FOXM1-mediated hyperplasia rather than hypertrophy contributed to compensatory mechanisms in the kidney and that miRNAs regulated downstream FOXM1 signaling. These results will be beneficial for evaluating nephrotoxicity in chemical risk assessment and for developing new biomarkers to predict nephrotoxicity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144262" }, "primaryId" : "GEO:GSE144262", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144262" } ] }, "title" : "Comprehensive Expression Analysis of mRNA and microRNA for Investigation of Compensatory Mechanisms in the Rat Kidney after Unilateral Nephrectomy (Male_mRNA)", "dateAssigned" : "2020-01-26T00:00:00.000-06:00", "summary" : "Compensation is a physiological response that occurs during chemical exposure to maintain homeostasis. Because compensatory responses are not usually considered adverse effects, it is important to understand compensatory mechanisms for chemical risk assessment. Although the kidney is a major target organ for toxicity, there is controversy over whether hyperplasia or hypertrophy contributes to the compensatory mechanism, and there is limited information to apply for chemical risk assessment. In the current study, compensatory mechanisms of the kidney were investigated in a unilateral nephrectomy (UNx) model using adult male and female rats. In residual kidneys of male and female rats after UNx, 5-bromo-2'-deoxyuridine-labeling indices and mRNA expression of cell cycle-related genes were increased, although there were no fluctuations in mRNA expression of transforming growth factor-β1, which contributes to hypertrophy in renal tubules. Pathway analysis using mRNA expression data from a cDNA microarray revealed that canonical pathways related to cell proliferation were mainly activated and that forkhead box M1 (FOXM1) was an upstream regulator of compensatory cell proliferation in residual kidneys of male and female rats. cDNA microarray for microRNAs (miRNAs) demonstrated that 9 miRNAs were downregulated in residual kidneys, and mRNA/miRNA integrated analysis indicated that miRNAs were associated with the expression of factors downstream of FOXM1. Overall, these results suggested that FOXM1-mediated hyperplasia rather than hypertrophy contributed to compensatory mechanisms in the kidney and that miRNAs regulated downstream FOXM1 signaling. These results will be beneficial for evaluating nephrotoxicity in chemical risk assessment and for developing new biomarkers to predict nephrotoxicity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144263" }, "primaryId" : "GEO:GSE144263", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144263" } ] }, "title" : "Comprehensive Expression Analysis of mRNA and microRNA for Investigation of Compensatory Mechanisms in the Rat Kidney after Unilateral Nephrectomy (Female_mRNA)", "dateAssigned" : "2020-01-26T00:00:00.000-06:00", "summary" : "Compensation is a physiological response that occurs during chemical exposure to maintain homeostasis. Because compensatory responses are not usually considered adverse effects, it is important to understand compensatory mechanisms for chemical risk assessment. Although the kidney is a major target organ for toxicity, there is controversy over whether hyperplasia or hypertrophy contributes to the compensatory mechanism, and there is limited information to apply for chemical risk assessment. In the current study, compensatory mechanisms of the kidney were investigated in a unilateral nephrectomy (UNx) model using adult male and female rats. In residual kidneys of male and female rats after UNx, 5-bromo-2'-deoxyuridine-labeling indices and mRNA expression of cell cycle-related genes were increased, although there were no fluctuations in mRNA expression of transforming growth factor-β1, which contributes to hypertrophy in renal tubules. Pathway analysis using mRNA expression data from a cDNA microarray revealed that canonical pathways related to cell proliferation were mainly activated and that forkhead box M1 (FOXM1) was an upstream regulator of compensatory cell proliferation in residual kidneys of male and female rats. cDNA microarray for microRNAs (miRNAs) demonstrated that 9 miRNAs were downregulated in residual kidneys, and mRNA/miRNA integrated analysis indicated that miRNAs were associated with the expression of factors downstream of FOXM1. Overall, these results suggested that FOXM1-mediated hyperplasia rather than hypertrophy contributed to compensatory mechanisms in the kidney and that miRNAs regulated downstream FOXM1 signaling. These results will be beneficial for evaluating nephrotoxicity in chemical risk assessment and for developing new biomarkers to predict nephrotoxicity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144276" }, "primaryId" : "GEO:GSE144276", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144276" } ] }, "title" : "Gestational diabetes mellitus alters placental structure, efficiency, and plasticity", "dateAssigned" : "2020-01-27T00:00:00.000-06:00", "summary" : "The hemochorial placenta provides a critical barrier at the maternal-fetal interface to modulate maternal immune tolerance and enable gas and nutrient exchange between mother and conceptus. Pregnancy outcomes are adversely affected by gestational diabetes mellitus (GDM); however, the effects of GDM on placental formation, and subsequently fetal development, are not fully understood. In this report, streptozotocin was used to induce hyperglycemia in pregnant rats for the purpose of investigating the impact of GDM on placental formation and fetal development. GDM caused placentomegaly and placenta malformation, decreasing placental efficiency and fetal size. Elevated glucose disrupted rat trophoblast stem (TS) cell differentiation in vitro. Evidence of altered trophoblast differentiation was also observed in vivo, as hyperglycemia affected the junctional zone transcriptome and interfered with intrauterine trophoblast invasion and uterine spiral artery remodeling. When exposed to hypoxia, rats with GDM showed decreased proliferation and ectoplacental cone development on gestation day (gd) 9.5 and complete pregnancy loss by gd 13.5. Furthermore, elevated glucose concentrations inhibited TS cell responses to hypoxia in vitro. Overall, these results indicate that alterations in placental development, efficiency, and plasticity could contribute to the suboptimal fetal outcomes in offspring from pregnancies complicated by GDM.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32595139" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144438" }, "primaryId" : "GEO:GSE144438", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144438" } ] }, "title" : "LncRNA-mRNA expression profiles and functional networks of hyposalivation in the submandibular gland in hypertension", "dateAssigned" : "2020-01-29T00:00:00.000-06:00", "summary" : "Hyposalivation is a complication of hypertension. Although the lncRNA have recently been identified to play a role in the pathogenesis of hypertension, the specific effects of lncRNAs on hyposalivation caused by hypertension remain unclear. The aim of the current study was to construct and systematically analyze the lncRNA-miRNA-mRNA network and reveal its potential roles in hyposalivation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32811845" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144439" }, "primaryId" : "GEO:GSE144439", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144439" } ] }, "title" : "LncRNA-mRNA expression profile and functional network of vascular dysfunction in endotoxemic rats", "dateAssigned" : "2020-01-29T00:00:00.000-06:00", "summary" : "In our study, we used a rat model of LPS intervention to extract blood vessels. Differentially expressed LncRNA and mRNA were screened in lps rat blood vessels and normal rat blood vessels by microarray analysis. And through CNC and ceRNA analysis, lncRNA, miRNA, and mRNA regulatory network diagrams were constructed using verified lncRNA. This has the potential to highlight specific molecular functions and mechanisms. Later, we performed functional enrichment analysis and annotation to further explore the importance of lncRNA in vascular cell injury in sepsis. This work helps to reveal the underlying mechanism of vascular cell damage caused by sepsis and provides a new therapeutic target for controlling vascular damage in sepsis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36611198" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144485" }, "primaryId" : "GEO:GSE144485", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144485" } ] }, "title" : "Changes in Expressions of Spermatogenic Marker Genes and Spermatogenic Cell Population Caused by Stress", "dateAssigned" : "2020-01-29T00:00:00.000-06:00", "summary" : "Conclusions: Our study suggest that chronic psychosomatic stress can affect the spermatogenic transcriptome of the testes, leading to a significant change in the expression of the spermatogenic genes. At the same time, histopathological and immunohistochemical results showed that chronic stress may lead to pathological changes in spermatogenic cells and to a significant decrease in key regulatory proteins", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34707565" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144547" }, "primaryId" : "GEO:GSE144547", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144547" } ] }, "title" : "Gene expression in crossed cerebellar diaschisis in a transient middle cerebral artery occlusion rat model", "dateAssigned" : "2020-01-30T00:00:00.000-06:00", "summary" : "Crossed cerebellar diaschisis (CCD) is hypoperfusion and hypometabolism in the contralateral cerebellar hemisphere caused by supratentorial lesion. We evaluated chronological change of cerebellar blood flow (CbBF) and gene expressions in cerebellum using a rat model of focal ischemic stroke.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32531947" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144548" }, "primaryId" : "GEO:GSE144548", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144548" } ] }, "title" : "Integrated analysis of miRNA-mRNA interactions reveals novel target pathways in hypertension-induced cardiac remodeling (mRNA-seq dataset)", "dateAssigned" : "2020-01-30T00:00:00.000-06:00", "summary" : "The goals of the study are to compare differently expressed genes in heart tissues of hypertensive rats (spontaneously Hypertension Rats, SHR) with age-matched control rats (wistar Rats, WKY), identify new targets to reverse hypertension induced cardiac remodeling and idetify the targets of Traditional Chinese Medicine QDG.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144549" }, "primaryId" : "GEO:GSE144549", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144549" } ] }, "title" : "Integrated analysis of miRNA-mRNA interactions reveals novel target pathways in hypertension-induced cardiac remodeling (miRNA-seq dataset)", "dateAssigned" : "2020-01-30T00:00:00.000-06:00", "summary" : "The goals of the study are to compare differently expressed genes in heart tissues of hypertensive rats (spoutaneously Hypertension Rats, SHR) with age-matched control rats (wistar Rats, WKY), identify new targets to reverse hypertension induced cardiac remodeling and idetify the targets of Traditional Chinese Medicine QDG.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144606" }, "primaryId" : "GEO:GSE144606", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144606" } ] }, "title" : "Environmental enrichment during abstinence from cocaine self-administration opposes gene network expression changes associated with the incubation effect", "dateAssigned" : "2020-01-31T00:00:00.000-06:00", "summary" : "Environmental enrichment (EE) is a robust intervention for reducing cocaine-seeking behaviors in animals when given during abstinence. However, the mechanisms that underlie these effects have not been well-established. We investigated the adult male rat transcriptome using RNA-sequencing (RNA-seq) following differential housing during abstinence from cocaine self-administration for either 1 or 21 days. Rats housed for 21 days of abstinence in EE displayed a significant reduction in cocaine-seeking behavior compared to rats housed in isolation. RNA-seq of the nucleus accumbens shell revealed hundreds of differentially regulated transcripts between rats of different abstinence length and housing environment, as well as within specific contrasts such as enrichment (isolated 21 days vs. enriched 21 days) or incubation (isolated 1 day vs. isolated 21 days). Ingenuity Pathway Analysis affirmed several pathways as differentially enriched based on housing condition and abstinence length including RELN, the Eif2 signaling pathway, synaptogenesis and neurogenesis pathways. Additionally, multiple pathways reversed their directionality between enrichment and incubation contrasts, potentially indicating oppositional roles across housing and abstinence length. Together, these findings reveal novel mechanisms potentially involved in the protective effects of EE against cocaine seeking, which may inform efforts to develop new pharmacological and gene therapies for treating cocaine use disorders.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32647308" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144974" }, "primaryId" : "GEO:GSE144974", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144974" } ] }, "title" : "RNAseq of NRVMs infected with AdCryABR120G by the manipulation of Ube2v1 expression", "dateAssigned" : "2020-02-07T00:00:00.000-06:00", "summary" : "Neonatal rat ventricle myocytes (NRVMs) were infected with CryABR120G adenovirus. Knockdown or overexpression of Ube2v1 was performed by siUbe2v1 transfection or AdUbe2v1 infection in CryABR120G-expressing cells. Total RNA was extracted from NRVMs of four groups: CTR (untreated control), R120G (AdCryABR120G infection), RSIV1 (AdCryABR120G infection with siUbe2v1 transfection), and RADV1 (coinfection with AdCryABR120G and AdUbe2v1), in triplicate, for gene expression profiling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32081062" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144985" }, "primaryId" : "GEO:GSE144985", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE144985" } ] }, "title" : "Integrated analysis of genome-wide profiling of lncRNA and mRNA expression and functional networks after botulinum toxin type A injection into submandibular gland of rats.", "dateAssigned" : "2020-02-09T00:00:00.000-06:00", "summary" : "Abstract: Backgroud: This study was to explore long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles and construct functional networks to analyze their biological functions when botulinum toxin type A (BTXA) inhibited salivary secretion. Methods: BTXA and saline were injected into the submandibular gland of rats as the BTXA group and control group, respectively. Morphological and secretory function tests validated the animal models. Microarray analysis was applied to identify the expression variation of lncRNA and mRNA and were confirmed by qRT-PCR. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to explicit the biological functions. The construction of functional networks including lncRNA-mRNA co-expression network and competing endogenous RNA (ceRNA) network was to reveal the interaction between coding and noncoding genes. Results: A total of 254 lncRNAs and 631 mRNAs were differentially expressed (DE) between the control group and the BTXA group. Ten lncRNAs and eleven mRNAs were confirmed by qRT-PCR and the results were consistent with the microarray analysis. The bioinformatic analysis found that most of mRNAs were closely related to transmembrane transporter activity. LncRNA-mRNA co-expression network and ceRNA network were constructed and identified several critical mRNA-lncRNA axes and key microRNAs related to salivary secretion, respectively. Conclusions: Our study identified DE lncRNAs and mRNAs through microarray analysis and explored the biological functions and interaction between coding and noncoding genes through bioinformatics analysis. These findings may provide new directions for the mechanism of BTXA to inhibit salivary secretion.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32892462" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145167" }, "primaryId" : "GEO:GSE145167", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145167" } ] }, "title" : "Gene expression changes in the conceptus following maternal exposure to PolyI:C", "dateAssigned" : "2020-02-12T00:00:00.000-06:00", "summary" : "We report the global transcript changes in the rat conceptus following maternal exposure to PolyI:C", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145199" }, "primaryId" : "GEO:GSE145199", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145199" } ] }, "title" : "Analysis of miRNA Changes in the prelimbic cortex of Rat with Chronic Neuropathic Pain", "dateAssigned" : "2020-02-12T00:00:00.000-06:00", "summary" : "Neuropathic pain (NP) is a complex, chronic pain condition caused by injury or dysfunction affecting the somatosensory nervous system. This study aimed to identify crucial miRNA in prelimbic cortex (PL) involved in NP rats. miRNA microarrays were applied in the present study.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145222" }, "primaryId" : "GEO:GSE145222", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145222" } ] }, "title" : "Expression data from rat dorsal root ganglion after chronic compression", "dateAssigned" : "2020-02-13T00:00:00.000-06:00", "summary" : "All rats were divided into the sham and CCD groups randomly. Rats in CCD groups were anesthetized, followed by the implantation of two stainless steel rods in the intervertebral foramina between L4 and L5. Rats in the sham-operated group underwent the same procedure without steel rod insertion. DRG were harvested on the 7th day post-surgery.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145223" }, "primaryId" : "GEO:GSE145223", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145223" } ] }, "title" : "To investigate gene expression changes in neurons lacking cap methyltransferase 1 (CMTR1)", "dateAssigned" : "2020-02-13T00:00:00.000-06:00", "summary" : "Transcriptomic profiles of control and CMTR1-knockdown neurons.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33086056" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145226" }, "primaryId" : "GEO:GSE145226", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145226" } ] }, "title" : "Analysis of mRNA Changes in the prelimbic cortex of Rat with Chronic Neuropathic Pain", "dateAssigned" : "2020-02-13T00:00:00.000-06:00", "summary" : "Neuropathic pain (NP) is a complex, chronic pain condition caused by injury or dysfunction affecting the somatosensory nervous system. This study aimed to identify crucial mRNA in prelimbic cortex (PL) involved in NP rats. mRNA microarrays were applied in the present study.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145367" }, "primaryId" : "GEO:GSE145367", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145367" } ] }, "title" : "GeneChip Expression Array", "dateAssigned" : "2020-02-16T00:00:00.000-06:00", "summary" : "We transfected cDNA of human umbilical vein endothelial cells into rat myeloma cells, and sorted cells bound to patient IgG. Sorted cells were analyzed using the Affymetrix Human Genome U133 Plus 2.0 Array to investigate the cDNA inserted into the sorted cells. Array data was processed by Affymetrix GeneChip Command Console Software and Affymetrix Expression Console Software. No techinical replicates were performed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145431" }, "primaryId" : "GEO:GSE145431", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145431" } ] }, "title" : "Physiological and Transcriptomic Changes in the Hypothalamic-Neurohypophysial System after 24 H of Furosemide-Induced Sodium Depletion", "dateAssigned" : "2020-02-18T00:00:00.000-06:00", "summary" : "Conclusions: We thus have identified novel genes that might regulate vasopressin gene expression in the hypothalamus controlling the magnocellular neurons secretory response to body sodium depletion and consequently hypotonic stress.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31955161" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145460" }, "primaryId" : "GEO:GSE145460", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145460" } ] }, "title" : "Expression data from INS1E cells stimulated with vitamin D metabolites and glucose", "dateAssigned" : "2020-02-18T00:00:00.000-06:00", "summary" : "We used an established β-cell line, INS1E. INS1E cells were pre-treated with 10 nM 1,25(OH)2vitamin D or 10 nM 25(OH)vitamin D for 72 hours and stimulated with 22 mM glucose for 60 minutes. RNA was extracted for gene expression analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32251702" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145479" }, "primaryId" : "GEO:GSE145479", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145479" } ] }, "title" : "Inhaled titanium dioxyde-induced gene expression profile in rat lung", "dateAssigned" : "2020-02-18T00:00:00.000-06:00", "summary" : "In this work we study the pulmonary toxicological properties of titanium dioxyde nanoparticles using molecular toxicological approach. For this, we exposed F344 rats by nose-only inhalation 6 hours/day, 5 days/week for 4 weeks. Lung samples have been collected up to 28 days after the end of exposure and transcriptomics analysis were performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34206090" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145504" }, "primaryId" : "GEO:GSE145504", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145504" } ] }, "title" : "Coding transcriptome analyses reveal altered functions underlying immunotolerance of PEG-fused rat sciatic nerve allografts", "dateAssigned" : "2020-02-18T00:00:00.000-06:00", "summary" : "Conclusions: This study is the first to characterize the coding transcriptome of PEG-fused PNAs, and identifies possible links between alterations of the extracellular matrix and suppression of the allorejection response. The results establish a molecular-basis to understand mechanisms underlying PEG-mediated immunosuppression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33008419" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145516" }, "primaryId" : "GEO:GSE145516", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145516" } ] }, "title" : "Platform effects on regeneration by pulmonary basal cells as evaluated by single-cell RNA sequencing [array]", "dateAssigned" : "2020-02-19T00:00:00.000-06:00", "summary" : "Cell-based therapies have shown promise for treating myriad chronic pulmonary diseases through direct application of epithelial progenitors or by way of engineered tissue grafts or whole organs. To elucidate environmental effects on epithelial regenerative outcomes in vitro, we isolated and cultured a population of pharmacologically expanded basal cells (peBC) from rat tracheas. At peak basal marker expression we simultaneously split peBC into four in vitro platforms – organoid, air-liquid interface (ALI), engineered trachea, and engineered lung. Following differentiation, these samples were evaluated using single-cell RNA sequencing (scRNAseq) and computational pipelines were developed to compare samples both globally and at the population level. A sample of native rat tracheal epithelium was also evaluated by scRNAseq as a control for engineered epithelium. Overall this work identifies platform-specific effects that support the use of engineered models to achieve the most physiologic differential outcomes in pulmonary epithelial regenerative applications.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145517" }, "primaryId" : "GEO:GSE145517", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145517" } ] }, "title" : "Platform effects on regeneration by pulmonary basal cells as evaluated by single-cell RNA sequencing [RNA-seq]", "dateAssigned" : "2020-02-19T00:00:00.000-06:00", "summary" : "Cell-based therapies have shown promise for treating myriad chronic pulmonary diseases through direct application of epithelial progenitors or by way of engineered tissue grafts or whole organs. To elucidate environmental effects on epithelial regenerative outcomes in vitro, we isolated and cultured a population of pharmacologically expanded basal cells (peBC) from rat tracheas. At peak basal marker expression we simultaneously split peBC into four in vitro platforms – organoid, air-liquid interface (ALI), engineered trachea, and engineered lung. Following differentiation, these samples were evaluated using single-cell RNA sequencing (scRNAseq) and computational pipelines were developed to compare samples both globally and at the population level. A sample of native rat tracheal epithelium was also evaluated by scRNAseq as a control for engineered epithelium. Overall this work identifies platform-specific effects that support the use of engineered models to achieve the most physiologic differential outcomes in pulmonary epithelial regenerative applications.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145854" }, "primaryId" : "GEO:GSE145854", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145854" } ] }, "title" : "Genome-wide Profiling of Long Noncoding RNA Expression Patterns in Thoracic Aorta from Spontaneously Hypertensive Rats.", "dateAssigned" : "2020-02-24T00:00:00.000-06:00", "summary" : "We used lncRNA-mRNA micro-array to analyze the transcriptome in the thoracic aorta tissue of 24 wees-old WKY and spontaneously hypertensive rats (SHRs).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145882" }, "primaryId" : "GEO:GSE145882", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145882" } ] }, "title" : "Progesterone, via yes-associated protein (YAP), promotes cardiomyocyte proliferation and cardiac repair", "dateAssigned" : "2020-02-25T00:00:00.000-06:00", "summary" : "To explore effect of progesterone on gene expression of primary cultured cardiomyocytes isolated from 7-day-old SD rats", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145917" }, "primaryId" : "GEO:GSE145917", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145917" } ] }, "title" : "Gene expression profiling in dorsolateral prostates of prepubertal and adult Sprague-Dawley rats dosed with Estradiol Benzoate, Estradiol and Testosterone", "dateAssigned" : "2020-02-25T00:00:00.000-06:00", "summary" : "Using rat prostate disease models that Prins and colleagues have developed (Ho et al., 2006 - PMID: 16740699), the purpose of the study is to identify gene(s) for diagnosing early stage of prostate diseases and monitoring the development of prostate diseases. To identify the genes, we analyzed whole genome expression profiling on the prostate from Sprague-Dawley rats dosed postnatally with estradiol benzoate, estradiol and testosterone at PNDs 30, 100 and 145.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32741896" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145965" }, "primaryId" : "GEO:GSE145965", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE145965" } ] }, "title" : "Coordinated Regulation of Smooth Muscle Cell Remodeling by Non-coding and Coding products of Phenotype Switching Regulator Gene.", "dateAssigned" : "2020-02-26T00:00:00.000-06:00", "summary" : "We identified a novel nuclear peptide Arteridin encoded by an annotated lncRNA Phenotype Swithching Regulator (PSR). To test the DNA binding capacity of Arteridin, we perfomed Arteridin ChIP-seq. We found both Arteridin and lncPSR transcript could induce vascular smooth muscle cell phenothype switching. We also found the interaction between Arteridin, lncPSR and transcription factor YBX1. To further illustrate how Arteridin and lncPSR work coordinately, we performed YBX1 ChIP-seq in VSMCs with Arteridin-FLAG overexpression or lncPSR ATT mutant overexpression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146051" }, "primaryId" : "GEO:GSE146051", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146051" } ] }, "title" : "131I exposured young and adult rat thyroid", "dateAssigned" : "2020-02-27T00:00:00.000-06:00", "summary" : "Transcriptional profiling of rat thyroid cells comparing control untreated thyroid cells with 131I irradiated thyroid cells. Goal was to invesigate radiation induced gene expression profiles", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35136135" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146098" }, "primaryId" : "GEO:GSE146098", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146098" } ] }, "title" : "The effects of low-level Er:YAG laser irradiation on proliferation and calcification of primary osteoblast-like cells isolated from rat calvaria", "dateAssigned" : "2020-02-28T00:00:00.000-06:00", "summary" : "A number of reports showed that photo-bio-modulation by various lasers has favorable biological effects on cells. However, the effects of low-level Er:YAG laser irradiation on osteoblasts remain unclear. The purpose of this study was to evaluate the effects on proliferation and osteogenic differentiation of primary osteoblast-like cells by low-level Er:YAG laser irradiation. Osteoblast-like cells isolated from the calvariae of 3–5-day-old Wistar rats were irradiated by Er:YAG laser at energy fluences of 2.2, 3.3, or 4.3 J/cm2, respectively. After irradiation, cell surface temperature was measured and cell proliferation was evaluated by flow cytometry. Calcification was evaluated by measuring the Alizarin red S staining area after 7-day-culture with osteoinductive medium. Gene expressions in non-irradiated and laser-irradiated cells were evaluated by qPCR at 3, 6, and 12 hours after irradiation. Microarray analysis was performed to comprehensively evaluate gene expressions of non-irradiated cells and irradiated cells at 3.3 J/cm2 at 6 hours after irradiation. No pronounced increase of cell surface temperature was induced by low-level Er:YAG laser irradiation, and the Er:YAG laser irradiation did not affect osteoblast-like cell proliferation. Osteoblast-like cell calcification was significantly increased 7 days after Er:YAG laser irradiation at 3.3 J/cm2. Bglap expression was significantly increased in cells irradiated at 3.3 J/cm2 at 6 hours post-irradiation. Microarray analysis showed that irradiation at 3.3 J/cm2 caused up-regulation of inflammation-related genes and down-regulation of Wisp2. Gene set enrichment analysis also clarified enrichment of inflammation-related gene sets and Notch signaling pathway. In conclusion, Low-level Er:YAG laser irradiation enhanced calcification of primary osteoblast-like cells via enhanced Bglap expression and enriched Notch signaling pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32656208" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146155" }, "primaryId" : "GEO:GSE146155", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146155" } ] }, "title" : "Fetal cortical transcriptomic changes after oxytocin induced aberrant uterine contractility", "dateAssigned" : "2020-03-01T00:00:00.000-06:00", "summary" : "We report changes in the fetal brain cortical transcriptome after oxytocin-induced aberrant uterine contractility using unbiased RNA-seq analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32434985" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146180" }, "primaryId" : "GEO:GSE146180", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146180" } ] }, "title" : "Er:YAG laser irradiation decreases Sost expressions in bone and osteogenic cell (6h after surgery)", "dateAssigned" : "2020-03-02T00:00:00.000-06:00", "summary" : "The purpose of this study was to evaluate comprehensive and sequential gene expressions in Er;YAG laser ablated bone, bur-drilled bone, and non-treated control bone to clarify the biological responses for bone healing.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146181" }, "primaryId" : "GEO:GSE146181", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146181" } ] }, "title" : "Er:YAG laser irradiation decreases Sost expressions in bone and osteogenic cell (24h after surgery)", "dateAssigned" : "2020-03-02T00:00:00.000-06:00", "summary" : "The purpose of this study was to evaluate comprehensive and sequential gene expressions in Er;YAG laser ablated bone, bur-drilled bone, and non-treated control bone to clarify the biological responses for bone healing.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146182" }, "primaryId" : "GEO:GSE146182", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146182" } ] }, "title" : "Er:YAG laser irradiation decreases Sost expressions in bone and osteogenic cell (72h after surgery)", "dateAssigned" : "2020-03-02T00:00:00.000-06:00", "summary" : "The purpose of this study was to evaluate comprehensive and sequential gene expressions in Er;YAG laser ablated bone, bur-drilled bone, and non-treated control bone to clarify the biological responses for bone healing.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146193" }, "primaryId" : "GEO:GSE146193", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146193" } ] }, "title" : "Genome-wide identification and analysis of circular RNAs in the pineal in rats between day and night", "dateAssigned" : "2020-03-02T00:00:00.000-06:00", "summary" : "Circular RNAs (circRNAs) are a new class of RNAs with covalently closed circular structures that are involved in many biological processes. However, information about circRNAs in the pineal gland is limited, especially in rats. In this study, 331 circRNAs were identified by the Illumina platform as being expressed in the pineal glands of rats during the night and day. Forty circRNAs with differential expression were found. A total of 737 GO terms were significantly enriched, and 121 KEGG pathways were found to contain differentially expressed genes. We predicted 6837 interactions between 65 cicRNAs and 549 miRNAs by using miRanda. We also found that high expression of miR-328a-3p in the daytime inhibits AANAT translation through targeting of the AANAT 3’UTR region. CircRNA-WNK2, which is highly expressed in the rat pineal gland during the night and functions as a miRNA sponge, removes this inhibitory effect and promotes the AANAT expression and melatonin secretion. The circadian expression profile of circRNAs in the rat pineal gland may provide more information on the roles of circRNAs in the regulation of melatonin circadian rhythm changes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146261" }, "primaryId" : "GEO:GSE146261", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146261" } ] }, "title" : "RNA Seq Analysis of BMSC cell line Transcriptomes under the different conditions.", "dateAssigned" : "2020-03-03T00:00:00.000-06:00", "summary" : "The goal of this study are to compare the transcriptome profiling (RNA-seq) of rat bone marrow mesenchymal stem cells (BMSC) transcriptome profiling (RNA-seq) under the condition of infection of different lentiviruses(shRac1 or shLuci) and/or oxygen-glucose deprivation (OGD).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146291" }, "primaryId" : "GEO:GSE146291", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146291" } ] }, "title" : "Impact of oligodendrocyte secreted factors on hippocampal GABAergic neurons: an electrophysiological and transcriptomic study", "dateAssigned" : "2020-03-03T00:00:00.000-06:00", "summary" : "In the present work, we gain insight into the impact of oligodendrocyte secreted factors on hippocampal GABAergic neuron physiology, and performed patch-clamp recordings followed by single-cell RNA sequencing of neurons. Our results demonstrate that the GABAergic neuron excitability is influenced by glial cells and oligodendrocyte-secreted factors. Moreover, we show specific ion channels alterations and find a correlation with electrophysiological parameters suggesting possible mechanisms for the OCM-induced regulation of neuronal function.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146299" }, "primaryId" : "GEO:GSE146299", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146299" } ] }, "title" : "Gamma aminobutyric acid increases erythropoietin overexpression of hypoxia inducible factors in rats", "dateAssigned" : "2020-03-03T00:00:00.000-06:00", "summary" : "In this study, we investigated the effect of γ-aminobutyric acid (GABA) on serum EPO level and erythropoiesis, and its mechanism was elucidated in rat. GABA significantly (P < 0.05) increased EPO level in serum and expression levels of EPO and EPOR in a dose dependent manner. GABA increased the expression levels of HIF-1 and HIF-2 in a dose dependent manner compared with the negative control; while GABA did not affect the expression of prolyl-hydroxylase domain protein-2α (PHD-2α) gene, an oxygen sensor. GABA supplementation alters energy production pathway resulted in hypoxic condition, which increases EPO level in rat through overexpression of HIF-1 and HIF-2. This study shows a new physiological role of GABA in EPO production and thus GABA could contribute to the prevention of anemia by using alone or in combination with other anemia treating drugs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32290638" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146485" }, "primaryId" : "GEO:GSE146485", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146485" } ] }, "title" : "Chronic Dosed-Feed Toxicity/Carcinogenicity Study of 2-Hydroxy-4-Methoxybenzophenone (HMB, C10260; CAS No. 131-57-7) in Sprague-Dawley rats (G822872B)", "dateAssigned" : "2020-03-05T00:00:00.000-06:00", "summary" : "2-Hydroxy-4-methoxybenzophenone (HMB) is an approved Food and Drug Administration (FDA) over-the-counter Category I product considered to be a deterrent to ultraviolet (UV) radiation-induced skin cancer. HMB is used in pharmaceuticals, plastic products, fabric coatings, finishes, and cosmetics. Exposure to HMB occurs through both occupational and consumer routes. HMB is used in skin moisturizing products and sunscreen lotions. In plastics manufacturing, HMB is used in surface coatings and polymers including ABS resins, cellulosic esters, polyesters, polystyrenes, rubber, flexible and rigid vinyl, and vinylidene chloride. HMB readily penetrates the skin and bioaccumulates in lipid-rich tissues. Uptake from the gastrointestinal tract is rapid. This study will characterize the toxicologic and carcinogenic potential of HMB administered in dosed feed to Sprague-Dawley rats given its potential for widespread human exposure as a broad-spectrum sunscreen.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146489" }, "primaryId" : "GEO:GSE146489", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146489" } ] }, "title" : "Expression data from female rat retroperinoneal fat tissue", "dateAssigned" : "2020-03-05T00:00:00.000-06:00", "summary" : "Obesity is a complex disease with many causes, including a possible role of environmental chemicals. Perfluorohexane sulfonate (PFHxS) is one of many per- and polyfluoroalkyl substances (PFASs) frequently detected in humans and it is a suspected obesogenic compound. We examined the potential long-term effects of PFHxS on metabolic parameters in rats after developmental exposure to 0.05, 5 or 25 mg/kg bw/day, with or without co-exposure to a background mixture of 12 endocrine disrupting chemicals (EDmix). Both male and female offspring showed signs of lower birth weight following intrauterine exposure. Female offspring exposed to both PFHxS and EDmix showed increased body weight in adulthood. Furthermore, the retroperitoneal fat pad was larger in these female offspring when compared to those exposed to EDmix alone. An attempt to detect putative molecular markers in the fat tissue by performing whole transcriptome profiling resulted in no significant changes between groups and there were no significant effects on plasma leptin levels in exposed females. These results show that early life exposure to endocrine disrupting chemicals can influence body weight later in life, but the effect is not necessarily reflected in changed gene expression in the fat tissue.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146493" }, "primaryId" : "GEO:GSE146493", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146493" } ] }, "title" : "Transcriptional analysis of sodium valproate and lithium in a serotonergic cell line", "dateAssigned" : "2020-03-06T00:00:00.000-06:00", "summary" : "Sodium valproate (VPA) and lithium are mood stabilizers, widely prescribed in the treatment of bipolar disorder, and yet the precise modes of therapeutic action for these drugs are not fully understood. After exposure of the rat serotonergic cell line RN46A to VPA, RNA-sequencing (RNA-Seq) analysis showed widespread changes in gene expression but no changes with lithium. Analysis by multiple pipelines revealed that as many as 230 genes were significantly upregulated and 72 genes were significantly downregulated in response to VPA exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33649518" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146638" }, "primaryId" : "GEO:GSE146638", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146638" } ] }, "title" : "Effect of chronic uremia on the transcriptional profile of the calcified aorta analyzed by RNA sequencing.", "dateAssigned" : "2020-03-09T00:00:00.000-05:00", "summary" : "1. We used RNA-seq to examine vascular tissue (aorta) transcriptomes from chronic kidney disease rat model (uremic) developing vascular calcifications, compared with controls. Uremic calcified aortas have extensive changes in the transcriptional profile. Among the 10,153 genes with an expression level of >1 reads/kilobase transcript/million mapped reads, 2,663 genes were differentially expressed with 47% upregulated genes and 53% downregulated genes in uremic rats. Significantly deregulated genes were enriched for ontologies related to the extracellular matrix, response to wounding, organic substance, and ossification. The individually affected genes were of relevance to osteogenic transformation, tissue calcification, and Wnt modulation. 2. We demonstrated extensive changes in the transcriptional profile of the uremic calcified aorta, which were consistent with a shift in phenotype from vascular tissue toward an osteochondrocytic transcriptome profile. 3. Moreover, neither the normal vasculature nor calcified uremic vasculature expresses Klotho.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26739890" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146739" }, "primaryId" : "GEO:GSE146739", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146739" } ] }, "title" : "mRNA expression of spinal dorsal horn in oxaliplatin-treated rats", "dateAssigned" : "2020-03-10T00:00:00.000-05:00", "summary" : "Oxaliplatin-induced neuropathic pain is a common dose-limiting side effect of cancer treatment but the underlying mechanisms are largely unknown. The neuropathic pain model was established by oxaliplatin intraperitoneal administration for five consecutive days. In the present study, we performed whole genome expression microarray analysis by using spinal dorsal horn from oxaliplatin-treated and vehicle-treated rats on day 10.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146813" }, "primaryId" : "GEO:GSE146813", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146813" } ] }, "title" : "Intraarticular injection of liposomal adenosine reduces cartilage damage in established murine and rat models of osteoarthritis", "dateAssigned" : "2020-03-11T00:00:00.000-05:00", "summary" : "Osteoarthritis (OA) affects nearly 10% of the population of the United States and other industrialized countries and, at present, short of surgical joint replacement, there is no therapy available that can reverse the progression of the disease OA. Adenosine, acting at its A2A receptor (A2AR), is a critical autocrine factor for maintenance of cartilage homeostasis. Here we report that injection of liposomal suspensions of a selective A2AR agonist, CGS21680, significantly reduced OA cartilage damage in a rat model of established post-traumatic OA (PTOA). Differential expression analysis of mRNA from chondrocytes harvested from knees of rats with PTOA treated with liposomal A2AR agonist revealed downregulation of genes associated with matrix degradation and upregulation of genes associated with cell proliferation as compared to liposomes alone.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146881" }, "primaryId" : "GEO:GSE146881", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146881" } ] }, "title" : "Transcriptome analysis of dorsal root ganglion in rats with knee rheumatoid arthritis", "dateAssigned" : "2020-03-12T00:00:00.000-05:00", "summary" : "To determine the LncRNA expression profile in dorsal root ganglia tissues of 7 days after rats received 150 μl of CFA (1 mg/ml Mycobacterium tuberculosis, Sigma, USA) through the patella tendon into the right knee joint. CFA injection rats macthed saline injection rats, we uesed LncRNA microArray analysis form Arraystar to examine the expression of LncRNAs and mRNAs in dorsal root ganglia tissues of 7 days after rats received CFA through the patella tendon into the right knee joint and matched Saline through the patella tendon into the right knee joint.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33149663" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146883" }, "primaryId" : "GEO:GSE146883", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146883" } ] }, "title" : "Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth (injured sciatic nerve microarray data)", "dateAssigned" : "2020-03-12T00:00:00.000-05:00", "summary" : "Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are essential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, including known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesenchymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons. These data therefore identify an unexpected paracrine role for nerve mesenchymal cells and suggest that multiple cell types contribute to creating a highly pro-growth environment for peripheral axons.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32349983" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146891" }, "primaryId" : "GEO:GSE146891", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146891" } ] }, "title" : "RNA-sequencing of Imiquimod-induced rat skin treated with or without epidural lidocaine injection", "dateAssigned" : "2020-03-12T00:00:00.000-05:00", "summary" : "We use back skin of WT SD rats, or imiquimod(IMQ)-induced psoraisis-like rat model treated with or without epidural injection of 1% lidocaine. We isolate total RNA for RNA-sequencing.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146898" }, "primaryId" : "GEO:GSE146898", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146898" } ] }, "title" : "Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth (sympathetic neuron microarray data)", "dateAssigned" : "2020-03-12T00:00:00.000-05:00", "summary" : "Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are essential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, including known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesenchymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons. These data therefore identify an unexpected paracrine role for nerve mesenchymal cells and suggest that multiple cell types contribute to creating a highly pro-growth environment for peripheral axons.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32349983" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146927" }, "primaryId" : "GEO:GSE146927", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146927" } ] }, "title" : "RNA-sequencing of Imiquimod-induced rat dorsal root ganglion (DRG) tissues treated with or without epidural lidocaine injection", "dateAssigned" : "2020-03-13T00:00:00.000-05:00", "summary" : "We use dorsal root ganglion tissues of WT SD rats, or imiquimod(IMQ)-induced psoraisis-like rat model treated with or without epidural injection of 1% lidocaine. We isolated total RNA for RNA-sequencing.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146957" }, "primaryId" : "GEO:GSE146957", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146957" } ] }, "title" : "Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth (sensory neuron microarray data)", "dateAssigned" : "2020-03-13T00:00:00.000-05:00", "summary" : "Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are essential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, including known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesenchymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons. These data therefore identify an unexpected paracrine role for nerve mesenchymal cells and suggest that multiple cell types contribute to creating a highly pro-growth environment for peripheral axons.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32349983" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146976" }, "primaryId" : "GEO:GSE146976", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE146976" } ] }, "title" : "Comparison of age-related changes in gene expression of 2 rat skeletal muscles (20 months, 22 months)", "dateAssigned" : "2020-03-13T00:00:00.000-05:00", "summary" : "In this study we compared Gastrocnemius and Triceps gene expression with age. Our results show that gene expression is massively modulated with age in Gastroc but on the contrary very stable in Triceps, suggesting that Triceps is resistant to age-related defects.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33580198" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147072" }, "primaryId" : "GEO:GSE147072", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147072" } ] }, "title" : "Evaluation of 5-Day In Vivo Rat Liver and Kidney with High-Throughput Transcriptomics for Estimating Benchmark Doses of Apical Outcomes", "dateAssigned" : "2020-03-16T00:00:00.000-05:00", "summary" : "The Division of the National Toxicology Program (DNTP) is currently evaluating high-throughput transcriptomics (HTT) as an approach to provide estimates of chemical exposure that may pose minimal risk. HTT was evaluated in a 5-day in vivo rat model (with repeated dosing) with the objective to determine if benchmark doses (BMD) values for transcriptional pathway changes in the liver and kidney could estimate BMD values for traditional toxicological (apical) endpoints. Eighteen chemicals, most having been tested by the NTP in 2-year bioassays, were chosen for this study. Some of these chemicals are known to be potent hepatotoxicants (e.g. DE71, PFOA, furan, and methyl eugenol) in rodents, some exhibit toxicity but have minimal effects on the liver (e.g. acrylamide and α,β-thujone), and some exhibit little overt toxicity (e.g. ginseng and milk thistle extract) based on traditional toxicological evaluations. Male Sprague Dawley rats were exposed daily for 5 consecutive days by oral gavage to 8 to 10 dose levels of each chemical. Liver and kidney were collected 24 hours after the final exposure and assayed using HTT with the rat S1500+ platform. HTT dose-response data were analyzed using BMD Express 2.2 to determine transcriptional BMD values for liver and kidney. BMDS Wizard was used to determine apical BMD values for histopathological effects from historical chronic or sub-chronic toxicity studies. For many of the chemicals, the lowest transcriptional BMDs from the 5-day assays were within a factor of 5 of the lowest histopathological BMDs estimated from the traditional toxicity studies. These data suggest that using HTT in a 5-day in vivo model provides reasonable estimates of BMD values for traditional apical endpoints. This approach may be useful to prioritize chemicals for further testing while providing actionable data in a timely and cost-effective manner.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32492150" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147073" }, "primaryId" : "GEO:GSE147073", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147073" } ] }, "title" : "Stimulation of glycolysis via the pyruvate dehydrogenase axis promotes cardiomyocyte proliferation after injury in adult zebrafish.", "dateAssigned" : "2020-03-16T00:00:00.000-05:00", "summary" : "Cardiac metabolism plays a crucial role in producing sufficient energy to sustain cardiac contractions. However, the role of metabolism in cardiomyocyte proliferation remains unclear. Working with the adult zebrafish heart regeneration model, we first find an increase in the levels of mRNAs encoding enzymes regulating glucose and pyruvate metabolism, including pyruvate kinase M1/2 (Pkm) and pyruvate dehydrogenase kinases (Pdks), specifically in tissues bordering the damaged area. We proceed to show that impaired glycolysis decreases the number of proliferating cardiomyocytes following cardiac injury. These observations are further supported by analyses using loss-of-function models for the metabolic regulators Pkm2a and peroxisome proliferator-activated receptor gamma coactivator 1 alpha (Ppargc1a). Cardiomyocyte-specific loss- and gain-of-function manipulations of pyruvate metabolism using Pdk3 and a catalytic subunit of the pyruvate dehydrogenase complex (PDC) reveal its importance in cardiomyocyte dedifferentiation and proliferation. Furthermore, we find that PDK activity can modulate cell cycle progression and protrusive activity in mammalian cardiomyocytes in culture. Our findings reveal new roles for cardiac metabolism and the PDK-PDC axis in cardiomyocyte behavior following cardiac injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32648304" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147079" }, "primaryId" : "GEO:GSE147079", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147079" } ] }, "title" : "Genome-wide identification of estrogen receptor binding sites reveals novel estrogen-responsive pathways in adult male germ cells", "dateAssigned" : "2020-03-16T00:00:00.000-05:00", "summary" : "Spermatogenesis occurs in the seminiferous epithelium that shows presence of estrogen receptors alpha (ERα) and beta (ERβ), both of which regulate gene transcription by binding to the DNA. Hormone responsive phases of spermatogenesis are well documented; yet, the genes regulated remain inexplicit. To study the regulation of genes by estrogen in male germ cells, we performed chromatin immunoprecipitation (ChIP) sequencing for ERα and ERβ under normal physiological conditions. We observed a total of 27,221 peaks in ERα and 20,926 peaks in ERβ. Majority of the peaks were present in the intronic regions and located 20kb upstream or downstream from the transcription start site (TSS). Upon pathway analysis, the genes enriched showed involvement in several biological pathways. Genes involved in pathways whose role in spermatogenesis is unexplored were validated; these included prolactin, GnRH and oxytocin signalling. All the genes showed presence of estrogen response elements (EREs) and majority of them showed significant enrichment by ChIP-qPCR. Functional validation using seminiferous tubule culture after treatment with receptor specific agonist and antagonist confirmed the regulation of these genes by estrogen through its receptors. This study provides new insights about the estrogen regulated genes during spermatogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32478811" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147186" }, "primaryId" : "GEO:GSE147186", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147186" } ] }, "title" : "RNASeq of undifferentated and two types of differentiated 50B11 cells", "dateAssigned" : "2020-03-18T00:00:00.000-05:00", "summary" : "RNASeq of 50B11 cells before and after differentiation with forskolin and nerve growth factor or with forskolin and glial-derived neurotrophic factor", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33307981" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147248" }, "primaryId" : "GEO:GSE147248", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147248" } ] }, "title" : "In vivo transcriptomic responses to mercury chloride exposure in rat kidney tissue", "dateAssigned" : "2020-03-19T00:00:00.000-05:00", "summary" : "In this study we tested the ability to predict organ injury from transcriptomics data in Sprague-Dawley rats at early time points after exposure to mercury chloride (10 and 34 hours). We selected mercury chloride, a compound extensively used in animal studies for its ability to cause acute kidney and liver damage.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147335" }, "primaryId" : "GEO:GSE147335", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147335" } ] }, "title" : "Gene expression profile of metabolic dysfunction in the aorta of male Sprague-Dawley rats following a short-term high fat diet", "dateAssigned" : "2020-03-21T00:00:00.000-05:00", "summary" : "Diet-induced metabolic dysfunction precedes multiple disease states, including diabetes, heart disease, and atherosclerosis. The critical role of the vasculature in disease progression is established, yet the details of how gene expression changes in early cardiovascular disease remain an enigma. The objective of the current project was to evaluate whether a quantitative assessment of gene expression within the aorta of six-week old healthy male Sprague-Dawley rats compared to those exhibiting metabolic dysfunction symptoms could reveal potential mediators of vascular dysfunction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34285833" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147379" }, "primaryId" : "GEO:GSE147379", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147379" } ] }, "title" : "Examination of gene expression changes after exposure to 29 chemicals in rat primary hepatocytes", "dateAssigned" : "2020-03-23T00:00:00.000-05:00", "summary" : "In this study we examined transcriptional responses to 29 ToxCast chemicals in dose-response format. The chemicals were selected because in vitro transcriptional effects could be extrapolated to in vivo effects including liver cancer and steatosis incidences using in vitro to in vivo extrapolation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147402" }, "primaryId" : "GEO:GSE147402", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147402" } ] }, "title" : "Differential activation of P-TEFb complexes in the development of cardiomyocyte hypertrophy following activation of distinct GPCRs", "dateAssigned" : "2020-03-23T00:00:00.000-05:00", "summary" : "Pathological cardiac hypertrophy is driven by neurohormonal activation of specific G protein-coupled receptors (GPCRs) in cardiomyocytes and is accompanied by large-scale changes in cardiomyocyte gene expression. These transcriptional changes require activity of positive transcription elongation factor b (P-TEFb), which is recruited to target genes by the bromodomain protein Brd4 or the Super Elongation Complex (SEC). Here we describe GPCR-specific regulation of these P-TEFb complexes and a novel mechanism for activating Brd4 in primary neonatal rat cardiomyocytes. The SEC was required for the hypertrophic response downstream of either the α1-adrenergic receptor (α1-AR) or the endothelin receptor (ETR). In contrast, Brd4 inhibition selectively impaired the α1-AR response. This was corroborated by the finding that activation of α1-AR, but not ETR, increased Brd4 occupancy at promoters and super enhancers of hypertrophic genes. Transcriptome analysis demonstrated that activation of both receptors initiated similar gene expression programs, but that Brd4 inhibition attenuated hypertrophic genes more robustly following α1-AR activation. Finally, we show that protein kinase A (PKA) is required for α1-AR stimulation of Brd4 chromatin occupancy. The differential role of the Brd4/P-TEFb complex in response to distinct GPCR pathways has potential clinical implications as therapies targeting this complex are currently being explored for heart failure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32341082" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147416" }, "primaryId" : "GEO:GSE147416", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147416" } ] }, "title" : "An interaction between Gβγ and RNA polymerase II regulates transcription in cardiac fibroblasts", "dateAssigned" : "2020-03-23T00:00:00.000-05:00", "summary" : "Gβγ subunits are involved in an array of different signalling processes in various compartments of the cell, including the nucleus. To gain further insight into the functions of nuclear Gβγ, we investigated the functional role of Gβγ signalling in the regulation of GPCR-mediated gene expression in primary rat neonatal cardiac fibroblasts. Here, we demonstrate that following activation of the angiotensin II type I receptor in these cells, Gβγ dimers interact with RNA polymerase II (RNAPII). Our findings suggest that Gβ1 recruitment to RNAPII negatively regulates the fibrotic transcriptional response, which can be overcome by strong fibrotic stimuli. The Gβγ-RNAPII interaction was also investigated in HEK 293 cells and was regulated by signaling pathways that diverged from those operating in cardiac fibroblasts, suggesting that although it may be a conserved feature of transcriptional regulation, such regulation may be cell-specific. Taken together, our studies reveal a novel interaction between Gβγ subunits and RNA polymerase II and expand the role for Gβγ signalling in cardiac fibrosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36841480" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147432" }, "primaryId" : "GEO:GSE147432", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147432" } ] }, "title" : "TDP-43 dysfunction restricts dendritic complexity by inhibiting CREB activation and altering gene expression", "dateAssigned" : "2020-03-23T00:00:00.000-05:00", "summary" : "Identified TDP-43 targets in rat cortical neurons, many related to the CREB pathway", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32393629" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147473" }, "primaryId" : "GEO:GSE147473", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147473" } ] }, "title" : "Expression data from rat vocal fold at different periods after vocal fold injury (miRNA)", "dateAssigned" : "2020-03-24T00:00:00.000-05:00", "summary" : "Vocal cord healing is a dynamic process, and many genes and proteins are involved, which play varying roles at different regeneration stages after injury. Previous studies have shown that inflammatory responses occur at the early stage of vocal cord injury, where the fibroblasts proliferate exuberantly with intensive secretion and deposition of ECM. These activities reach the peak at 3-7 days and their intensity begins to decline 15 days later. A study based on the dermal system has shown that ECM remodeling during the repair of injury can last for several months. However, few studies have been conducted as to the dynamic changes of gene and microRNA expressions during the healing process of vocal cord injury. Plotting these changes will facilitate the understanding about the physiological changes during healing and the identification of key time points and target genes and microRNAs in fibrosis formation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147569" }, "primaryId" : "GEO:GSE147569", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147569" } ] }, "title" : "Diurnal patterns of gene expression in the dorsal vagal complex and the central nucleus of the amygdala", "dateAssigned" : "2020-03-26T00:00:00.000-05:00", "summary" : "Micropunches of dorsal vagal complex (DVC) and central nucleus of the amygdala (CeA) were collected from male, Sprague Dawley rats at three different times of the day. Animals were not experimentally different in any way except for the time of sacrifice and collction. Gene expression of 145 genes were measured with Fluidigm's Biomark 96.96 platform.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32477043" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147578" }, "primaryId" : "GEO:GSE147578", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147578" } ] }, "title" : "Comparison of miRNA between normal rat plasma exosomes and melatonin pretreated rat plasma exosomes", "dateAssigned" : "2020-03-26T00:00:00.000-05:00", "summary" : "Stroke places a huge burden on society today, and great of studies were devoted for seeking safe and effective therapeutic strategy to improve the prognosis of stroke. Plasma exosome has exhibited its therapeutic potential against ischemia and reperfusion injury via ameliorating inflammation. To enhance therapeutic potential in patients with ischemic injury, we isolated exosomes from melatonin pretreated rat plasma and assessed the neurological protective effect in a rat model of focal cerebral ischemia. Treatment with melatonin enhanced plasma exosome therapeutic effect against ischemia induced inflammatory response and inflammasome mediated pyroptosis. In addition, we confirmed ischemic stroke induced pyroptotic cell death mainly occurred in microglia, while administration of melatonin treated exosome further effectively decreased infract volume and improved function recovery via regulation of TLR-4/NF-κB signaling pathway. Finally, the altered miRNAs profile in melatonin treated plasma exosomes demonstrated the regulatory mechanisms. This study suggests plasma exosome with melatonin pretreatment might be a more effective strategy for patients with ischemic brain injury. Further exploration of key molecules in plasma exosome may devote more therapeutic value for cerebral ischemic injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33013286" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147615" }, "primaryId" : "GEO:GSE147615", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147615" } ] }, "title" : "Single-cell RNA-seq reveals the difference between Schwann cells in dorsal root ganglion and sciatic nerve", "dateAssigned" : "2020-03-27T00:00:00.000-05:00", "summary" : "Schwann cells are important glial cells in peripheral nervous system. In this study, we performed single cell RNA-sequencing (scRNA-seq) analysis of Schwann cells exist in both dorsal root ganglion(DRG) and sciatic nerve.We categorized DRG and sciatic nerve Schwann cells into different subtypes,and found common subtypes and different subtypes.In addition, we discovered the proliferation and migration ability of Schwann cells were distinct in different tissues.Our current study revealed the distinctive characteristics of Schwann cells in DRG and sciatic nerve.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33079428" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147663" }, "primaryId" : "GEO:GSE147663", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147663" } ] }, "title" : "A deletion in Eml1 leads to bilateral subcortical heterotopia in the tish rat", "dateAssigned" : "2020-03-27T00:00:00.000-05:00", "summary" : "Malformations of cortical development (MCD) are present in up to 40% of children with pharmacoresistant epilepsy. Although epilepsy surgery can be successful in a subset of children, not all forms of MCD are operable. Understanding the genetic and neurobiological mechanisms underlying MCD and MCD-related epilepsy are necessary for the development of novel anti-epilepsy drugs. The tish (telencephalic internal structural heterotopia) rat is a unique model of MCD and spontaneous seizures, but the underlying genetic mutation has been, heretofore, unknown. DNA and RNA-sequencing revealed that a deletion encompassing a previously unannotated exon markedly diminished EML1 transcript and protein abundance in the tish brain. Developmental electrographic characterization of the tish rat demonstrated spontaneous spike-wave discharge (SWD) bursts beginning as early as postnatal day (P) 17. A dihybrid cross demonstrated that the mutantEml1 allele segregates with the observed dysplastic cortex and SWD bursts in monogenic autosomal recessive frequencies. Our data link the development of the bilateral, heterotopic dysplastic cortex of the tish rat to a mutation in Eml1 and provide a novel rat model of MCD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32179177" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147706" }, "primaryId" : "GEO:GSE147706", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147706" } ] }, "title" : "RNA-Sequencing Characterisation of the Renal Cortical Response to Roux-en-Y Gastric Bypass Surgery Alone and Combined Roux-en-Y Gastric Bypass Surgery and Medical Therapy in the Zucker Diabetic Sprague Dawley Rat Model of Diabetic Kidney Disease", "dateAssigned" : "2020-03-29T00:00:00.000-05:00", "summary" : "We report results from renal cortical transcriptomic analysis of responses to RYGB surgery alone and the combination of RYGB surgery and medical therapy in the Zucker Diabetic Sprague Dawley (ZDSD) rat model of diabetic kidney disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35222262" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147732" }, "primaryId" : "GEO:GSE147732", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147732" } ] }, "title" : "Gene expression profiling of sciatic nerves from rats with diabetic peripheral neuropathy", "dateAssigned" : "2020-03-30T00:00:00.000-05:00", "summary" : "To identify the key genes and pathways which might play critical roles in the pathogenesis of experimental DPN via microarray analysis. Adult male Sprague-Dawley rats (initial weight 250-300g, from the department of laboratory animal science of Fudan University) were randomly assigned into two groups: control rats and diabetic rats. Diabetes was induced with a single intraperitoneal injection of STZ (55mg/kg). Control rats were performed with a single intraperitoneal injection of 0.9% saline solution. Glucose level was evaluated using Sannuo strips on tail vein blood at day 3 after STZ injection and verified again at day 7 after STZ injection. Only rats with blood glucose level 16.7 mmol/L were considered diabetic.Six weeks after diabetes induction, nerve tissue samples (about 1cm long) were harvested from the right sciatic nerve of rats in control (n=3) and diabetic (n=3) groups for total RAN isolation. Microarray hybridization was then performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies). Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). The univariate t-test with a fold-change >2 and P value < 0.001 was applied to identify the DEGs between control rats and diabetic rats. Credibility of the microarray data was validated through qRT-PCR on 4 genes. Total RNA was independently extracted from the right sciatic nerve of rats in both groups (n=3) 6 weeks after diabetes induction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32566679" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147772" }, "primaryId" : "GEO:GSE147772", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147772" } ] }, "title" : "Identification of circRNA and mRNA expression profiles and functional networks of vascular tissue in lipopolysaccharide-induced rat septic shock model [circRNA]", "dateAssigned" : "2020-03-30T00:00:00.000-05:00", "summary" : "Septic shock is the most common cause of death in intensive care units. The aim of this study is to investigate the role of circular RNA (circRNA) and mRNA expression profiles and functional networks in aortic tissue of septic shock.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32452125" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147774" }, "primaryId" : "GEO:GSE147774", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147774" } ] }, "title" : "Identification of circRNA and mRNA expression profiles and functional networks of vascular tissue in lipopolysaccharide-induced rat septic shock model [mRNA]", "dateAssigned" : "2020-03-30T00:00:00.000-05:00", "summary" : "Septic shock is the most common cause of death in intensive care units. The aim of this study is to investigate the role of circular RNA (circRNA) and mRNA expression profiles and functional networks in aortic tissue of septic shock.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32452125" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147806" }, "primaryId" : "GEO:GSE147806", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147806" } ] }, "title" : "Stress regulation of sustained attention and the cholinergic attention system", "dateAssigned" : "2020-03-31T00:00:00.000-05:00", "summary" : "Results: VS impaired attentional performance in SAT and increased the dendritic complexity of NBM cholinergic neurons in both sexes. NBM cholinergic neurons are mainly under inhibitory control, so this morphological change could increase inhibition on these neurons, reducing downstream ACh release to impair attention. Indeed, VS decreased ACh release in the prefrontal cortex of males. Quantification of global transcriptional changes revealed that, although VS induced many sex-specific changes in gene expression, it increased several signaling molecules in both sexes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147845" }, "primaryId" : "GEO:GSE147845", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147845" } ] }, "title" : "DNA Methyltransferase 3A Mediates the Sustained Effects of Stress on Synaptic Functions and Behaviors [RNA-seq]", "dateAssigned" : "2020-03-31T00:00:00.000-05:00", "summary" : "Emerging evidence suggests that epigenetic mechanisms regulate aberrant gene transcription in stress-associated mental disorders. However, it remains to be elucidated about the role of DNA methylation and its catalyzing enzymes, DNA methyltransferases (DNMTs), in this process. Here we found that rats exposed to chronic (2-week) unpredictable stress exhibited a substantial reduction of Dnmt3a after stress cessation in the prefrontal cortex (PFC), a key target region of stress. Treatment of unstressed control rats with DNMT inhibitors recapitulated the effect of chronic unpredictable stress on decreased AMPAR expression and function in PFC. In contrast, overexpression of Dnmt3a in PFC of stressed animals prevented the loss of glutamatergic responses. Moreover, the stress-induced behavioral abnormalities, including the impaired recognition memory and aggressive behaviors, were ameliorated by Dnmt3a expression in PFC of stressed animals. Lastly, we found genome-wide DNA methylation changes in PFC of stressed rats are selectively enriched at several pathways, such as axon guidance, Wnt signaling and neurotransmission. These findings have therefore recognized the role of DNA epigenetic modification in stress-induced disturbance of synaptic functions and cognitive & emotional processes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147846" }, "primaryId" : "GEO:GSE147846", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147846" } ] }, "title" : "DNA Methyltransferase 3A Mediates the Sustained Effects of Stress on Synaptic Functions and Behaviors [RRBS]", "dateAssigned" : "2020-03-31T00:00:00.000-05:00", "summary" : "Emerging evidence suggests that epigenetic mechanisms regulate aberrant gene transcription in stress-associated mental disorders. However, it remains to be elucidated about the role of DNA methylation and its catalyzing enzymes, DNA methyltransferases (DNMTs), in this process. Here we found that rats exposed to chronic (2-week) unpredictable stress exhibited a substantial reduction of Dnmt3a after stress cessation in the prefrontal cortex (PFC), a key target region of stress. Treatment of unstressed control rats with DNMT inhibitors recapitulated the effect of chronic unpredictable stress on decreased AMPAR expression and function in PFC. In contrast, overexpression of Dnmt3a in PFC of stressed animals prevented the loss of glutamatergic responses. Moreover, the stress-induced behavioral abnormalities, including the impaired recognition memory and aggressive behaviors, were ameliorated by Dnmt3a expression in PFC of stressed animals. Lastly, we found genome-wide DNA methylation changes in PFC of stressed rats are selectively enriched at several pathways, such as axon guidance, Wnt signaling and neurotransmission. These findings have therefore recognized the role of DNA epigenetic modification in stress-induced disturbance of synaptic functions and cognitive & emotional processes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147864" }, "primaryId" : "GEO:GSE147864", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147864" } ] }, "title" : "The Molecular Effects of a High Fat Diet on Endometrial Tumour Biology", "dateAssigned" : "2020-03-31T00:00:00.000-05:00", "summary" : "We sought to validate the BDII/Han rat model as a model for diet-induced obesity in endometrial cancer (EC) and determine if transcriptomic changes induced by a high fat diet (HFD) in an EC rat model can be used to identify novel biomarkers in human EC. Nineteen BDII/Han rats were included. Group A (n = 7) were given ad lib access to a normal calorie, normal chow diet (NCD) while Group B (n = 12) were given ad lib access to a calorie rich HFD for 15 months. RNAseq was performed on endometrial tumours from both groups. The top-ranking differentially expressed genes (DEGs) were examined in the human EC using The Cancer Genome Atlas (TCGA) to assess if the BDII/Han rat model is an appropriate model for human obesity-induced carcinogenesis. Weight gain in HFD rats was double the weight gain of NCD rats (50 g vs. 25 g). The incidence of cancer was similar in both groups (4/7-57% vs. 4/12-33%; p = 0.37). All tumours were equivalent to a Stage 1A, Grade 2 human endometrioid carcinoma. A total of 368 DEGs were identified between the tumours in the HFD group compared to the NCD group. We identified two upstream regulators of the DEGs, mir-33 and Brd4, and a pathway analysis identified downstream enrichment of the colorectal cancer metastasis and ovarian cancer metastasis pathways. Top-ranking DEGs included Tex14, A2M, Hmgcs2, Adamts5, Pdk4, Crabp2, Capn12, Npw, Idi1 and Gpt. A2M expression was decreased in HFD tumours. Consistent with these findings, we found a significant negative correlation between A2M mRNA expression levels and BMI in the TCGA cohort (Spearman's Rho = -0.263, p < 0.001). A2M expression was associated with improved overall survival (HR = 0.45, 95% CI 0.23-0.9, p = 0.024). Crabp2 expression was increased in HFD tumours. In human EC, CRABP2 expression was associated with reduced overall survival (HR = 3.554, 95% CI 1.875-6.753, p < 0.001). Diet-induced obesity can alter EC transcriptomic profiles. The BDII/Han rat model is a suitable model of diet-induced obesity in endometrial cancer and can be used to identify clinically relevant biomarkers in human EC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32927694" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147945" }, "primaryId" : "GEO:GSE147945", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147945" } ] }, "title" : "High-throughput RNA sequencing of basilar artery smooth muscle cells in wild type and high-salt diet induced hypertension rats", "dateAssigned" : "2020-04-01T00:00:00.000-05:00", "summary" : "We utilized high-throughput sequencing and subsequent signaling pathway analyses to find 2 fold change or greater upregulated expression of 230 transcripts and downregulated expression of 165 transcripts in basilar artery smooth muscle cells derived from rats fed a high-salt diet compared with those from control rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33083107" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147992" }, "primaryId" : "GEO:GSE147992", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE147992" } ] }, "title" : "Genome-wide maps of chromatin state in rat IUGR islets at 2 time points", "dateAssigned" : "2020-04-02T00:00:00.000-05:00", "summary" : "Intrauterine growth restriction (IUGR) increases the risk of developing type 2 diabetes in adulthood. A rat model of IUGR induced by bilateral uterine artery ligation at day 18 of gestation, which reduces the blood supply and critical substrates to the fetus, was used to assess the alterations of genome-wide histone modifications in IUGR islets. At 2 and 10 weeks of age, pancreatic islets were isolated and chromatins were extracted for ChIP-Seq study. Chromatin state of H3K4me3, H3K27me3, and H3K27Ac modifications was compared in the study.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32527043" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148007" }, "primaryId" : "GEO:GSE148007", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148007" } ] }, "title" : "Mu opioid receptor (Oprm1) knockdown in the medial preoptic area (MPOA) on patterns of gene expression in the MPOA of adolescent male rats", "dateAssigned" : "2020-04-02T00:00:00.000-05:00", "summary" : "We investigate effects of Oprm1 downregulation in the MPOA on gene expression profiles in adolescent male rats using RNA-Seq. We conducted differential gene expression analysis of RNA-Seq data using the EdgeR Bioconductor Package. We evaluated differential gene expression between Oprm1 knockdown and control groups and found 349 genes were differentially expressed, with some genes being involved in neuronal signaling exhibited altered expression due to Oprm1 knockdown.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32388931" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148151" }, "primaryId" : "GEO:GSE148151", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148151" } ] }, "title" : "Strain differences in responsiveness to chronic restraint stress affect remote contextual fear memory and blood transcriptomics", "dateAssigned" : "2020-04-06T00:00:00.000-05:00", "summary" : "Fear memory regulation is thought to be similar between humans and animals, and the role of stress in altering remote memory is little explored. Since individual variation in stress reactivity exists, should stress alter remote memory, invividuals with differing stress-reactivity would affect it to various degree. We evaluate this question using two strains of rats with differing stress-reactivity. The Fisher 344 (F344) strain is known to have active coping style and represent normal stress-reactivity, while the Wistar–Kyoto (WKY) rat shows passive coping strategies and heightened stress-reactivity. Male animals were exposed contextual fear conditioning (CFC) and four weeks later, chronic restraint stress (CRS) or no stress (NS) was administered for two weeks. Remote memory, immediate stress response to a second CFC, and reinstated fear memory was measured. Both recent and reinstated fear memory were greater in F344s, regardless of the stress status, In contrast, remote memory was attenuated in F344 only, concurring with their increased immediate stress responsive behavior after CRS. To find if this strain-specific response to CRS can be mirrored by transcriptomic changes in the blood, RNA sequencing was carried out. Overlapping differentially expressed genes (DEGs) between NS vs. CRS in the blood of F344 and WKY suggest a convergence of stress-related molecular mechanisms, independent of stress-reactivity. In contrast, DEGs unique to the F344 and the WKY stress responses are divergent in their functionality and networks, beyond that of strain differences in their non-stressed state. These unique DEGs than could be implicated as biomarkers stress-reactivity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148155" }, "primaryId" : "GEO:GSE148155", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148155" } ] }, "title" : "CELL CONTRACTILITY AND AN ACTIN GRADIENT DRIVE POLAR ALIGNMENT OF FIBROBLASTS IN CONSTRAINED GEOMETRIES", "dateAssigned" : "2020-04-06T00:00:00.000-05:00", "summary" : "When REF 2c cells were placed on circular micro-contact printed patterns, the boundary cells radially aligned over a period of 48 h. Video tracking of specific boundary and inner cells showed that this phenomenon was not caused by cells migrating towards or away from the periphery. Cell contractility, intercellular junctions, and cell-cell adhesion are required for radial alignment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34542405" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148174" }, "primaryId" : "GEO:GSE148174", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148174" } ] }, "title" : "Direct Formalin Fixation Induces Widespread Transcriptomic Effects in Archival Tissue Samples", "dateAssigned" : "2020-04-06T00:00:00.000-05:00", "summary" : "Archival formalin-fixed paraffin-embedded (FFPE) tissue samples hold a wealth of transcriptomic information; however, little is known about potential artifacts. Previously, we identified a consistent shift in global RNA-sequencing profiles between matching frozen and FFPE samples. We hypothesized that this shift was from fixing fresh tissue in formalin. To test this idea, RNA-sequencing was performed on liver samples collected from male mice treated with 600 ppm of a reference chemical (phenobarbital, 600 ppm phenobarbital) or vehicle control for 7 days. Samples were divided into: (1) fresh-frozen (FR); (2) directly fixed in 10% buffered formalin for 18 hours followed by paraffin embedding (FFPE); (3) frozen then fixed as FFPE (FR>FFPE); or (4) frozen then fixed in 70% ethanol followed by paraffin embedding (FR>OH) (n=6/group/condition). Direct fixation resulted in 2946 differentially expressed genes (DEGs), 98% of which were down-regulated. Freezing prior to fixation resulted in ≥95% fewer DEGs vs. FR, indicating that most formalin-derived transcriptional effects occurred with fixation. This was supported by follow-up studies, which identified consistent enrichment in oxidative stress, mitochondrial dysfunction, and transcription elongation pathways with formalin fixation. Notably, formalin fixation in the parent study did not significantly impact chemical response profiles, which were consistent with CAR/PXR activation and 600 ppm phenobarbital exposure. Our results demonstrate distinct transcriptional effects of formalin fixation that could impact gene expression studies using FFPE samples.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32879405" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148253" }, "primaryId" : "GEO:GSE148253", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148253" } ] }, "title" : "Effects of repetitive Iodine Thyroid Blocking on the Fetal Brain and Thyroid in rats: a Systems Biology approach [Thyroid]", "dateAssigned" : "2020-04-07T00:00:00.000-05:00", "summary" : "Our group showed that repetitive dose of KI for eight days offers efficient protection against radiation exposure during nuclear accidents without toxic effects in adult rats. However, the effect of repetitive KI on the developing fetus still unknown especially on brain development, but a correlation between the impaired maternal thyroid status and a decrease in intelligence quotient has been observed. In this study, gene expression analysis of the progeny of repetitive KI-administered pregnant rats performed by our group showed distinct gene expression profile from two different organs: thyroid and cortex. To understand how these differentially expressed genes are implicated in the observed behaviour change, a systems biology approach was used to construct networks using three different techniques; Bayesian statistics using ShrinkNet, sPLS-DA on the DIABLO platform using mixOmics and manual construction of a Process Descriptive network. For each organ, we were able to construct gene expression network, to select genes that are most contributing to either control or KI-treated groups, respectively, and to construct the PD network from differentially expressed (DE) gene enriched with data from publications. Furthermore, we were able to connect DE genes from both organs into one network with genes from both organ participating in the same cellular processes that affect mitophagy and neuronal outgrowth.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32616734" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148255" }, "primaryId" : "GEO:GSE148255", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148255" } ] }, "title" : "Biological effects of inhaled hydraulic fracturing sand dust in rats", "dateAssigned" : "2020-04-07T00:00:00.000-05:00", "summary" : "The pulmonary inflammatory response to inhalation exposure to fracking sand dust (FSD) was investigated in a rat model. Adult male Sprague-Dawley rats were exposed by whole-body inhalation to air or an aerosol of FSD at concentrations of 10 or 30 mg/m3, 6 hours/day for 4 days. The control and FSD-exposed rats were euthanized at post-exposure time intervals of 1, 7 or 27days and pulmonary inflammatory, cytotoxic and oxidant responses were determined. Deposition of FSD particles was detected in the lungs of all the FSD-exposed rats. Analysis of bronchoalveolar lavage parameters of toxicity, oxidant generation, and inflammation did not reveal any significant persistent pulmonary toxicity in the FSD- exposed rats. Similarly, the lung histology of the FSD-exposed rats showed only minimal changes in influx of macrophages following the exposure. Determination of global gene expression profiles detected significant differential expressions of only six and five genes in the 10 mg/m3, 1 day post-exposure, and the 30 mg/m3, 7-day post-exposure FSD groups, respectively. Taken together, data obtained from the present study demonstrated that FSD inhalation exposure resulted in minimal/no toxicity or gene expression changes in the lungs of the rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33065154" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148266" }, "primaryId" : "GEO:GSE148266", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148266" } ] }, "title" : "Effects of Prenatal Exposure to a Mixture of Organophosphate Flame Retardants on Placental Gene Expression and Serotonergic Innervation in the Developing Rat Brain", "dateAssigned" : "2020-04-07T00:00:00.000-05:00", "summary" : "There is a growing need to understand the potential neurotoxicity of organophosphate ester flame retardants (OPFRs) and plasticizers because use and, consequently, human exposure, is rapidly expanding. We have previously shown in rats that developmental exposure to the commercial FR mixture Firemaster® 550 (FM 550), which contains OPFRs, results in sex-specific behavioral effects, and identified the placenta as a potential target of toxicity. The placenta is a critical coordinator of fetal growth and neurodevelopment, and a source of neurotransmitters (NTs) for the developing brain. We have shown in rats and humans that FRs accumulate in placental tissue, and induce functional changes, including altered neurotransmitter (NT) production. Here we sought to establish if OPFRs (triphenyl phosphate, TPHP, and a mixture of isopropylated triarylphosphate isomers, ITPs) alter placental function and fetal forebrain development, with disruption of tryptophan (Trp) metabolism as a primary pathway of interest. Wistar rat dams were orally exposed to OPFRs (0, 500, 1,000, or 2,000 μg/day) or a serotonin (5-HT) agonist (5-MT) for 14 days during gestation and placenta and fetal forebrain tissues collected for analysis by transcriptomics and metabolomics. Relative abundance of genes responsible for the transport and synthesis of placental 5-HT were disrupted, and multiple neuroactive metabolites in the 5-HT and kynurenine (Kyn) metabolic pathways were upregulated. Additionally, 5-HTergic projections were significantly longer in the fetal forebrains of exposed males. These findings suggest that OPFRs have the potential to impact the 5-HTergic system in the fetal forebrain by disrupting placental Trp metabolism.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148280" }, "primaryId" : "GEO:GSE148280", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148280" } ] }, "title" : "Effects of repetitive Iodine Thyroid Blocking on the Fetal Brain and Thyroid in rats: a Systems Biology approach [Cortex]", "dateAssigned" : "2020-04-08T00:00:00.000-05:00", "summary" : "Our group showed that repetitive dose of KI for eight days offers efficient protection against radiation exposure during nuclear accidents without toxic effects in adult rats. However, the effect of repetitive KI on the developing fetus still unknown especially on brain development, but a correlation between the impaired maternal thyroid status and a decrease in intelligence quotient has been observed. In this study, gene expression analysis of the progeny of repetitive KI-administered pregnant rats performed by our group showed distinct gene expression profile from two different organs: thyroid and cortex. To understand how these differentially expressed genes are implicated in the observed behaviour change, a systems biology approach was used to construct networks using three different techniques; Bayesian statistics using ShrinkNet, sPLS-DA on the DIABLO platform using mixOmics and manual construction of a Process Descriptive network. For each organ, we were able to construct gene expression network, to select genes that are most contributing to either control or KI-treated groups, respectively, and to construct the PD network from differentially expressed (DE) gene enriched with data from publications. Furthermore, we were able to connect DE genes from both organs into one network with genes from both organ participating in the same cellular processes that affect mitophagy and neuronal outgrowth.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32616734" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148331" }, "primaryId" : "GEO:GSE148331", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148331" } ] }, "title" : "Expression and Possible Mechanism of circular RNA rno_CIRCpedia_1953 in Deep Venous Thrombosis (RNA)", "dateAssigned" : "2020-04-08T00:00:00.000-05:00", "summary" : "Conclusions: Animal model of DVT in rats was successfully established by stenosis method. High-throughput sequencing analysis of circRNAs showed that circRNAs participated in the evolution of DVT. According to STEM functional analysis of mRNA sequencing, a target circRNA rno_CIRCpedia _1953 was screened, verified and identified. rno_CIRCpedia_1953 may participate in the development of DVT by acting as miRNA molecular sponge.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148332" }, "primaryId" : "GEO:GSE148332", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148332" } ] }, "title" : "Expression and Possible Mechanism of circular RNA rno_CIRCpedia_1953 in Deep Venous Thrombosis (circular RNA)", "dateAssigned" : "2020-04-08T00:00:00.000-05:00", "summary" : "Conclusions: Animal model of DVT in rats was successfully established by stenosis method. High-throughput sequencing analysis of circRNAs showed that circRNAs participated in the evolution of DVT. According to STEM functional analysis of mRNA sequencing, a target circRNA rno_CIRCpedia _1953 was screened, verified and identified. rno_CIRCpedia_1953 may participate in the development of DVT by acting as miRNA molecular sponge.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148350" }, "primaryId" : "GEO:GSE148350", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148350" } ] }, "title" : "Microglia transcriptome in a rat model of ischemic stroke", "dateAssigned" : "2020-04-08T00:00:00.000-05:00", "summary" : "We identified an extensive and persistent upregulation of anti-inflammatory M2-like patterns after stroke and a mild up-regulation of pro-inflammatory M1-like patterns at later stage. We also found that younger brains showed larger microglial response than middle aged brains. Moreover, beyond the standard M1/M2 dichotomy, a wide spectrum of novel microglial polarization states was activated in response to stroke, particularly the phenotypes related to Tlr2 and dietary fatty acids stimulation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33208001" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148420" }, "primaryId" : "GEO:GSE148420", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148420" } ] }, "title" : "Immunohistochemical Investigation for Renal Tubules in Adaptive and Maladaptive Repair Process after Renal Tubular Injury in the Kidney of Rats", "dateAssigned" : "2020-04-09T00:00:00.000-05:00", "summary" : "Acute kidney injury (AKI) have been thought to be reversible condition, however, emerging evidence demonstrated association between AKI and subsequent development of irreversible fibrosis and chronic kidney disease. In the present study, since recovery of AKI depends on renal tubular regeneration, factors expressing in renal tubules in adaptive or maladaptive repair process were investigated to predict reversibility of kidney injury. In the kidney of female F344 rats subjected to ischemia/reperfusion (I/R), regenerative tubules and dilated tubules were observed at 3 and 7 days after I/R. In fibrotic areas of the kidney of male SD rats subjected to I/R, renal tubules were dilated or atrophied. From microarray data of regenerative tubules, survivin, sex-determining region Y (SRY)-box 9 (SOX9), and CD44 were extracted as factors possibly relating to tubular regeneration or fibrosis. Immunohistochmical analysis demonstrated that survivin and SOX9 expressed in regenerative tubules, while SOX9 also expressed in renal tubules in fibrotic area, indicating that survivin and SOX9 contribute renal tubular regeneration, but sustained SOX9 expression may lead fibrosis. CD44 expressed in dilated tubules at day 3 and 7, and tubules in fibrotic area, suggesting that CD44 expressed in maladaptive tubules. These information will be helpful to consider reversibility of kidney injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148453" }, "primaryId" : "GEO:GSE148453", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148453" } ] }, "title" : "RNA-seq to characterize estrogen receptor alpha mutation in the female rat right ventricle with pressure overload", "dateAssigned" : "2020-04-10T00:00:00.000-05:00", "summary" : "Conclusions: ERα in females is protective against RV-pulmonary vascular uncoupling, diastolic dysfunction, and fibrosis in response to pressure overload. ERα appears to be dispensable for RV adaptation in males. ERα may be a mediator of superior RV adaptation in female patients with PAH.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33064565" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148559" }, "primaryId" : "GEO:GSE148559", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148559" } ] }, "title" : "RNA sequencing of rodent myocardial tissue when subjected to mitral regurgitation (MR) for different time-points, compared to normal Sham tissue.", "dateAssigned" : "2020-04-13T00:00:00.000-05:00", "summary" : "Conclusions: RNA sequencing revealed an early activation of multiple cellular pathways.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148598" }, "primaryId" : "GEO:GSE148598", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148598" } ] }, "title" : "Finding two synergized compounds from Chinese herbal medicine in rheumatoid arthritis therapy", "dateAssigned" : "2020-04-13T00:00:00.000-05:00", "summary" : "Conclusion: A pair of compound combination has been found. RNA sequencing and IPA analysis revealed that the synergistic mechanism of combination treatment was related to several canonical signaling pathways and key targets.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148751" }, "primaryId" : "GEO:GSE148751", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148751" } ] }, "title" : "Analyses of circRNAs and mRNAs profiling in the submandibular gland in hypertension [circRNA]", "dateAssigned" : "2020-04-15T00:00:00.000-05:00", "summary" : "The aim of this study is to explore the role of circRNAs in the mechanism of submandibulargland (SMG)dysfunction in hypertension.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148752" }, "primaryId" : "GEO:GSE148752", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148752" } ] }, "title" : "Analyses of circRNAs and mRNAs profiling in the submandibular gland in hypertension [mRNA]", "dateAssigned" : "2020-04-15T00:00:00.000-05:00", "summary" : "The aim of this study is to explore the role of circRNAs in the mechanism of submandibulargland (SMG)dysfunction in hypertension.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148828" }, "primaryId" : "GEO:GSE148828", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148828" } ] }, "title" : "In vivo transciptomic responses to acetaminophen exposure from liver and kidneys of Sprague Dawley rats", "dateAssigned" : "2020-04-17T00:00:00.000-05:00", "summary" : "In this study we tested the ability to identify early perturbations in the organ (liver and kidney) metabolism due to acetaminopen exposure at two early time points (5 and 10 h) using RNA-sequencing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30974156" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148852" }, "primaryId" : "GEO:GSE148852", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148852" } ] }, "title" : "In vivo transciptomic responses to bromobenzene exposure from liver and kidneys of Sprague Dawley rats", "dateAssigned" : "2020-04-17T00:00:00.000-05:00", "summary" : "In this study we tested the ability to identify early perturbations in the organ (liver and kidney) metabolism due to bromobenzene exposure at two early time points (5 and 10 h) using RNA-sequencing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32479839" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148869" }, "primaryId" : "GEO:GSE148869", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE148869" } ] }, "title" : "Lung response to multi-walled carbon nanotube exposure in rats.", "dateAssigned" : "2020-04-17T00:00:00.000-05:00", "summary" : "The projected increase in the production and use of nanomaterials is expected to result in a corresponding increase in human exposure, potentially resulting in significant morbidity and mortality. Currently, the lung toxicity of multi-walled carbon nanotubes (MWCNT), a prototype nanomaterial, was investigated in a rat model. The rats were exposed by whole-body inhalation to air (controls) or MWCNT (6 hours/day, 3 days) to result in cumulative doses of 180, 90, 45, 22.5, or 11.25 mg/m3. Lung toxicity and gene expression profiles were determined in the lungs of the control and MWCNT exposed rats one day following termination of the exposures. Moderate lung histological changes, indicative of toxicity, were detected in rats exposed to MWCNT at doses > 45 mg/m3. Changes in toxicity parameters including, lactate dehydrogenase (LDH) activity, oxidant production, cell counts of phagocytes, and cytokine levels were detected in the bronchoalveolar lavage of rats exposed to > 22.5 mg/m3 MWCNT, compared with the air controls. Lung gene expression profiling detected differences in transcript levels (fold change >1.5 and FDR p<0.05) of several genes in the rats exposed to >22.5 mg/m3 MWCNT, compared with the controls. The changes in lung toxicity and gene expression profiles exhibited a dose-response to the MWCNT administered in the rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35648795" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149006" }, "primaryId" : "GEO:GSE149006", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149006" } ] }, "title" : "Transcriptomic analysis of Resp18mutant rat kidneys reveals up-regulation of Renin-Angiotensin system", "dateAssigned" : "2020-04-21T00:00:00.000-05:00", "summary" : "Regulated endocrine specific protein 18 (Resp18), expression has been specifically located in a series of tissues and cell types however the exact cellular function is unknown. In previous studies we have showed that a targeted disruption of Resp18 in Dahl SS rats (Resp18mutant) resulted in higher blood pressure (BP), increased renal fibrosis, and decreased survival rate on a long term (6-week) 2% high salt (HS) diet treatment compared with wild type SS rats. In the current study we studied whether a short term (1 week) exposure to HS diet shows a similar effect in Resp18mutant rats. Furthermore, previously we have shown that in addition to BP phenotype Resp18mutant rats have demonstrated deteriorative kidney phenotype evident through renal fibrosis, protein urea and protein cast formation. Based on this background we conducted BP study and performed transcriptomic profiling of the kidney after one-week exposure to HS diet treatment. Through radio-telemetry procedure, we found that the systolic BP was increased in the Resp18mutant rats compared with SS rats even with short term HS diet exposure. Therefore, we sought out to investigate if there was any alteration in the transcriptomic response by HS diet treatment in the Resp18mutant rat kidneys. Using RNA sequencing approach, we found that Resp18mutant rats showed a differential expression of 25 genes of which one was an upregulation of Ren. We confirmed the upregulation of Ren and other differentially expressed genes via qRT-PCR analysis. Upon KEGG pathway enrichment we found that the Resp18mutant rat showed upregulation in the renin angiotensin system (RAAS), and renin secretion pathway. Furthermore, the renin activity is found to be higher in Resp18mutant rats serum compared with SS rats. Therefore, these observations demonstrate that upon disruption of Resp18 gene in SS rats associated with the increase in renin secretion and thus increase BP.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34340197" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149072" }, "primaryId" : "GEO:GSE149072", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149072" } ] }, "title" : "Gene expression profiling of tissue and hMSC xenografts in a rat postpartum urinary injury model", "dateAssigned" : "2020-04-21T00:00:00.000-05:00", "summary" : "Periurethral human mesenchymal stem cell (hMSC) injections are associated with functional improvement in animal models of post-partum stress urinary incontinence (SUI). However, limited data exists on the role of hMSCs in modulating gene expression in tissue repair after urethral injury. We quantified temporal gene expression modulation in hMSCs, and injured rat urethral tissue, using RNA seq in an animal model of SUI, over a 3-day time period following urethral injury, and local hMSC therapy. We injected PKH fluorescent-labeled human hMSC into the periurethral space of rats, following a 4h vaginal distention (3 rats per time point). Control rats underwent vaginal distention injury only, and were sacrificed at 12h, 24h, 36h, 72h post injury. Rat urethral and vaginal tissues were frozen and sectioned. Fluorescent labeled hMSCs were distinguished from adjacent, unlabeled rat urethral tissue. RNA was prepared from urethral tissue obtained by laser dissection of frozen tissue sections and sequenced on an Illumina HiSeq 2500. Differentially expressed genes (DEGs) over 72h were evaluated using a 2-group t-test (p<0.05). Our transcriptional analyses identified candidate genes involved in tissue injury, that were broadly sorted by injury and exposure to hMSC, throughout the first 72h of acute phase of injury. DEGs in treated urethra, compared with untreated urethra, were functionally associated with tissue repair, angiogenesis, neurogenesis, and oxidative stress suppression. DEGs included a variety of cytokines, extracellular matrix stabilization and regeneration genes, cytokine signaling modification, cell cycle regulation, muscle differentiation and stabilization. Moreover, our results revealed DEGs changes in the hMSCs (PKH-labelled), which were harvested from injured urethra. The expressions are related to DNA damage repair, transcription activation, stem cell regulation, cell survival, apoptosis, self-renewal, cell proliferation, migration and injury response.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149188" }, "primaryId" : "GEO:GSE149188", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149188" } ] }, "title" : "Whole transcriptome deep sequencing to rat vein graft", "dateAssigned" : "2020-04-23T00:00:00.000-05:00", "summary" : "a rat vein graft model was constructed by the “cuffâ€� technique, and whole transcriptome deep sequencing was applied.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149227" }, "primaryId" : "GEO:GSE149227", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149227" } ] }, "title" : "RNA-seq analysis of brain tissue treated by VEGFC in BDL-induced cirrhotic rat with hepatic encephalopathy", "dateAssigned" : "2020-04-23T00:00:00.000-05:00", "summary" : "Conclusion: Promoting meningeal lymphatic drainage and enhancing waste clearance improves HE. Manipulation of meningeal lymphangiogenesis could be a new therapeutic strategy for the treatment of HE.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149230" }, "primaryId" : "GEO:GSE149230", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149230" } ] }, "title" : "Comparison of the hepatic effects of phenobarbital in chimeric mice containing either rat or human hepatocytes with humanized constitutive androstane receptor (CAR) and pregnane X receptor (PXR) mice (hCAR/hPXR mice) [rat liver experiments]", "dateAssigned" : "2020-04-23T00:00:00.000-05:00", "summary" : "Using a chimeric mouse humanized liver model, we provided evidence that human hepatocytes are refractory to the mitogenic effects of rodent constitutive androstane receptor (CAR) activators. To evaluate the functional reliability of this model, the present study examined mitogenic responses to phenobarbital (PB) in chimeric mice transplanted with rat hepatocytes, since rats are responsive to CAR activators. Treatment with 1000 ppm PB for 7 days significantly increased replicative DNA synthesis (RDS) in rat hepatocytes of the chimeric mice, demonstrating that the transplanted hepatocyte model is functionally reliable for cell proliferation analysis. Treatment of humanized CAR and pregnane X receptor (PXR) mice (hCAR/hPXR mice) with 1000 ppm PB for 7 days significantly increased hepatocyte RDS together with increases in several mitogenic genes. Global gene expression analysis was performed with liver samples from this and from previous studies focusing on PB-induced Wnt/β-catenin signaling, and showed that altered genes in hCAR/hPXR mice clustered most closely with liver tumor samples from a diethylnitrosamine/PB initiation/promotion study than with wild type mice. However, different gene clusters were observed for chimeric mice with human hepatocytes for Wnt/ß-catenin signaling when compared to those of hCAR/hPXR mice, wild type mice and liver tumor samples. The results of this study demonstrate clear differences in the effects of PB on hepatocyte RDS and global gene expression between human hepatocytes of chimeric mice and hCAR/hPXR mice, suggesting that the chimeric mouse model is relevant to humans for studies on the hepatic effects of rodent CAR activators, whereas the hCAR/hPXR mouse is not.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32735318" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149285" }, "primaryId" : "GEO:GSE149285", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149285" } ] }, "title" : "Transcriptome analysis of mesothelial cells induced by intraperitoneal injections of crocidolite in rats", "dateAssigned" : "2020-04-24T00:00:00.000-05:00", "summary" : "Malignant mesothelioma (MM) is an aggressive tumor strongly associated with asbestos exposure. The granuloma capturing crocidolite contribute to mutagenesis, cell death and regenerative activity. To clarify the biological responses of mesothelial cells after crocidolite exposure, we compared the microarray gene expression profiles of no treatment and crocidolite exposure (1 wks) mesothelial cells induced by intraperitoneal injections.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32863225" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149286" }, "primaryId" : "GEO:GSE149286", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149286" } ] }, "title" : "Role of tobacco smoke on lung response to crystalline silica exposure in rats", "dateAssigned" : "2020-04-24T00:00:00.000-05:00", "summary" : "Previous studies have shown that smoking induces oxidative stress and inflammation, known factors that coincide with the development and progression of lung toxicity in response to crystalline silica exposure. Nevertheless, the precise role of tobacco smoke exposure on the lung response to tobacco smoke exposure and the underlying mechanisms remain largely elusive. Therefore, the objective of the present study was to determine the effect of smoking, if any, on silica-induced pulmonary toxicity and the underlying molecular mechanisms. Pulmonary toxicity and lung gene expression profiles were determined in rats exposed to air, crystalline silica, tobacco smoke, or crystalline silica plus tobacco smoke. Silica exposure resulted in significant pulmonary toxicity which was further exacerbated by tobacco smoke exposure in the rats. Significant differences in the gene expression profiles were detected in the lungs of the rats exposed to tobacco smoke, silica or a combination of both compared with the air exposed control rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149297" }, "primaryId" : "GEO:GSE149297", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149297" } ] }, "title" : "ADRB3 overexpression in rat", "dateAssigned" : "2020-04-24T00:00:00.000-05:00", "summary" : "Effect of endothelial overexpression of ADBR3 in rats on the cardiac transcriptome", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33034410" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149317" }, "primaryId" : "GEO:GSE149317", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149317" } ] }, "title" : "Transcriptome profiling of rat brain samples in two age groups in responding to intracerebral hemorrhage", "dateAssigned" : "2020-04-24T00:00:00.000-05:00", "summary" : "Aging-induced decline of endogenous neuroprotection has been shown to aggravate intracerebral hemorrhage (ICH)-induced acute brain injury, however, the underlying mechanisms in brain are still little known. In this study, we applied a rat ICH model to study the transcriptional responses in the early and late aging (13-month and 22-month old) rats that show substantial differences in brain damage and recovery. Transcriptome analysis (RNA-seq) reveals that brain expression of neuroinflammation genes is similarly and selectively upregulated in ICH, which includes genes in the cellular response to interferon gamma function. We show that the anti-IFN-γ treatment effectively reduces ICH-induced acute brain injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33071720" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149364" }, "primaryId" : "GEO:GSE149364", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149364" } ] }, "title" : "RNA sequencing of rodent myocardial tissue when subjected to a myocardial infarction (MI) or an MI and a surgical device (TRD) for 12 weeks.", "dateAssigned" : "2020-04-26T00:00:00.000-05:00", "summary" : "Conclusions: RNA sequencing revealed an activation of multiple cellular pathways with the device group.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149498" }, "primaryId" : "GEO:GSE149498", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149498" } ] }, "title" : "LncRNA sequencing in dorsal root ganglion cultured with high sugar content", "dateAssigned" : "2020-04-28T00:00:00.000-05:00", "summary" : "Primary isolated rat dorsal root ganglion nerve cells (DRGs) were cultured with high glucose in vitro and divided into normal culture group and high glucose culture group", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149514" }, "primaryId" : "GEO:GSE149514", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149514" } ] }, "title" : "Identification of gene modulating vascular inflammation using chromosome 2 fragment substitutions and RNA sequencing [RNA-Seq]", "dateAssigned" : "2020-04-28T00:00:00.000-05:00", "summary" : "Chromosome 2 introgression from normotensive Brown Norway (BN) rats into hypertensive Dahl salt-sensitive (SS) background (consomic S2B) reduced blood pressure (BP) and vascular inflammation under normal salt diet (NSD). We hypothesized that BN chromosome 2 contains anti-inflammatory genes that could reduce BP elevation and vascular inflammation in rats fed NSD and high salt diet (HSD). We used chromosome 2 fragment substitutions to map chromosome 2 portion associated with vascular inflammation changes and next generation sequencing (NGS) to profile messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs) in thoracic descending aorta of SS and congenic rats fed NSD or HSD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33161775" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149515" }, "primaryId" : "GEO:GSE149515", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149515" } ] }, "title" : "Identification of gene modulating vascular inflammation using chromosome 2 fragment substitutions and RNA sequencing [miRNA-Seq]", "dateAssigned" : "2020-04-28T00:00:00.000-05:00", "summary" : "Chromosome 2 introgression from normotensive Brown Norway (BN) rats into hypertensive Dahl salt-sensitive (SS) background (consomic S2B) reduced blood pressure (BP) and vascular inflammation under normal salt diet (NSD). We hypothesized that BN chromosome 2 contains anti-inflammatory genes that could reduce BP elevation and vascular inflammation in rats fed NSD and high salt diet (HSD). We used chromosome 2 fragment substitutions to map chromosome 2 portion associated with vascular inflammation changes and next generation sequencing (NGS) to profile microRNAs in thoracic descending aorta of SS and congenic rats fed NSD or HSD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33161775" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149517" }, "primaryId" : "GEO:GSE149517", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149517" } ] }, "title" : "Profiling the immune cell gene signature of in vivo model of IBD", "dateAssigned" : "2020-04-28T00:00:00.000-05:00", "summary" : "Identification of genes differentially expressed in inflamed and intact colon samples of TNBS treated in vivo rat model of Inflammatory Bowel Disease", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36177008" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149540" }, "primaryId" : "GEO:GSE149540", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149540" } ] }, "title" : "Alzheimer's disease-related dysregulation of mRNA translation causes key pathological features with ageing", "dateAssigned" : "2020-04-28T00:00:00.000-05:00", "summary" : "Primary rat cortical neurons and treated with AB for 24h. RNA-seq on total and ribosome-enriched sucrose cushion", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32546772" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149542" }, "primaryId" : "GEO:GSE149542", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149542" } ] }, "title" : "Evidence of superior and inferior sinoatrial nodes in the mammalian heart [Rat]", "dateAssigned" : "2020-04-28T00:00:00.000-05:00", "summary" : "We report the application of RNA sequencing technology for high-throughput profiling of regionally separated sinoatrial nodal tissues from rat hearts. We find that both the superior and inferior regions of these sinoatrial nodal tissues (termed sSAN and iSAN, respectively) possess statistically comparable levels of cardiac ion channels, receptors, neural proteins, and transcription factors. This study provides new insights into regional molecular expression of pacemaking tissue in the right atria.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33357580" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149561" }, "primaryId" : "GEO:GSE149561", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149561" } ] }, "title" : "The cytoplasmic SYNCRIP mRNA interactome of mammalian neurons", "dateAssigned" : "2020-04-29T00:00:00.000-05:00", "summary" : "SYNCRIP, a member of the cellular heterogeneous nuclear ribonucleoprotein (hnRNP) family of RNA binding proteins, regulates various aspects of neuronal development and plasticity. Although SYNCRIP has been identified as a component of cytoplasmic RNA granules in dendrites of mammalian neurons, only little is known about the specific SYNCRIP target mRNAs that mediate its effect on neuronal morphogenesis and function. Here, we present a comprehensive characterization of the cytoplasmic SYNCRIP mRNA interactome using iCLIP in primary rat cortical neurons. We identify hundreds of bona fide SYNCRIP target mRNAs, many of which encode for proteins involved in neurogenesis, neuronal migration and neurite outgrowth. From our analysis, the stabilization of mRNAs encoding for components of the microtubule network, such as doublecortin (Dcx), emerges as a novel mechanism of SYNCRIP function in addition to the previously reported control of actin dynamics. Furthermore, we found that SYNCRIP interacts with miRISC and synergizes with pro-neural miRNAs, such as miR-9. Based on our findings, we propose a model whereby SYNCRIP promotes early neuronal differentiation by a two-tier mechanism involving the stabilization of pro-neural mRNAs by direct 3’UTR interaction and the repression of anti-neural mRNAs in a complex with neuronal miRISC. Together, our findings provide a rationale for future studies investigating the function of SYNCRIP in mammalian brain development and disease.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149648" }, "primaryId" : "GEO:GSE149648", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149648" } ] }, "title" : "A transcriptomic analysis of dorsal root ganglia (DRG) with tumor cell injection (TCI, Walker 256 mammary gland carcinoma cell)", "dateAssigned" : "2020-04-30T00:00:00.000-05:00", "summary" : "The present study is aimed to analyze the transcriptomic changes across the generation and development of cancer induced bone pain (CIBP) in primary afferent neuron, which would provide a comprehensive understanding of the molecular mechanisms of CIBP. The transcriptomic profiles of primary afferent neuron in DRG from different time points were examined by RNAseq technique, including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Our study provide the first detailed analysis of DRG transcriptomes during the generation and development of CIBP.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34025351" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149657" }, "primaryId" : "GEO:GSE149657", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149657" } ] }, "title" : "RNA-seq analysis lncRNA and mRNA between crushed sciatic nerves and intact contralateral nerves", "dateAssigned" : "2020-04-30T00:00:00.000-05:00", "summary" : "To investigate the potential function of lncRNAs in Schwann cell (SCs) response to sciatic nerve damage and repair, we extracted the total RNA of crushed sciatic nerves and intact contralateral nerves for RNA-sequencing (RNA-seq). A total of 98 differentially expressed lncRNAs (including 46 up-regulated and 52 down-regulated lncRNAs) and 77 differentially expressed mRNAs (including 55 up-regulated and 22 down-regulated mRNAs) were identified between crushed sciatic nerves and normal control (log 2 FC > 1 and p < 0.001).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35768768" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149678" }, "primaryId" : "GEO:GSE149678", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149678" } ] }, "title" : "Gene expression changes in rat liver induced by 6 PA", "dateAssigned" : "2020-04-30T00:00:00.000-05:00", "summary" : "Transcriptomic analysis with six structurally different PA heliotrine, echimidine, lasiocarpine, senecionine, senkirkine, and platyphylline after subacute treatment of rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32419051" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149713" }, "primaryId" : "GEO:GSE149713", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149713" } ] }, "title" : "RNA sequencing analysis of monocrotaline-induced pulmonary arterial hypertension", "dateAssigned" : "2020-05-01T00:00:00.000-05:00", "summary" : "Inflammation and immunity play a causal role in the pathogenesis of pulmonary vascular remodeling and pulmonary arterial hypertension (PAH). However, the pathways and mechanisms by which inflammation and immunity contribute to pulmonary vascular remodeling remain unknown. RNA sequencing was used to analyze the transcriptome in control and rats injected with monocrotaline (MCT) for 1, 2, 3 and 4 weeks. Using the transcriptional profiling of MCT-induced PAH coupled with bioinformatics analysis, we clustered the differentially expressed genes (DEGs) and chose the increased expression patterns associated with inflammatory and immune response. We found the enrichment of Toll-like receptor (TLR) and NOD-like receptor (NLR) pathways and identified NF-κB-mediated inflammatory and immune profiling in MCT-induced PAH. Pathway-based data integration and visualization showed the dysregulated TLR and NLR pathways, including increased expression of TLR2 and NLRP3, and their downstream molecules. Further analysis revealed that the activation of TLR and NLR pathways was associated with upregulation of damage-associated molecular patterns (DAMPs) and RIPK3-mediated necroptosis was involved in the generation of DAMPs in MCT-induced PAH. Collectively, we identify RIPK3-mediated necroptosis and its triggered TLR and NLR pathways in the progression of pulmonary vascular remodeling, thus, providing novel insights into the mechanisms underlying inflammation and immunity in the pathogenesis of PAH.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34635097" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149734" }, "primaryId" : "GEO:GSE149734", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149734" } ] }, "title" : "Application of a Rat Liver Drug Bioactivation Transcriptional Response Assay Early in Drug Development that informs Chemically Reactive Metabolite formation", "dateAssigned" : "2020-05-01T00:00:00.000-05:00", "summary" : "Transcriptional responses in rat liver following treatment with compounds with a range of in vitro covalent binding measurements", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32559301" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149777" }, "primaryId" : "GEO:GSE149777", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149777" } ] }, "title" : "Single-cell RNA-sequencing of mesenteric artery and aorta of 16-18 week old Wistar Kyoto rats or Spontaneously hypertensive rats", "dateAssigned" : "2020-05-03T00:00:00.000-05:00", "summary" : "We reported the cellular heterogeneity in the mesenteric artery and aortic artery", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32589721" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149828" }, "primaryId" : "GEO:GSE149828", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149828" } ] }, "title" : "Developmental Alterations in the Transcriptome of Three Distinct Rodent Models of Schizophrenia", "dateAssigned" : "2020-05-04T00:00:00.000-05:00", "summary" : "Schizophrenia is a debilitating disorder affecting just under 1% of the population. While the symptoms of this disorder do not appear until late adolescence, pathological alterations likely occur earlier, during development in utero. While there is an increasing literature examining transcriptome alterations in patients, it is not possible to examine the changes in gene expression that occur during development in humans that will develop schizophrenia. Here we utilize three distinct rodent developmental disruption models of schizophrenia to examine potential overlapping alterations in the transcriptome, with a specific focus on markers of interneuron development. Specifically, we administered either methylazoxymethanol acetate (MAM), Polyinosinic:polycytidylic acid (Poly I:C), or chronic protein malnutrition, on GD 17 and examined mRNA expression in the developing hippocampus of the offspring 18 hours later. Here, we report alterations in gene expression that may contribute to the pathophysiology of schizophrenia, including significant alterations in interneuron development and ribosome function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32497066" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149829" }, "primaryId" : "GEO:GSE149829", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149829" } ] }, "title" : "Transcriptional response of rat skeletal muscle to prolonged fasting", "dateAssigned" : "2020-05-04T00:00:00.000-05:00", "summary" : "Skeletal muscle is of primary importance for metabolism, thermogenesis and locomotion. However, muscle integrity is inevitably challenged throughout life, and muscle atrophy occurs in various situations, being associated with development of metabolic diseases. There is virtually no fully effective countermeasure today to fight the loss of muscle mass. It is therfore needed to understand in depth how muscle mass is regulated in wasting conditions. The aim of this study was to decipher the transcriptional regulations involved in prolonged fasting-induced muscle wasting during the phase of protein sparing (P2) and the late phase of increased body protein mobilization (P3). The main findings show that gene expression changes reflect well the intense use of lipids as fuels during P2 and increased use of muscle proteins during P3. Changes in muscle transcriptome for downstream signaling of anabolic and catabolic hormones (Smad, NFKB, EiF2alpha-ATF4, autophagy, ubiquitin-proteasome, Foxo, AMPK, PI3K/AKT, and mTOR pathways) and for the response to oxidative stress, transcription and translation processes, and myogenesis are generally consistent with increased muscle protein degradation and repressed synthesis, in a more marked manner during P3 than P2 compared to the fed state. Nevertheless, several changes appeared to be in favour of muscle protein synthesis during fasting, notably at the level of PI3K/AKT and mTOR pathways, transcription and translations processes, and the response to oxidative stress. They could constitute mechanisms that promote protein sparing during P2 and anticipate refeeding during P3 for restoration of the protein compartment. Future studies should examine validity of such targets for improving nitrogen balance during catabolic diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32825252" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149899" }, "primaryId" : "GEO:GSE149899", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE149899" } ] }, "title" : "Reversible and irreversible PAH in a rat model for MCT+Shunt-induced PAH and hemodynamic unloading.", "dateAssigned" : "2020-05-05T00:00:00.000-05:00", "summary" : "PAH was induced by 60mg/kg MCT and an aorto-caval shunt. At different timepoints of PAH progression (day 14, 21 and 28 after MCT-injection), the left lung with PAH was hemodynamically unloading by unilateral orthotopic transplatation into a syngeneic, healthy recipient. All day 14 and 7/10 day 21 transplanted lungs showed reversal of PAH after LTx. All day 28 and 3/10 day 21 transplanted lungs showed PAH progression after LTx. Lung tissue of Reversible and Irreversible PAH and normal controls, acquired at LTx, was compared using RNA-seq.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32727916" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150069" }, "primaryId" : "GEO:GSE150069", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150069" } ] }, "title" : "Development and Application of a Transcriptomic Signature of Bioactivation in an Advanced In Vitro Liver Model to Reduce Drug-induced Liver Injury Risk Early in the Pharmaceutical Pipeline", "dateAssigned" : "2020-05-07T00:00:00.000-05:00", "summary" : "Translation of NRF1/NRF2-mediated liver tissue biomarkers to an in vitro assay using an advanced micropatterned co-culture system (HEPATOPAC®) with primary hepatocytes from male Wistar-Hannover rats or humans", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32559289" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150091" }, "primaryId" : "GEO:GSE150091", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150091" } ] }, "title" : "The gut microbiome regulates memory function.", "dateAssigned" : "2020-05-07T00:00:00.000-05:00", "summary" : "The mammalian gastrointestinal tract contains a diverse ecosystem of microbial species collectively making up the gut microbiome. Emerging evidence highlights a critical relationship between gut microbiota and neurocognitive development. Consumption of unhealthy yet palatable dietary factors associated with obesity and metabolic dysfunction (e.g., saturated fat, added sugar) produces microbiota dysbiosis and negatively impacts neurocognitive function, particularly when consumed during early life developmental periods. Here we explore whether excessive early life consumption of added sugars negatively impacts neurocognitive development via the gut microbiome. Using a rodent model of habitual sugar-sweetened beverage (SSB) consumption during the adolescent stage of development, we first show that excessive early life sugar intake impairs hippocampal-dependent memory function when tested during adulthood while preserving other neurocognitive domains. Gut microbiome genomic sequencing analyses reveal that early life SSB consumption alters the abundance of various bacterial populations, including elevations in operational taxonomic units within the genus Parabacteroides (P. distasonis and P. johnsonii) whose abundance negatively correlated with memory task performance. Additional results reveal that in vivo Parabacteroides enrichment of cultured P. distasonis and P. johnsonii bacterial species in adolescent rats severely impairs memory function during adulthood. Hippocampus transcriptome analyses identify gene expression alterations in neurotransmitter synaptic signaling, intracellular kinase signaling, metabolic function, neurodegenerative disease, and dopaminergic synaptic signaling-associated pathways as potential mechanisms linking microbiome outcomes with memory impairment. Collectively these results identify microbiota dysbiosis as a mechanism through which early life unhealthy dietary patterns negatively impact neurocognitive outcomes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33790226" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150331" }, "primaryId" : "GEO:GSE150331", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150331" } ] }, "title" : "Effects of lipid-specific antibodies (sulphatide, O4) on dissociated myelinating cultures", "dateAssigned" : "2020-05-11T00:00:00.000-05:00", "summary" : "Analysis of the effects of sulphatide specific antibody (O4, 20microg/ml) on myelinating cultures generated from dissociated embryonic rat spinal cord after 24 hours treatment to give insights into effects of lipid-specific antibodies and its implication in demyelinating diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32792006" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150499" }, "primaryId" : "GEO:GSE150499", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150499" } ] }, "title" : "RNA-seq datasets for enhancer RNA quantification in \"Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems\"", "dateAssigned" : "2020-05-13T00:00:00.000-05:00", "summary" : "This dataset contains total RNA sequencing results from rat embryonic cortical, hippocampal, and striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 1hr prior to RNA extraction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37333110" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150567" }, "primaryId" : "GEO:GSE150567", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150567" } ] }, "title" : "Lung response to crystalline nanocellulose exposure in rats", "dateAssigned" : "2020-05-14T00:00:00.000-05:00", "summary" : "Crystalline nanocellulose (CNC) is an emerging nanomaterial with multiple commercial and industrial applications. Occupational exposure to CNC during the production and/or use of products containing the nanomaterial potentially resulting in adverse health effects among workers is possible. Therefore, there is an immediate need to determine the toxicity potential of CNC. Rats were exposed to either air or CNC (20 mg/m^3, 6 hours/day, 5 days/week, 14 days) and lung toxicity was determined one day following termination of the exposures. Compared to the control rats, the CNC exposed rats exhibited moderate changes in lung histology. Lactate dehydrogenase activity and the number of phagocytes present in the bronchoalveolar lavage were higher in the CNC exposed rats, compared with the controls. Global gene expression profiling identified 531 genes whose expressions were significantly different (fold change >1.5 and FDR p <0.05) in the lungs of the CNC exposed rats, compared with the controls. In summary, the data demonstrated the induction of pulmonary toxicity and global gene expression changes in the lungs of the rats in response to inhalation exposure to CNC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33602020" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150589" }, "primaryId" : "GEO:GSE150589", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150589" } ] }, "title" : "ATAC-seq datasets for chromatin accessibility quantification in \"Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems\"", "dateAssigned" : "2020-05-14T00:00:00.000-05:00", "summary" : "This dataset contains Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat embryonic cortical, hippocampal, and striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 1hr.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37333110" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150598" }, "primaryId" : "GEO:GSE150598", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150598" } ] }, "title" : "ATP mediates neuropathic pain of neuromyelitis optica spectrum disorder via microglial activation", "dateAssigned" : "2020-05-14T00:00:00.000-05:00", "summary" : "Intractable neuropathic pain is recognized as a common symptom of neuromyelitis optica spectrum disorder (NMOSD). However, the underlying mechanism of NMOSD pain remains to be elucidated. Here, we established NMOSD pain model by injecting anti-AQP4 recombinant autoantibodies (AQP4-Ab) generated from NMOSD patient’s plasmablasts into rat spinal cords and confirmed the development of mechanical allodynia. AQP4-Ab mediated extracellular ATP release from astrocytes and pharmacological inhibition of ATP receptor reversed mechanical allodynia in NMOSD pain model. Furthermore, transcriptome analysis revealed microglia activation and IL-1β elevation in NMOSD spinal cord. Inhibition of microglia activation and neutralization of IL-1β also attenuated neuropathic pain in NMOSD rat model. In addition, the human CSF ATP concentration was significantly higher in the acute and remission phase of NMOSD than in multiple sclerosis and other neurological disorder patients. These findings indicate ATP, microglial activation and IL-1β secretion orchestrates the pathogenesis of NMOSD neuropathic pain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34419102" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150646" }, "primaryId" : "GEO:GSE150646", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150646" } ] }, "title" : "Increased expression of myelin-associated genes in frontal cortex of SNCA overexpressing rats and Parkinson’s disease patients", "dateAssigned" : "2020-05-15T00:00:00.000-05:00", "summary" : "Parkinson’s disease is an age-dependent neurodegenerative disorder. Besides characteristic motor symptoms, patients suffer from cognitive impairments linked to pathology in cortical areas. Due to obvious challenges in tracing molecular perturbations underlying alterations in human brain over time, we took advantage of a well-characterized rat model. Using RNA sequencing, we profiled the frontocortical transcriptome of post-mortem patient samples and aligned expression changes with perturbation patterns obtained in the model at 5 and 12 months of age reflecting a presymptomatic and symptomatic time point. Integrating cell type-specific reference data, we identified a shared expression signature between both species that pointed to oligodendrocyte-specific, myelin-associated genes. Drawing on longitudinal information from the model, their nearly identical upregulation in both species allowed tracing them to two distinctive perturbance modes they originate from. While one mode exhibited age-independent alterations that affected genes like PLP1, the other mode, impacting on genes like MAG, was characterized by interferences of disease gene and adequate adaptations of gene activity along ageing. Our results highlight that even for a small set of functionally linked genes distinct interference mechanisms may underly disease progression that cannot be distinguished by examining the terminal point alone but instead require longitudinal interrogation of the system.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33017301" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150649" }, "primaryId" : "GEO:GSE150649", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150649" } ] }, "title" : "Maternal High Fat Diet and Diabetes Disrupts Transcriptomic Pathways that Regulate Cardiac Metabolism and Cell Fate in Newborn Rat Hearts", "dateAssigned" : "2020-05-15T00:00:00.000-05:00", "summary" : "We used gene expression profiling to investigate the overall transcriptional signature of newborn rat offspring exposed to the combination of maternal diabetes and maternal high fat diet.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33042024" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150689" }, "primaryId" : "GEO:GSE150689", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150689" } ] }, "title" : "Lung response to crystalline silica exposure in rats", "dateAssigned" : "2020-05-15T00:00:00.000-05:00", "summary" : "Exposure to crystalline silica results in serious health effects, most notably, silicosis and cancer. An understanding of the silica-induced lung toxicity is critical for the intervention and/or prevention of its adverse health effects. Rats were exposed by inhalation to air or crystalline silica (15 mg/m3, 6 hours/day for 5 days). At post-exposure time intervals of 1, 3, 6, 9, 12, and 18 months, the control and silica exposed rats were euthanized, and lung toxicity and gene expression profiles determined. Histological changes indicative of lung toxicity detected in the silica exposed rats included infiltration of neutrophils, thickening of alveolar epithelium, and fibrosis. Significant increases in lactate dehydrogenase activity, number of phagocytes, and inflammatory cytokine levels were detected in the bronchoalveolar lavage (BAL) obtained from the silica exposed rats compared with the corresponding time-matched controls. Significant changes in lung gene expression profiles, corresponding to the changes in the lung toxicity parameters analyzed, were detected in the silica exposed rats. The BAL parameters of toxicity and inflammation peaked at the 12-months post-exposure time interval and declined subsequently. However, lung fibrosis continued to progress being highest at the 18-month post-exposure time interval. These results suggest that inflammation may be required for the initiation but not for the progression and/or maintenance of lung fibrosis in response to silica exposure in the rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150710" }, "primaryId" : "GEO:GSE150710", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150710" } ] }, "title" : "Next Generation Sequencing Facilitates Quantitative Analysis of TRAP from grafted human neural stem cells in stroke and naïve rat brains", "dateAssigned" : "2020-05-17T00:00:00.000-05:00", "summary" : "Conclusions: Our study represents the first detailed analysis of grafted hNSC transcriptome, with biologic replicates, generated by TRAPseq technology. TRAPseq and RSEM could be applied to many xenograft cell transplantation paradigms. With this approach we can start to predict upstream regulators that signal between the host and graft, and to predict the downstream signaling pathways and biological processes these upstream regulators might affect.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37043353" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150841" }, "primaryId" : "GEO:GSE150841", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150841" } ] }, "title" : "S-allylmercaptocysteine Improves NAFLD by Enhancing AhR/Nrf2-mediated Drug Metabolising Enzymes and Reducing NF-κB/IκBα and NLRP3/6-mediated Inflammation", "dateAssigned" : "2020-05-19T00:00:00.000-05:00", "summary" : "We investigated the novel molecular mechanisms of the antioxidant and anti-inflammatory properties of S-allylmercaptocysteine (SAMC) based on a transcriptomic study in a non-alcoholic fatty liver disease (NAFLD) rat model. NAFLD was induced in Sprague-Dawley rats by feeding with a high fat diet (HFD) for 12 weeks. 200mg/kg SAMC was fed by oral gavage for 4 weeks from 9-12 week. We found that SAMC co-administration attenuated HFD-induced liver injury, including the increased serum ALT, hepatic oxidative stress and inflammation. Transcriptomic analysis revealed that SAMC dramatically induced the XRE- and ARE-driven drug metabolising enzymes (DMEs) including Akr7a3, Akr1b8, and NQO1. The nuclear translocation of the upstream regulator of xenobiotics metabolism, AhR, and regulator of antioxidant responses, Nrf2, were significantly increased by SAMC treatment. Furthermore, SAMC counteracted the effects of HFD on NF-κB/IκB and NLRP3/6 pathways with decreasing protein levels of ASC, cleaved caspase-1, IL-18 and IL-1β. These results were further verified in another mice NASH model induced by an MCD diet with SAMC co-administration. Conclusion: we propose that SAMC triggers AhR/Nrf2-mediated antioxidant responses which may further suppress the NLRP3/6 inflammasome pathway and NF-κB activation, contributing to the improvement of NAFLD/NASH.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150939" }, "primaryId" : "GEO:GSE150939", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150939" } ] }, "title" : "Gene expression within the periaqueductal gray in Pink1 knockout rats", "dateAssigned" : "2020-05-20T00:00:00.000-05:00", "summary" : "Conclusions: Overall, this work supports the premise that gene expression changes in the PAG may contribute to the vocal behavioral and deficits observed in this PD rat model. Additionally, this dataset identifies genes that represent new therapeutic targets for PD voice disorders.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36172466" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150950" }, "primaryId" : "GEO:GSE150950", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE150950" } ] }, "title" : "Distinct transcriptomic profiles in the dorsal hippocampus and prelimbic cortex are transiently regulated following episodic learning", "dateAssigned" : "2020-05-20T00:00:00.000-05:00", "summary" : "A fundamental, evolutionarily conserved biological mechanism required for long-term memory formation is rapid induction of gene transcription upon learning in relevant brain areas. For episodic types of memories, two regions undergoing this transcription are the dorsal hippocampus (dHC) and prelimbic (PL) cortex. Whether and to what extent these regions regulate similar or distinct transcriptomic profiles upon learning remains to be understood. Here, we used RNA sequencing in the dHC and PL cortex of male rats to profile their transcriptomes in untrained conditions (baseline) and at 1 hour and 6 days after inhibitory avoidance learning. We found that, out of 33,713 transcripts, over 14,000 were significantly expressed at baseline in both regions and approximately 3,000 were selectively enriched in each region. Gene Ontology biological pathway analyses indicated that commonly expressed pathways included synapse organization, regulation of membrane potential, and vesicle localization. The enriched pathways in the dHC were gliogenesis, axon development, and lipid modification, while in the PL cortex included vesicle localization and synaptic vesicle cycle. At 1 hour after learning, 135 transcripts changed significantly in the dHC and 478 in the PL cortex; of these, only 34 were shared. Biological pathways most significantly regulated by learning in the dHC were protein dephosphorylation, glycogen and glucan metabolism, while in the PL cortex were axon development and axonogenesis. The transcriptome profiles returned to baseline by 6 days after training. Thus, a significant portion of dHC and PL cortex transcriptomic profiles is divergent and their regulation upon learning is largely distinct and transient.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33536202" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151209" }, "primaryId" : "GEO:GSE151209", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151209" } ] }, "title" : "Thyroarytenoid muscle gene expression in Pink1 knockout rats", "dateAssigned" : "2020-05-26T00:00:00.000-05:00", "summary" : "Loss of function in the PTEN-induced kinase 1 gene (Pink1) causes an early-onset, autosomal recessive form of PD. The translational Pink1-/- rat shows cranial sensorimotor deficits including: declines in ultrasonic vocalization, negative impacts on social vocal function, and alterations to thyroarytenoid muscle structure. The aim of this study was to identify differentially expressed genes using RNA-sequencing and bioinformatic analysis of the thyroarytenoid muscle of male Pink1-/- rats compared to wildtype controls. To construct gene co-expression networks and gene modules, a WGCNA was used to identify biological networks of interest including where Pink1 was a central node with interconnecting genes. Data are congruent with previous findings demonstrating changes to thyroarytenoid muscle structure. These data are consistent with the hypothesis that differences in peripheral biology may influence the early pathogenesis of vocalizations at the level of the thyroarytenoid muscle.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36172466" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151220" }, "primaryId" : "GEO:GSE151220", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151220" } ] }, "title" : "RNA-seq data of liver samples in FMT recipient rats", "dateAssigned" : "2020-05-26T00:00:00.000-05:00", "summary" : "DHEA-shaped gut microbiota was transplantated to pseudo germ- free rats. Glucose intolerance, liver lipid accumulation and dyslipidemia were observed in recipient rats. Therefore, liver gene expression of these recipient rats were investigated.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33957990" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151252" }, "primaryId" : "GEO:GSE151252", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151252" } ] }, "title" : "RNA polymerase II (RNAPII) ChIP-seq analysis evaluating effects of Cdk7 inhibitor THZ1 on responses of neonatal rat ventricular myocytes (NRVM) to adrenergic receptor agonist phenylephrine (PE)", "dateAssigned" : "2020-05-27T00:00:00.000-05:00", "summary" : "RNA polymerase II (RNAPII) ChIP-seq analysis evaluating effects of Cdk7 inhibitor THZ1 on responses of NRVM to adrenergic receptor agonist PE", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35896549" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151253" }, "primaryId" : "GEO:GSE151253", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151253" } ] }, "title" : "RNA-seq analysis evaluating effects of Cdk7 inhibitor THZ1 on responses of neonatal rat ventricular myocytes (NRVM) to adrenergic receptor agonist phenylephrine (PE)", "dateAssigned" : "2020-05-27T00:00:00.000-05:00", "summary" : "RNA-seq analysis evaluating effects of Cdk7 inhibitor THZ1 on responses of NRVM to adrenergic receptor agonist PE", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35896549" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151402" }, "primaryId" : "GEO:GSE151402", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151402" } ] }, "title" : "Effect of Maternal Separation (MatSep) on renal vasculature isolated from male neonates (Postnatal day 10) and adult (Postnatal day 180)", "dateAssigned" : "2020-05-28T00:00:00.000-05:00", "summary" : "In this dataset, gene expression changes by MatSep at P10 in renal vasculature isolated from neonates, modulate extracellular structure organization, vasculature development, inflammation and angiogenesis. The long -term effects of MatSep on renal vasculature gene expression is assessed at P180, which reveal clusters of genes with short, long, and downstream changes in expression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151458" }, "primaryId" : "GEO:GSE151458", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151458" } ] }, "title" : "Primordial Germ Cell Transgenerational Sperm DNA Methylation Epimutations Following Ancestral Vinclozolin Exposure", "dateAssigned" : "2020-05-29T00:00:00.000-05:00", "summary" : "Previously the agricultural fungicide vinclozolin was found to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs) termed epimutations that help mediate this epigenetic inheritance. The current study was designed to investigate the developmental origins of the transgenerational DMRs during gametogenesis. Male control and vinclozolin lineage F3 generation rats were used as a source of embryonic day 13 (E13) primordial germ cells. The DMRs between the control versus vinclozolin lineage samples were determined for this stage.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151477" }, "primaryId" : "GEO:GSE151477", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151477" } ] }, "title" : "Transcriptional profile changes in dedifferentiating Müller glia in mammalian cell culture after treatment with an α7 nicotinic acetylcholine receptor agonist", "dateAssigned" : "2020-05-29T00:00:00.000-05:00", "summary" : "Conclusions: PNU-282987 activation of RPE causes signficant transcript profile changes in MG cell culture that leads to upregulation of the HB-EGF/Ascl1/Lin28 pathway that was seen with RNA-seq profiles and validated with qRT-PCR. Further, these gene expression changes lead to dedifferentation of MG to an RPC-like fate and expression of several retinal RPC markers were found in RNA-seq data set and was validated with immunocytochemistry. Our study is the first to show that activaiton of the α7 nAChR on RPE can lead to MG dedifferentiation and that the HB-EGF/Ascl1/Lin28 pathway is upregulated in these cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151568" }, "primaryId" : "GEO:GSE151568", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151568" } ] }, "title" : "SATB1 promotion of trophoblast stem cell renewal", "dateAssigned" : "2020-06-01T00:00:00.000-05:00", "summary" : "Trophoblast stem (TS) cell renewal and differentiation are essential processes in placentation. Here, we have identified the mechanism/targets of chromatin organizer/transcription factor called special AT-rich binding protein 1 (SATB1) action on TS cell renewal by RNA-seq analysis in Rcho-1 TS cells expressing Satb1 shRNAs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151572" }, "primaryId" : "GEO:GSE151572", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151572" } ] }, "title" : "Effect of emodin on long non-coding RNA-mRNA networks in rats with severe acute pancreatitis-induced acute lung injury", "dateAssigned" : "2020-06-01T00:00:00.000-05:00", "summary" : "Long non-coding RNAs (lncRNAs) reportedly contribute to disease pathogenesis and drug treatment effects. Both emodin and dexamethasone (DEX) have been used for the treatment of severe acute pancreatitis-associated acute lung injury (SAP-ALI). However, lncRNA regulation networks related to SAP-ALI pathogenesis and drug treatment are unreported. In this study, lncRNAs and mRNAs in the lung tissue of SAP-ALI and control rats, with or without drug treatment (emodin or DEX), were assessed by RNA sequencing. Results showed that both emodin and DEX were therapeutic for SAP-ALI and that mRNA and lncRNA levels differed between untreated and treated SAP-ALI rats. Gene expression profile relationships for emodin treated and control rats were higher than DEX treated and untreated animals. By comparison of control and SAP-ALI animals, more upregulated than downregulated mRNAs and lncRNAs were observed with emodin treatment. For DEX treatment, more downregulated than upregulated mRNAs and lncRNAs were observed. Functional analysis demonstrated both upregulated mRNA and co-expressed genes with upregulated lncRNAs were enriched in inflammatory and immune response pathways. Further, emodin associated lncRNAs and mRNAs co-expressed modules were different from those associated with DEX. Quantitative polymerase chain reaction demonstrates that selected lncRNA and mRNA co-expressed modules were different in the lung tissue of emodin and DEX treated rats. Also, emodin had different effects compared to DEX on the co-expression network of lncRNAs Rn60_7_1164.1 and AABR07062477.2 for the blue lncRNA module and Nrp1 for the green mRNA module. In conclusion, this study provides evidence that emodin may be a suitable alternative or complementary medicine for treatment of SAP-ALI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33438315" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151608" }, "primaryId" : "GEO:GSE151608", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151608" } ] }, "title" : "Histone methylation regulates gene expression in the round spermatids to set the RNA payloads of sperm", "dateAssigned" : "2020-06-02T00:00:00.000-05:00", "summary" : "Gene expression during spermatogenesis undergoes significant changes due to a demanding sequence of mitosis, meiosis and differentiation. Round spermatids have to prepare for DNA condensation as well as synthesize transcripts of genes required for the differentiation process. However, the mechanisms of gene activation and silencing in round spermatids remain largely unknown. We employed ChIP-seq to figure out the correlation of H3K4me3 and H3K9me3 marks with transcriptional activation and silencing in round spermatids. Out of about 2800 genes identified by H3K4me3 chipseq, transcriptome sequencing in purified round spermatids showed the presence of transcripts corresponding to about 64% of the genes. On the other hand, only about 25% of H3K9me3 enriched genes showed transcription in round spermatids, that too at very low levels. In conclusion, H3K4me3 enrichment in round spermatids correlates significantly with gene expression and H3K9me3 correlates with gene silencing, both of which are equally important for successful spermatogenesis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151615" }, "primaryId" : "GEO:GSE151615", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151615" } ] }, "title" : "Axon-enriched lincRNA ALAE is required for axon elongation via regulating local mRNA translation", "dateAssigned" : "2020-06-02T00:00:00.000-05:00", "summary" : "Long intergenic noncoding RNAs (lincRNAs) are critical regulators involved in diverse biological processes. However, the roles and related mechanisms of lincRNAs in axon development are largely unknown. To seek the axon-enriched lincRNAs in DRG neurons, we performed high-throughput RNA-seq of cultured rat dorsal root ganglion (DRG) neurons at P0 to profile lincRNAs. Profiling of highly expressed lincRNAs in RNA-seq and their enrichment in the axon of DRG neurons. We report a previously unappreciated axon-enriched lincRNA regulating axon elongation, thus referred to as ALAE. ALAE functionally associates with KHSRP for preventing KHSRP binding on Gap43 mRNA, thereby maintaining GAP43 synthesis and facilitating axon elongation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151684" }, "primaryId" : "GEO:GSE151684", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151684" } ] }, "title" : "Genome-wide maps of DNA methylation state in 2-week rat IUGR islets", "dateAssigned" : "2020-06-02T00:00:00.000-05:00", "summary" : "Intrauterine growth restriction (IUGR) increases the risk of developing type 2 diabetes in adulthood. A rat model of IUGR induced by bilateral uterine artery ligation at day 18 of gestation, which reduces the blood supply and critical substrates to the fetus, was used to assess the alterations of genome-wide DNA methylation in IUGR islets. At 2 weeks of age, pancreatic islets were isolated and genomic DNA were extracted for TruSeq-HELP tagging assay. Cytosine methylation was compared in the study.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34894232" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151690" }, "primaryId" : "GEO:GSE151690", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151690" } ] }, "title" : "Isthmin-1 is a novel mediator of experimental glomerulonephritis through a pro-apoptotic action in podocytes", "dateAssigned" : "2020-06-03T00:00:00.000-05:00", "summary" : "Focal segmental glomerulosclerosis (FSGS) is a leading cause of end stage renal disease and remains without specific treatment. To identify novel actors involved in the progression of FSGS, we used an experimental model of nephroangiosclerosis with FSGS in rats and performed a differential transcriptomic analysis. Among the genes that were several-fold upregulated in glomeruli, was Isthmin-1 (ISM), an ‘unknown’ to the kidney gene. The objective of the present study was to find if and what role plays ISM to renal pathophysiology.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36769045" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151881" }, "primaryId" : "GEO:GSE151881", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151881" } ] }, "title" : "Infection of rat epithelial cells with a Salmonella typhimurium strain expressing Rck, PagN and the T3SS1 system (14028Sur) and two Salmonella typhimurium strains invalidated for entry factors (i.e. D(rck, pagN) and DinvASur)", "dateAssigned" : "2020-06-05T00:00:00.000-05:00", "summary" : "The aim of this work was to study the cellular gene expression profiles associated with the entry mechanism of Salmonella typhimurium. Whatever the bacterial strain used for infection, the expression of numerous genes associated with the extracellular matrix was modified.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36600181" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151882" }, "primaryId" : "GEO:GSE151882", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151882" } ] }, "title" : "Evaluation of the physiological effects of a biotechnologically produced oyster mushroom in the liver of obese Zucker rats by transcriptomics", "dateAssigned" : "2020-06-05T00:00:00.000-05:00", "summary" : "The hypothesis was tested that biotechnologically produced Pleurotus sajor-caju (PSC) influences metabolic health of obese Zucker rats. To test this, obese Zucker rats were randomly assigned to 2 groups of 12 rats each with similar body weights (BW) and fed diets either without (OC) or with 5 % PSC (OPSC) for 4 weeks and hepatic transcript profiling was performed. Transcriptomics of the liver revealed a total of 580 transcripts differentially expressed between OPSC and OC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32997875" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151971" }, "primaryId" : "GEO:GSE151971", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE151971" } ] }, "title" : "Site-specific Wnt signalling explains regional differences in bone physiology – Evidence from a cross-species RNA-Seq study comparing osteocyte transcriptomes in the tibia and skull", "dateAssigned" : "2020-06-07T00:00:00.000-05:00", "summary" : "Local site-specific differences between bones in different regions of the skeleton account for their different properties and functions. To identify mechanisms behind these differences, we have performed a cross-species study comparing RNA transcriptomes of cranial and tibial osteocytes, from bones with very different primary functions and physiological responses, collected from the same individual mouse, rat and rhesus macaque. Bioinformatic analysis was performed to identify 32 genes changed in the same direction between sites and shared across all three species. Several well-established key genes in bone growth and remodelling were upregulated in the tibias of all three species (BMP7, DKK1, FGF1, FRZB, SOST). Many of them associate or crosstalk with the canonical Wnt signalling pathway. These results suggest Wnt signalling-related candidates for different control of regulatory mechanisms in bone homeostasis in the skull and tibia and indicate a different balance between genetically determined structure and feedback mechanisms to strains induced by mechanical loading at the different sites.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33071985" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152126" }, "primaryId" : "GEO:GSE152126", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152126" } ] }, "title" : "Single cell RNA-seq of forebrain cells isolated from wild-type mouse, rat, and chimeric mouse", "dateAssigned" : "2020-06-09T00:00:00.000-05:00", "summary" : "We performed single cell RNA-seq to quantify gene expression in forebrain tissue from the wild-type mouse, rat, and chimeric mouse. Single cell data from WT mouse or rat was used to perform integrative analysis for identifying rat cells and mouse cells in the chimaeras, respectively.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152128" }, "primaryId" : "GEO:GSE152128", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152128" } ] }, "title" : "High-throughput transcriptomics platform for screening hepatotoxicants", "dateAssigned" : "2020-06-09T00:00:00.000-05:00", "summary" : "We introduce a new high-throughput transcriptomics (HTTr) platform comprised of a collagen sandwich primary rat hepatocyte culture and the TempO-Seq assay for screening and prioritizing potential hepatotoxicants. We selected 14 chemicals based on their risk of drug-induced liver injury (DILI) and tested them in hepatocytes at two treatment concentrations. HTTr data was generated using the TempO-Seq whole transcriptome and S1500+ assays. The HTTr platform exhibited high reproducibility between technical replicates (r>0.9) but biological replication was greater for TempO-Seq S1500+ (r>0.85) than for the whole transcriptome (r>0.7). Reproducibility between biological replicates was dependent on the strength of transcriptional effects induced by a chemical treatment. Despite targeting a smaller number of genes, the S1500+ assay clustered chemical treatments and produced gene set enrichment analysis (GSEA) scores comparable to those of the whole transcriptome. Connectivity mapping showed a high-level of reproducibility between TempO-Seq data and Affymetrix GeneChip data from the Open TG-GATES project with high concordance between the S1500+ gene set and whole transcriptome. Taken together, our results provide guidance on selecting the number of technical and biological replicates and support the use of TempO-Seq S1500+ assay for a high-throughput platform for screening hepatotoxicants.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34467220" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152187" }, "primaryId" : "GEO:GSE152187", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152187" } ] }, "title" : "Lung response to oil vapor exposure in rats", "dateAssigned" : "2020-06-10T00:00:00.000-05:00", "summary" : "The lung response to inhalation exposure to oil vapor particles was investigated in a rat model. Adult male Sprague-Dawley rats were exposed by whole-body inhalation to air or an aerosol containing oil vapor particles at concentrations of 300 ppm, 6 hours/day for 1 day (shot-term) or 300 ppm, 6 hours/day, 4 days/week for 4 weeks (long-term). The control and oil vapor exposed rats were euthanized at post-exposure time intervals of 1 and 28 days and lung toxicity determined. Analysis of bronchoalveolar lavage parameters of toxicity such as lactate dehydrogenase activity, oxidant generation, and inflammation did not reveal any significant lung toxicity in the oil vapor exposed rats. Approximately 50 genes each were found significantly differentially expressed in both the short- and long-term exposure groups of the rats at the one-day post-exposure time interval. The data obtained from the present study demonstrated that oil vapor inhalation exposure, under the exposure conditions employed in the present study, did not result in any significant lung toxicity in the rats despite the gene expression changes detected.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152250" }, "primaryId" : "GEO:GSE152250", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152250" } ] }, "title" : "Metabolic dysfunction is integral to TGFb signaling and tissue fibrosis", "dateAssigned" : "2020-06-10T00:00:00.000-05:00", "summary" : "Fibrosis, or the accumulation of extracellular matrix, causes loss of organ function and is a common feature of many chronic diseases. To interrogate core molecular pathways underlying fibrosis, we cross–examine human primary cells from various tissues treated with TGFβ, as well as rodent kidney and liver fibrosis models. Transcriptome analyses reveal that in addition to the known TGFβ signature, cluster of genes involved in fatty acid oxidation are significantly perturbed. Furthermore, defective mitochondrial oxidative phosphorylation and acylcarnitine accumulation are found in fibrotic tissues. Substantial down-regulation of the PGC1α gene is evident in both in vitro and in vivo fibrosis models, suggesting a common node of metabolic signature for all tissue fibrosis. In order to identify suppressors of fibrosis, we carry out a compound library phenotypic screen and identify AMPK and PPAR as highly enriched targets. We further show that pharmacological treatment of MK-8722 (AMPK activator) and MK-4074 (ACC inhibitor) reduce fibrosis in vivo. Altogether, our work demonstrate that metabolic defect is integral to TGFβ signaling and fibrosis, targeting which represents a promising therapeutic approach for multiple fibrotic diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33205063" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152339" }, "primaryId" : "GEO:GSE152339", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152339" } ] }, "title" : "Transcriptome of the Wistar audiogenic rat (WAR) strain following audiogenic seizures", "dateAssigned" : "2020-06-12T00:00:00.000-05:00", "summary" : "The Wistar Audiogenic Rat (WAR) is a model whose rats are predisposed to develop seizures following acoustic stimulation. We aimed to establish the transcriptional profile of the WAR model, searching for genes that help in understanding the molecular mechanisms involved in the predisposition and seizures expression of this strain. RNA-Seq of the corpora quadrigemina of WAR and Wistar rats subjected to acoustic stimulation revealed 64 genes differentially regulated in WAR. We validated twelve of these genes by qPCR in stimulated and naive (nonstimulated) WAR and Wistar rats. Among these, Acsm3 was upregulated in WAR in comparison with both control groups. In contrast, Gpr126 and Rtel1 were downregulated in naive and stimulated WAR rats in comparison with the Wistar controls. Qdpr was upregulated only in stimulated WAR rats that exhibited audiogenic seizures. Our data show that there are genes with differential intrinsic regulation in the WAR model and that seizures can alter gene regulation. We identified new genes that might be involved in the epileptic phenotype and comorbidities of the WAR model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34177758" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152443" }, "primaryId" : "GEO:GSE152443", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152443" } ] }, "title" : "Transcriptional profiling of brain tissues from a Q130 Long Evans Knock-in rat model of Huntington’s disease at 2-, 6- and 12-months of age", "dateAssigned" : "2020-06-14T00:00:00.000-05:00", "summary" : "Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that is characterized by motor, cognitive, and psychiatric alterations. The mutation responsible for this disease is an abnormally expanded and unstable CAG repeat within the coding region of the gene encoding huntingtin (Htt). A collaboration between the CHDI Foundation and Dr. H.P. Nguyen (huu.nguyen-r7w@ruhr-uni-bochum.de) at Universitat Bochum focused on generating a knock-in rat model of HD that contains expanded CAG repeats inserted within the rat huntingtin gene (Hdh) in order to provide a genetic reconstruction of the human causative mutation within the rat model. The goal of this study is RNA expression profiling by RNA sequencing (RNA-seq) in brain tissues of 2-, 6- and 12-month-old heterozygous knock-in rats with uninterrupted CAG length approaching 130 along with littermate control wild-type animals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152538" }, "primaryId" : "GEO:GSE152538", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152538" } ] }, "title" : "Development of gene expression signatures for vein graft restenosis following vascular grafting", "dateAssigned" : "2020-06-15T00:00:00.000-05:00", "summary" : "To further development of our gene expression approach to cardiovascular disease, we have employed microarray expression profiling as a discovery platform to identify genes with the potential to distinguish the therapeutic target of the vein graft restenosis following coronary artery bypass grafting. Vein graft samples were obtained from model rats which received external jugular vein-carotid bypass grafting at different postoperative timepoints (n=3/group; day 7, 14 and 28, respectively). Vein samples were also obtained from control rats without vascular grafting (n=3/group; day 0). Time-dependent gene expression profiles were described with microarray analysis. Expression of three lncRNA-mRNA pairs (AF062402-Src, BC091437-Edg1 and BC166461- Mcam) from this signature were quantified in the same RNA samples by real-time PCR, confirming the accuracy of the microarray data.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33968166" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152593" }, "primaryId" : "GEO:GSE152593", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152593" } ] }, "title" : "Expression data from rat lens epithelial cells after extracapsular lens extraction (ECLE)", "dateAssigned" : "2020-06-16T00:00:00.000-05:00", "summary" : "Using a microarray-based approach, herein we studied the changes in gene expression pattern during rat PCO formation in vivo as a model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33918979" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152616" }, "primaryId" : "GEO:GSE152616", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152616" } ] }, "title" : "Expression data from lens epithelial cells (LECs) from Shumiya cataract rats (SCR) with or without cataract (Cat+ or Cat-)", "dateAssigned" : "2020-06-16T00:00:00.000-05:00", "summary" : "Our study aimed to identify the gene expression patterns during cataract formation in SCRs, which may be responsible for cataractogenesis in SCR.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33204712" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152678" }, "primaryId" : "GEO:GSE152678", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152678" } ] }, "title" : "Glyphosate Induced Transgenerational DNA Methylation and Histone Retention Sperm Epigenetic Biomarkers for Disease", "dateAssigned" : "2020-06-17T00:00:00.000-05:00", "summary" : "The herbicide glyphosate has been shown to promote the epigenetic transgenerational inheritance of pathology and disease in subsequent great-grand offspring (F3 generation). This generational toxicology suggests the impacts of environmental exposures need to assess subsequent generations. The current study was designed to identify epigenetic biomarkers for glyphosate induced transgenerational disease. Following a transient glyphosate exposure of a gestating female rat (F0 generation), the subsequent transgenerational F3 generation, with no direct exposure, were aged to 1 year and animals with specific pathologies identified. The pathologies investigated included prostate disease, kidney disease, obesity, and presence of multiple disease. The sperm were collected from the males and used to identify specific differential DNA methylation regions (DMRs) associated with the pathologies. In addition, the differential histone retention sites (DHRs) were examined for the various pathologies as well. Unique signatures of DMRs and DHRs for each pathology were identified for the specific diseases. Interestingly, at a lower statistical threshold overlapping sets of DMRs and DHRs were identified that were common for all the pathologies. The DMR and DHR gene associations were identified and correlated with known pathology associated genes. While the disease biomarker DMR and DHR did not meet typical statistical significance levels, these results may help design future studies with reduced variability. Observations indicate transgenerational epigenetic biomarkers of disease pathology can potentially be identified in the sperm that can assess disease susceptibility. These biomarkers may also suggest epigenetic diagnostics could be used to facilitate preventative medicine.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35440735" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152720" }, "primaryId" : "GEO:GSE152720", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152720" } ] }, "title" : "Pulmonary effects of inhaled diesel particles in rats", "dateAssigned" : "2020-06-17T00:00:00.000-05:00", "summary" : "The pulmonary response to inhalation exposure to diesel exhaust particles (DEP) was investigated in a rat model. Adult male Sprague-Dawley rats were exposed by whole-body inhalation to air or an aerosol containing DEP at concentrations of 200 or 1000 mg/m3, 6 hours/day for 4 days. The control and DEP-exposed rats were euthanized at post-exposure time intervals of 1, 7, or 27 days and pulmonary inflammatory, cytotoxic and oxidant responses were determined. Analysis of bronchoalveolar lavage parameters of toxicity such as lactate dehydrogenase activity, oxidant generation, and inflammation did not reveal any significant pulmonary toxicity in the DEP-exposed rats. The lung gene expression profiles did not change significantly in the DEP exposed rats compared with the controls. The data obtained from the present study demonstrated that DEP inhalation exposure under the conditions employed in the present study did not result in any significant lung toxicity in the rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152877" }, "primaryId" : "GEO:GSE152877", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152877" } ] }, "title" : "Analysis of hepatic transcriptome modulation exerted by γ-conglutin from lupins in a streptozotocin-induced diabetes model", "dateAssigned" : "2020-06-19T00:00:00.000-05:00", "summary" : "Lupinus albus γ-conglutin is proposed to positively affect glucose metabolism through inhibition of hepatic glucose production and insulin-mimetic activity; however, the action mechanism is not entirely known. Besides, most studies had focused on its effect on molecular targets directly related to glucose metabolism, and few studies have investigated how γ-conglutin may affect the liver gene expression or if it plays a role in other metabolic processes. Therefore, we investigated the influence of γ-conglutin on the liver transcriptome of streptozotocin-induced diabetic rats using DNA microarrays, ontological analyses, and quantitative PCR. Of the 22,000 genes evaluated, 803 and 173 were downregulated and upregulated, respectively. The ontological analyses of the differentially expressed genes revealed that among others, the mitochondria, microtubules, cytoskeleton, and oxidoreductase activity terms were enriched, implying a possible role of γ-conglutin on autophagy. To corroborate the microarray results, we selected and quantified, by PCR, the expression of two genes associated with autophagy (Atg7 and Snx18) and found their expression augmented two and threefold, respectively; indicating a higher autophagy activity in animals treated with γ-conglutin. Although complementary studies are required, our findings indicate for the first time that the hypoglycaemic effects of γ-conglutin may involve an autophagy induction mechanism, a pivotal process for the preservation of cell physiology and glucose homeostasis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32777525" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152945" }, "primaryId" : "GEO:GSE152945", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE152945" } ] }, "title" : "Overexpression of α-SMA led to differential gene expression in INS-1 cells (RNA-seq)", "dateAssigned" : "2020-06-22T00:00:00.000-05:00", "summary" : "The goal of this study was to define the cohort of genes whose expression is regulated by α-SMA function in type 2 diabetic mellitus . Towards this goal, INS-1 cells stably expressing α-SMA (INS-SMA) were established. In addition, a control cells (INS-MOCK) was generated by transfection with empty vector. Subsequently, total RNA was isolated and then performed transcriptome RNA sequence.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153017" }, "primaryId" : "GEO:GSE153017", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153017" } ] }, "title" : "Defective mitochondrial dynamics underlie manganese-induced neurotoxicity", "dateAssigned" : "2020-06-22T00:00:00.000-05:00", "summary" : "Rats were exposed to manganese (Mn) at 25mg/kg for 15 days. After the exposure, the RNA was collected from the striatum tissue (specific part the brain) of the control group (untreated) and Mn-exposed group, and submitted for RNA sequencing to elucidate the transcriptional changes of Mn-induced toxicity in the striatum.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33666854" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153042" }, "primaryId" : "GEO:GSE153042", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153042" } ] }, "title" : "Early life stress leads to gene expression down-regulation in prefrontal cortex [microarray]", "dateAssigned" : "2020-06-23T00:00:00.000-05:00", "summary" : "Early life stress (ELS) is associated with adverse mental health outcomes including anxiety, depression and addiction-like behaviours. While ELS is known to affect the developing brain by leading to increased stress responsiveness and increased glucocorticoid levels, the molecular mechanisms underlying the detrimental effects of ELS remain incompletely characterised. Rodent models have been instrumental in beginning to uncover the molecular and cellular underpinnings of ELS. Limited nesting (LN), an ELS behavioural paradigm with significant improvements over maternal separation, mimics human maternal neglect. We have previously shown that LN leads to anxiety like-behaviours in rats. Here we assessed gene expression changes induced by ELS in rat prefrontal cortex by RNA-sequencing. We show that LN leads primarily to transcriptional repression and identify a molecular signature of LN in rat PFC that is robust to the behavioural paradigm and replicable across rodent species (mouse and rat).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33796639" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153043" }, "primaryId" : "GEO:GSE153043", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153043" } ] }, "title" : "Early life stress leads to gene expression down-regulation in prefrontal cortex [RNA-seq]", "dateAssigned" : "2020-06-23T00:00:00.000-05:00", "summary" : "Early life stress (ELS) is associated with adverse mental health outcomes including anxiety, depression and addiction-like behaviours. While ELS is known to affect the developing brain by leading to increased stress responsiveness and increased glucocorticoid levels, the molecular mechanisms underlying the detrimental effects of ELS remain incompletely characterised. Rodent models have been instrumental in beginning to uncover the molecular and cellular underpinnings of ELS. Limited nesting (LN), an ELS behavioural paradigm with significant improvements over maternal separation, mimics human maternal neglect. We have previously shown that LN leads to anxiety like-behaviours in rats. Here we assessed gene expression changes induced by ELS in rat prefrontal cortex by RNA-sequencing. We show that LN leads primarily to transcriptional repression and identify a molecular signature of LN in rat PFC that is robust to the behavioural paradigm and replicable across rodent species (mouse and rat).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33796639" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153081" }, "primaryId" : "GEO:GSE153081", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153081" } ] }, "title" : "Next Generation Sequencing Facilitates Quantitative Analysis of SPS and Control Rats Model", "dateAssigned" : "2020-06-23T00:00:00.000-05:00", "summary" : "In the present study, we used the single prolonged stress (SPS) model to mimic posttraumatic stress disorder. High-throughput sequencing were utilized to analyze differentially expressed genes (DEGs) in the hippocampus of control and SPS rats. RNA-seq analysis revealed 230 significantly DEGs between the control and SPS groups.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153086" }, "primaryId" : "GEO:GSE153086", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153086" } ] }, "title" : "Long non-coding RNA and mRNA expression profiles in rats with LPS-induced myocardial dysfunction", "dateAssigned" : "2020-06-23T00:00:00.000-05:00", "summary" : "Sepsis is a life-threatening disease that often causes multiple organ dysfunctions. Long noncoding RNAs (lncRNAs) are involved in the pathogenesis and development of sepsis. However, there is little known about the function of lncRNAs in sepsis-induced myocardial dysfunction.To test the hypothesis that dysregulating lncRNAs may be involved in sepsis-induced myocardial dysfunction, we identified differentially expressed (DE) lncRNAs and mRNAs in cardiac tissue by high-throughput sequencing. We constructed coding and non-coding co-expression (CNC) and lncRNA-micro RNA (miRNA)-mRNA competing endogenous networks. The findings will provide useful information for exploring therapeutic candidate targets and new molecular biomarkers of septic myocardial injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153217" }, "primaryId" : "GEO:GSE153217", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153217" } ] }, "title" : "Human placenta-derived mesenchymal stem cells ameliorate diabetic nephropathy", "dateAssigned" : "2020-06-25T00:00:00.000-05:00", "summary" : "The aim of this study is to compare renal transcriptome profiling between diabetic nephropathy (DN) and DN treated with human placenta-derived mesenchymal stem cells (PMSCs) groups. Twelve renal cortex samples (n=6 for each DN and treatment group) were sequenced using Illumina Hiseq 4000. We identified 90 differentially expressed genes between DN and treatment griups with |og2 FoldChange| ≥1 and p value <0.05. Our study represents the first detailed analysis of renal transcriptomes, with biologic replicates, generated by RNA-seq technology.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153275" }, "primaryId" : "GEO:GSE153275", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153275" } ] }, "title" : "Identification of dynamic RNA-binding proteins uncovers key regulators of gene expression in diseased cardiomyocytes", "dateAssigned" : "2020-06-25T00:00:00.000-05:00", "summary" : "Mutations or decreased expression of RNA-binding proteins (RBPs) can lead to cardiomyopathies in humans. Here we defined RBPs in healthy and diseased primary cardiomyocytes at a system-wide level by RNA Interactome Capture. This identified 67 novel cardiomyocyte specific RBPs including several contractile proteins. Furthermore, we identified Cytoplasmic polyadenylation element binding protein 4 (Cpeb4) as a dynamic RBP in diseased cardiomyocytes, regulating cardiac growth both in vitro and in vivo. To study Cpeb4 in cardiomyocytes, we identified mRNAs bound to and regulated by Cpeb4. Cpeb4 regulates cardiac remodeling by differential expression of transcription factors. Among Cpeb4 target mRNAs, two Zinc finger transcription factors (Zeb1 and Zbtb20) were identified. We show that Cpeb4 regulates the translation of these mRNAs and that Cpeb4 depletion increases their expression. Thus, Cpeb4 emerges as critical regulator of cardiomyocyte function by differential binding of specific mRNAs in response to pathological growth stimulation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153278" }, "primaryId" : "GEO:GSE153278", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153278" } ] }, "title" : "Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis [ncRNA-seq]", "dateAssigned" : "2020-06-25T00:00:00.000-05:00", "summary" : "Pulmonary fibrosis is a kind of interstitial lung disease with architectural remodeling of tissues and excessive matrix deposition. Apart from mRNA, microRNA, long non-coding RNA (lncRNA) and circular RNA (circRNA) could also play important roles in the regulatory processes of occurrence and progression of pulmonary fibrosis. In the present study, whole transcriptome sequencing analysis was applied to investigate the expression profiles of mRNAs, lncRNAs, circRNAs and miRNAs. After comparing bleomycin-induced pulmonary fibrosis model lung samples and controls, 286 lncRNAs, 192 mRNAs, 605 circRNAs, and 32 miRNAs were found to be differentially expressed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the potential functions of these DE mRNAs and ncRNAs. Various related GO-BP terms such as “inflammatory response”, “positive regulation of interleukin-2 biosynthetic process”, “Regulation of actin cytoskeleton”, “Notch signaling pathway”, “negative regulation of cellular response to vascular endothelial growth factor stimulus”, and KEGG signal pathways such as “Wnt signaling pathway”, “TNF signaling pathway”, “MAPK signaling pathway”, “Regulation of actin cytoskeleton” were enriched implying potential roles in regulatory process. In addition, two co-expression networks (lncRNA-miRNA-mRNA, circRNA-miRNA-mRNA) were also constructed to understand the internal regulating relationships of these mRNAs and ncRNAs. Our study provides a systematic perspective on the potential functions of these DE mRNAs and ncRNAs during PF process, and could help pave the way for effective therapeutics for this devastating and complex disease.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153294" }, "primaryId" : "GEO:GSE153294", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153294" } ] }, "title" : "Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis [miRNA-seq]", "dateAssigned" : "2020-06-25T00:00:00.000-05:00", "summary" : "Pulmonary fibrosis is a kind of interstitial lung disease with architectural remodeling of tissues and excessive matrix deposition. Apart from mRNA, microRNA, long non-coding RNA (lncRNA) and circular RNA (circRNA) could also play important roles in the regulatory processes of occurrence and progression of pulmonary fibrosis. In the present study, whole transcriptome sequencing analysis was applied to investigate the expression profiles of mRNAs, lncRNAs, circRNAs and miRNAs. After comparing bleomycin-induced pulmonary fibrosis model lung samples and controls, 286 lncRNAs, 192 mRNAs, 605 circRNAs, and 32 miRNAs were found to be differentially expressed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the potential functions of these DE mRNAs and ncRNAs. Various related GO-BP terms such as “inflammatory response”, “positive regulation of interleukin-2 biosynthetic process”, “Regulation of actin cytoskeleton”, “Notch signaling pathway”, “negative regulation of cellular response to vascular endothelial growth factor stimulus”, and KEGG signal pathways such as “Wnt signaling pathway”, “TNF signaling pathway”, “MAPK signaling pathway”, “Regulation of actin cytoskeleton” were enriched implying potential roles in regulatory process. In addition, two co-expression networks (lncRNA-miRNA-mRNA, circRNA-miRNA-mRNA) were also constructed to understand the internal regulating relationships of these mRNAs and ncRNAs. Our study provides a systematic perspective on the potential functions of these DE mRNAs and ncRNAs during PF process, and could help pave the way for effective therapeutics for this devastating and complex disease.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153304" }, "primaryId" : "GEO:GSE153304", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153304" } ] }, "title" : "Gene expression profiling of shRNA transduced rat hippocampal neurons", "dateAssigned" : "2020-06-26T00:00:00.000-05:00", "summary" : "Sirtuin 6 (SIRT6), a member of the sirtuin family, acts as nicotinamide adenine dinucleotide-dependent protein deacetylase, mono-adenosine diphosphate-ribosyltransferase, and fatty acid deacylase and plays critical roles in inflammation, aging, glycolysis, and DNA repair. Accumulating evidence has suggested that SIRT6 is involved in brain functions such as neuronal differentiation, neurogenesis, and learning and memory. However, the precise molecular roles of SIRT6 during neuronal circuit formation are not well understood. In this study, we attemped to elucidate the molecular roles of SIRT6 on neurite development using a primary culture of hippocampal neurons. We observed that SIRT6 was abundantly localized in the nucleus, and its expression was markedly increased during neurite outgrowth and synaptogenesis. Using shRNA-mediated SIRT6 knockdown, we showed that the dendritic length and number of dendrite branches were significantly reduced in SIRT6 knockdown neurons. Microarray and subsequent gene ontology analysis revealed that reducing SIRT6 caused the downregulation of immediate early genes (IEGs) and alteration of several biological processes including MAPK (ERK1/2) signaling. We found that nuclear accumulation of phosphorylated ERK1/2 was significantly reduced in SIRT6 knockdown neurons. Overexpression of SIRT6 promoted dendritic length and branching, but the mutants lacking deacetylase activity had no significant effect on the dendritic morphology. Collectively, the presented findings reveal a role of SIRT6 in dendrite morphogenesis and suggest that SIRT6 may act as an important regulator of the ERK1/2 signaling pathway that mediates IEG expression, which leads to dendritic development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33444676" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153351" }, "primaryId" : "GEO:GSE153351", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153351" } ] }, "title" : "Hepatic transcriptomic alterations for 1,2-bis(tribromophenoxy)ethane (BTBPE) (Firemaster 680) after 5-day exposure in rats", "dateAssigned" : "2020-06-26T00:00:00.000-05:00", "summary" : "A total of 0,0,0,0, and 0 gene transcripts were differentially expressed due to BTBPE treatment after exposure to 0.07, 0.69, 6.88, 68 or 680 mg/kg BTBPE (false discovery rate (FDR) < 0.05).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32904430" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153353" }, "primaryId" : "GEO:GSE153353", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153353" } ] }, "title" : "Hepatic transcriptomic alterations for decabromodiphenylethane (DBDPE) after 5-day exposure in rats", "dateAssigned" : "2020-06-26T00:00:00.000-05:00", "summary" : "A total of 0,0,0,2, and 3 gene transcripts were differentially expressed due to DBDPE treatment after exposure to 0.1, 0.97, 9.71, 97.1 or 970 mg/kg DBDPE (false discovery rate (FDR) < 0.05).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32904430" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153355" }, "primaryId" : "GEO:GSE153355", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153355" } ] }, "title" : "Hepatic transcriptomic alterations for decabromodiphenyl oxide (decaBDE) after 5-day exposure in rats", "dateAssigned" : "2020-06-26T00:00:00.000-05:00", "summary" : "A total of 0,11,27,25, and 30 gene transcripts were differentially expressed due to decaBDE treatment after exposure to 0.1, 0.959, 9.59, 95.9 or 959 mg/kg decaBDE (false discovery rate (FDR) < 0.05).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32904430" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153357" }, "primaryId" : "GEO:GSE153357", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153357" } ] }, "title" : "Hepatic transcriptomic alterations for 1,3,5,7,9,11-hexabromocyclododecane (HBCD) after 5-day exposure in rats", "dateAssigned" : "2020-06-26T00:00:00.000-05:00", "summary" : "A total of 1,2,1,23, and 247 gene transcripts were differentially expressed due to HBCD treatment after exposure to 0.06, 0.641, 6.41, 64.1 or 641 mg/kg HBCD (false discovery rate (FDR) < 0.05).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32904430" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153359" }, "primaryId" : "GEO:GSE153359", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153359" } ] }, "title" : "Hepatic transcriptomic alterations for hexachlorocyclopentadienyl-dibromocyclooctane (HCDBCO) after 5-day exposure in rats", "dateAssigned" : "2020-06-26T00:00:00.000-05:00", "summary" : "A total of 0,0,0,12, and 19 gene transcripts were differentially expressed due to HCDBCO treatment after exposure to 0.05, 0.54, 5.41, 54.1 or 541 mg/kg HCDBCO (false discovery rate (FDR) < 0.05).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32904430" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153360" }, "primaryId" : "GEO:GSE153360", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153360" } ] }, "title" : "Hepatic transcriptomic alterations for polybrominated diphenyl ether 47 (PBDE47) after 5-day exposure in rats", "dateAssigned" : "2020-06-26T00:00:00.000-05:00", "summary" : "A total of 44,28,111,999, and 3195 gene transcripts were differentially expressed due to PBDE47 treatment after exposure to 0.0485, 0.485, 4.85, 48.5 or 485 mg/kg PBDE47 (false discovery rate (FDR) < 0.05).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32904430" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153361" }, "primaryId" : "GEO:GSE153361", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153361" } ] }, "title" : "Hepatic transcriptomic alterations for 2-ethylhexyl-2,3,4,5-tetrabromobenzoate (TBB) after 5-day exposure in rats", "dateAssigned" : "2020-06-26T00:00:00.000-05:00", "summary" : "A total of 1,0,2,2, and 66 gene transcripts were differentially expressed due to TBB treatment after exposure to 0.05, 0.55, 5.50, 55 or 550 mg/kg TBB (false discovery rate (FDR) < 0.05).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32904430" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153363" }, "primaryId" : "GEO:GSE153363", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153363" } ] }, "title" : "Hepatic transcriptomic alterations for tetrabromobisphenol A-bis(2,3-dibromopropyl ether) (TBBPA-DBPE) after 5-day exposure in rats", "dateAssigned" : "2020-06-26T00:00:00.000-05:00", "summary" : "A total of 0,0,0,0,0, and 0 gene transcripts were differentially expressed due to TBBPA.DBPE treatment after exposure to 0.1, 0.94, 9.4, 94.3 or 943 mg/kg TBBPA.DBPE (false discovery rate (FDR) < 0.05).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32904430" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153365" }, "primaryId" : "GEO:GSE153365", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153365" } ] }, "title" : "Hepatic transcriptomic alterations for bis(2-ethylhexyl) tetrabromophthalate (TBPH) after 5-day exposure in rats", "dateAssigned" : "2020-06-26T00:00:00.000-05:00", "summary" : "A total of 0,0,0,0, and 0 gene transcripts were differentially expressed due to TBPH treatment after exposure to 0.07, 0.71, 7.06, 70.6 or 706 mg/kg TBPH (false discovery rate (FDR) < 0.05).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32904430" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153409" }, "primaryId" : "GEO:GSE153409", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153409" } ] }, "title" : "Identification of Cpeb4 binders in cardiomyocyte", "dateAssigned" : "2020-06-28T00:00:00.000-05:00", "summary" : "Mutations or decreased expression of RNA-binding proteins (mRBPs) can lead to cardiomyopathies in humans. Here we defined RBPs in healthy and diseased primary cardiomyocytes at a system-wide level by RNA Interactome Capture. This identified 67 novel cardiomyocyte specific RBPs including several contractile proteins. Furthermore, we identified Cytoplasmic polyadenylation element binding protein 4 (Cpeb4) as a dynamic mRBP in diseased cardiomyocytes, regulating cardiac growth both in vitro and in vivo. To study Cpeb4 in cardiomyocytes, we identified mRNAs bound to and regulated by Cpeb4. Cpeb4 regulates cardiac remodeling by differential expression of transcription factors. Among Cpeb4 target mRNAs, two Zinc finger transcription factors (Zeb1 and Zbtb20) were identified. We show that Cpeb4 regulates the translation of these mRNAs and that Cpeb4 depletion increases their expression. Thus, Cpeb4 emerges as critical regulator of cardiomyocyte function by differential binding of specific mRNAs in response to pathological growth stimulation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153524" }, "primaryId" : "GEO:GSE153524", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153524" } ] }, "title" : "microRNA regulation related to the protective effects of environmental enrichment against cocaine-seeking behavior", "dateAssigned" : "2020-06-29T00:00:00.000-05:00", "summary" : "MicroRNAs are “master regulators” of gene expression. To investigate microRNAs involved in the incentive motivation for cocaine elicited by exposure to cocaine-associated cues, we conducted NanoString nCounter analyses of microRNA expression in the nucleus accumbens shell of male rats that had been tested for cue reactivity in a previous study. These rats had been trained to self-administer cocaine while living in isolate housing, then during a subsequent 21-day forced abstinence period they either stayed under isolate housing or switched to environmental enrichment (EE), as this EE intervention is known to decrease cocaine seeking. This allowed us to create groups of “high” and “low” cocaine seekers using a median split of cocaine-seeking behavior. We conducted a differential expression analysis across these two groups that identified 33 miRNAs that were differentially altered in the nucleus accumbens shell. Predicted mRNA targets of these microRNAs are implicated in synaptic plasticity and neuronal signaling. Some of these microRNAs have previously been implicated in substance use disorders, while others are predicted to target large numbers of cocaine-related genes. Of the 33 differentially expressed microRNAs, 8 were specifically downregulated in the low-seeking group and another set of 8 had expression levels that were significantly correlated with cocaine-seeking. These findings suggest that processes involved in cocaine-seeking behavior may alter, or be altered by, multiple microRNAs. Further research examining the mechanisms involved in these microRNA changes and their effects on signaling may reveal novel therapeutic targets for attenuating drug craving.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33647589" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153604" }, "primaryId" : "GEO:GSE153604", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153604" } ] }, "title" : "Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in fetal and 2 weeks old rat islets", "dateAssigned" : "2020-07-01T00:00:00.000-05:00", "summary" : "Unlike adult β-cells, fetal and neonatal islets are functional immature and have blunted glucose responsiveness and decreased insulin secretion in response to stimuli. Pancreatic islets are a mixture of different cell types. Study of transcriptomes from intact islets would identify novel molecular mechanisms controlling islet functional development. At e19 and 2 weeks of age, pancreatic islets were isolated and total RNA were extracted for RNA-Seq study. Gene expression profiles were compared in the study.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153638" }, "primaryId" : "GEO:GSE153638", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153638" } ] }, "title" : "RNA-seq analysis of rat neurons treated with shRNA-mediated Trank1 knockdown", "dateAssigned" : "2020-07-01T00:00:00.000-05:00", "summary" : "Genetic analyses for bipolar disorder (BPD) have achieved prominent success in Europeans in recent years, whereas its genetic basis in other populations remains relatively less understood. We herein report that the lead risk locus for BPD in European genome-wide association studies (GWAS), the single nucleotide polymorphism (SNP) rs9834970 near TRANK1 at 3p22 region, is also genome-wide significantly associated with BPD in 5,748 cases and 65,361 controls of East Asian origin. In this study, we performed RAN-seq analysis of cultured rat neurons treated with shRNA knockdown of Trank1.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32791513" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153649" }, "primaryId" : "GEO:GSE153649", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153649" } ] }, "title" : "Next-generation sequencing of anterior cingulate cortex neurons in a social problem setting in rats", "dateAssigned" : "2020-07-01T00:00:00.000-05:00", "summary" : "We studied the brain mechanisms of ‘social problem’ where a worker’s credit is exploited in a group setting. A stable ‘worker-parasite’ relationship developed when three individually operant-conditioned rats were placed together in a Skinner box equipped with response lever and food dispenser on opposite sides. Specifically, one rat, the ‘worker,’ engaged in lever-pressing while the other ‘parasitic’ rats profited by crowding the feeder in anticipation. c-Fos expression in the anterior cingulate cortex (ACC) was significantly higher in worker rats than in parasite rats. ACC inactivation suppressed the worker’s lever-press behavior under the social dilemma settings. Importantly, our RNA sequencing and the differential expression analysis showed that GABA- and potassium channel-related mRNA expressions decreased in the worker’s ACC. In contrast, network disinhibition induced-activity responsive genes such as Cyr61, Arc, and Klf are upregulated. These results suggest that downregulation and upregulation of network inhibitory and excitatory factors, respectively, in the ACC of the worker compared to parasite rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34815341" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153681" }, "primaryId" : "GEO:GSE153681", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153681" } ] }, "title" : "Serum metabolomics associating with circulating microRNA profiles reveal the role of miR-383-5p in rat hippocampus under simulated microgravity", "dateAssigned" : "2020-07-02T00:00:00.000-05:00", "summary" : "MiRNA plays an important role during the adaptation to microgavity. In this study, effects of simulated microgravity on circulating microRNA profiles were performed to sreen different expression miRNA and gravity-sensitive miRNAs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33013433" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153709" }, "primaryId" : "GEO:GSE153709", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153709" } ] }, "title" : "Transcriptome profile of INS-1E Ctrl and DKO cells", "dateAssigned" : "2020-07-02T00:00:00.000-05:00", "summary" : "To analyse gene expression differences between the TFEB/TFE3 KO cells vs. Controls, under growing conditions (GC) vs. Fasting conditions (Fast)", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153763" }, "primaryId" : "GEO:GSE153763", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153763" } ] }, "title" : "RNA-seq transcriptonal profiling in neonatal rat ventricular myocytes under hypertrophic growth", "dateAssigned" : "2020-07-03T00:00:00.000-05:00", "summary" : "Heart failure is a leading cause of death in US. Hypertension is one of the most important risk factor of heart failure. In the presence of high blood pressure, the heart manifests hypertrophic growth to ameliorate ventricular wall stress. This once adaptive response may progress into decompensation and heart failure. The precise mechanisms governing this transition remain elusive. Here, we aimed to identify novel signaling pathways in cardiac hypertrophic growth. Primary neonatal rat ventricular myocytes (NRVMs) were isolated from 1-2 days old rats and treated with phenylephrine or IGF-1. Total RNA was isolated for RNA-seq analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32877669" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153986" }, "primaryId" : "GEO:GSE153986", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE153986" } ] }, "title" : "Transcriptomic analysis of hepatotoxicity induced by pesticides imazalil, thiacloprid and clothianidin alone or in binary mixtures in a 28-day study in female Wistar rats", "dateAssigned" : "2020-07-07T00:00:00.000-05:00", "summary" : "Co-occurrence of pesticide residues in food commodities raises a safety issue as their mixture effects on human health is largely unknown and need to be investigated. In a previous study, we reported the toxicological effects (pathology & histopathology) of imazalil (IMZ), thiacloprid (THI), and clothianidin (CTD) alone and in binary mixtures in a 28-day gavage study in female Wistar rats. Here, we undertook a transcriptomic analysis by means of total RNA sequencing (RNA-Seq). Ingenuity pathway analysis (IPA) was used to gain mechanistic information on the hepatotoxic pathways affected after treatment with pesticides, alone and in mixtures. Our data shows that 2986 genes were deregulated by CTD while IMZ and THI had effect on 194 and 225 genes, respectively. All three compounds share a common subset of genes whose network is associated with xenobiotic metabolism and nuclear receptors. Additionally, DNA repair process was predicted for CTD. The same networks were retrieved for the mixtures. Dose addition was indicated for the evaluated gene expressions. Our results bring new insight in the hepatotoxicity mechanisms of IMZ, THI, and CTD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35690182" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154012" }, "primaryId" : "GEO:GSE154012", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154012" } ] }, "title" : "3'DGE-seq analysis of fetal rat testis reveals limited transcriptional changes after exposure to azole fungicides triticonazole and flusilazole despite adverse in vivo effects", "dateAssigned" : "2020-07-08T00:00:00.000-05:00", "summary" : "Conclusions: Sequencing revealed few transcriptional changes in the fetal rat testes exposed to flusilazole or triticonazole. This suggests that flusilazole may be directly targeting steroidogenic enzyme activity in the testis at the protein level, whereas triticonazole may primarily disturbe androgen signaling in androgen-sensitive tissues. Expression of Calb2 and Gsta2 was altered by flusilazole but not triticonazole and may pinpoint novel pathways of disrupted testicular steroid synthesis. Our findings have wider implication for how we integrate omics data in chemical testing frameworks, including selection of non-animal test methods and building of Adverse Outcome Pathways for regulatory purposes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154013" }, "primaryId" : "GEO:GSE154013", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154013" } ] }, "title" : "Gene expression profiles in rat lung following intratracheal instillation with cellulose nanofibrils and multi-walled carbon nanotubes", "dateAssigned" : "2020-07-08T00:00:00.000-05:00", "summary" : "To evaluate the biological effects at the transcriptional level of manufactured nanomaterials, whole genome microarray analysis of rat lungs intratracheally instilled with cellulose nanofibrils (CNFs) with different physicochemical properties or multi-walled carbon nanotubes (MWCNTs) were performed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154019" }, "primaryId" : "GEO:GSE154019", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154019" } ] }, "title" : "RNA Sequencing reveals induction of specific renal inflammatory pathways in a rat model of malignant hypertension", "dateAssigned" : "2020-07-08T00:00:00.000-05:00", "summary" : "In malignant hypertension, far more severe kidney injury occurs than in the “benign” form of the disease. The role of high blood pressure and the renin-angiotensin-aldosterone system are well recognized, but the development of malignant nephrosclerosis remains incompletely understood. Using the rat model of two-kidney, one-clip renovascular hypertension in which some but not all animals develop malignant nephrosclerosis, we performed an unbiased analysis of genes by RNA-sequencing to identify transcriptional changes in the kidney specific for malignant nephrosclerosis. Differential gene expression was assessed in three groups: malignant hypertension (MH), non-malignant hypertension (NMH) and normotensive, sham operated controls (sham). To distinguish MH from NMH, we considered two factors: weight loss and typical renovascular lesions. Mean blood pressure measured intraarterially was elevated to a similar degree in MH (220.0±6.5 mmHg) and NMH (192.0±6.4 mmHg) compared to controls (119.5±1.7 mmHg, p<0.05). 886 genes were exclusively regulated in MH only. Principal component analysis revealed a separated clustering of the three groups. The data pointed to an upregulation of many inflammatory mechanisms in MH including pathways, which did previously attract relatively little attention in the setting of hypertensive nephrosclerosis: Transcripts from all three complement activation pathways were upregulated in MH compared to NMH but not in NMH compared with controls; immunohistochemistry confirmed complement deposition in MH exclusively. The expression of chemokines attracting neutrophil granulocytes (CXCL6) as well as actual granulocyte infiltration were increased only in MH rats. The data suggest that these pathways may contribute to the most severe forms of hypertensive nephrosclerosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34528115" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154022" }, "primaryId" : "GEO:GSE154022", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154022" } ] }, "title" : "Extracellular vesicles containing miR-146a-5p activate hepatocytic progenitor cells in regenerating retrorsin-treated rat livers", "dateAssigned" : "2020-07-08T00:00:00.000-05:00", "summary" : "We found that the transplantation of bone marrow mesenchymal cells (BM-MCs) transiently increased the liver mass by expanding resident small hepatocy-like progenitor cells (SHPCs). We used microarrays to detail the gene expression of SHPCs clusters with and without BM-MCs transplantation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34051870" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154098" }, "primaryId" : "GEO:GSE154098", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154098" } ] }, "title" : "Effect of Panax Notoginseng on gene expression in rats with cerebral ischemia-reperfusion injury", "dateAssigned" : "2020-07-09T00:00:00.000-05:00", "summary" : "Methods: Panax notoginseng was used to treat MCAO model rats, and the differentially expressed genes between Panax notoginseng group and model group were identified by RNA SEQ, and the possible mechanism of Panax notoginseng in regulating ischemic stroke was analyzed", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154274" }, "primaryId" : "GEO:GSE154274", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154274" } ] }, "title" : "RRBS, RNA-seq of placenta in women with PCOS and RNA-seq of hippocampus and hypothalamus in femal rats born to PCOS rats.", "dateAssigned" : "2020-07-12T00:00:00.000-05:00", "summary" : "Polycystic ovarian syndrome (PCOS) is characterized by hyperandrogenism, irregular ovulation and polycystic ovaries. In the present study, we utilized integrated analysis of whole transcriptome and DNA methylome by reduced representation bisulfite sequencing (RRBS) and RNA sequencing (RNA-seq) of the fetal side of placenta in women with PCOS. A cluster of neural function related genes, such as LIN7A and MAP1B, were identified with integrative analysis of methylome and transcriptome. Inflammatory disease and response process were spotlighted with GO enrichments analysis of differentially transcriptional gene cluster in PCOS, and the cellular growth and the development and function of nervous and endocrine system were also closely related to PCOS. With respect to neural function, the enriched GO terms in differential expressed gene cluster of PCOS group involved brain development, the proliferation and differentiation of neural precursor cell, neuron and neuroblast. Consistently, the enriched GO terms in differential methylated gene cluster of PCOS group were associated with neuropeptide and synaptic transmission, as well as cognition and learning or memory. As the gene expression changes in hypothalamus and hippocampus probably result in long standing neurobehavioural consequences in rodents, we conducted a global analysis of transcriptomic data of F1 pubertal female rats born to PCOS rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32949999" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154312" }, "primaryId" : "GEO:GSE154312", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154312" } ] }, "title" : "miRNA profiles of natural recovery in vitreous humor after NAION induction in rat", "dateAssigned" : "2020-07-13T00:00:00.000-05:00", "summary" : "We used microarray to find some new miRNAs that may participate in the natural recovery process after experience eye stroke.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154326" }, "primaryId" : "GEO:GSE154326", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154326" } ] }, "title" : "Cpxm2 as a novel candidate for cardiac hypertrophy and failure in hypertension [Illumina]", "dateAssigned" : "2020-07-13T00:00:00.000-05:00", "summary" : "To identify novel targets in left ventricular (LV) hypertrophy (LVH) we initiated comparative transcriptome analysis between genetic models derived from stroke-prone spontaneously hypertensive rats (SHRSP) and Fischer (F344). Previous genetic studies in the SHRSP/F344 model confirmed the presence of a major quantitative trait locus (QTL) for LV mass on rat chromosome (RNO) 1. We assigned carboxypeptidase X 2 (Cpxm2) to a genetic locus for LV mass identified in SHRSP. We assigned carboxypeptidase X 2 (Cpxm2) to a genetic locus for left ventricular mass.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154350" }, "primaryId" : "GEO:GSE154350", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154350" } ] }, "title" : "ASCL2 reciprocally controls key trophoblast lineage decisions during hemochorial placenta development", "dateAssigned" : "2020-07-13T00:00:00.000-05:00", "summary" : "Invasive trophoblast cells are critical to spiral artery remodeling in hemochorial placentation. Insufficient trophoblast invasion and vascular remodeling can lead to pregnancy disorders including preeclampsia, preterm birth, and intrauterine growth restriction. Previous studies in the mouse identified achaete-scute homolog 2 (ASCL2) as essential to extraembryonic development. We hypothesized that ASCL2 is a critical and conserved regulator of invasive trophoblast lineage development. In contrast to the mouse, the rat possesses deep intrauterine trophoblast cell invasion and spiral artery remodeling similar to human placentation. In this report, we investigated invasive/extravillous trophoblast (EVT) cell differentiation using human trophoblast stem (TS) cells and a loss-of-function mutant Ascl2 rat model. ASCL2 transcripts are expressed in the EVT column and junctional zone, which represent tissue sources of invasive trophoblast progenitor cells within human and rat placentation sites, respectively. Differentiation of human TS cells into EVT cells resulted in significant upregulation of ASCL2 and several other transcripts indicative of EVT cell differentiation. Disruption of ASCL2 impaired EVT cell differentiation as indicated by cell morphology and transcript profiles. RNA sequencing analysis of ASCL2-deficient trophoblast cells identified both downregulation of EVT cell-associated transcripts and upregulation of syncytiotrophoblast-associated transcripts, indicative of dual activating and repressing functions. ASCL2 deficiency in the rat impacted placental morphogenesis resulting in junctional zone dysgenesis and failed intrauterine trophoblast cell invasion. ASCL2 acts as a critical and conserved regulator of invasive trophoblast cell lineage development and a species-specific modulator of the syncytiotrophoblast lineage.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33649217" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154351" }, "primaryId" : "GEO:GSE154351", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154351" } ] }, "title" : "Gene Expression Signature in Rat Pituitary MMQ Cells Treated With DRD2 agonist UNC9994", "dateAssigned" : "2020-07-13T00:00:00.000-05:00", "summary" : "DRD2 agonists are effective in treating pituitary tumors. To fathom the β-arresin-dependent mechanisms underlying DRD2-mediated pituitary tumor growth suppression,we applied RNA-seq analysis to rat pituitary MMQ cells treated with a DRD2 β-arresin-biased agoinst, UNC9994.MMQ cells were treated with UNC9994(15μM) or vehecle control for 12 h or 24 h and then subject to RNA-seq analysis.We found oxidative-stress-related genes such as Nqo1 and Hmox1 were upregulated by UNC9994, revealing oxidative stress may be the basis of UNC9994-induced tumor growth suppression. Our study represents the first detailed analysis of transcriptomes in rat pituitary MMQ cells treated with DRD2 β-arresin-biased agonist.The significance of altered expression of specific transcripts will enhance our understanding of DRD2 signaling in pituitary tumor cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154533" }, "primaryId" : "GEO:GSE154533", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154533" } ] }, "title" : "Zonation of pancreatic acinar cells in diabetic mice", "dateAssigned" : "2020-07-16T00:00:00.000-05:00", "summary" : "We sequenced AR42J cell exposed to CCK or insulin in different concentrations. This enable us to uncover the possible effect of the different hormones on acinar cells in pathlogy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32814046" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154603" }, "primaryId" : "GEO:GSE154603", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154603" } ] }, "title" : "Targeting mitochondrial metabolism for detection and treatment of doxorubicin-induced heart failure", "dateAssigned" : "2020-07-16T00:00:00.000-05:00", "summary" : "We conducted RNAseq using mRNA extracted from rat hearts to elucidate the effect of doxorubicin chemotherapy on the heart. Rats were 250g at the start of the treatment protocol. Tissues were collected post five weekly intravenous injections of either sterile saline or 3mg/kg/week doxorubicin. Hearts were excised under deep isoflurane anaesthesia and rapidly frozen with liquid-nitrogen cooled Wallenberger tongs. Total mRNA was extracted with a Qiagen RNeasy fibrous tissue mini kit. Gene set enrichement analysis (GSEA) shows that unlike previously reported, oxidative stress is not involved in the cardiac pathology of our model (reduced cardiac function and atrophy). However, gene sets responsible for mRNA processing, ribosomes and protein synthesis and processing are decreased in doxorubicin-treated rat hearts compared to saline control hearts.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33214680" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154606" }, "primaryId" : "GEO:GSE154606", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154606" } ] }, "title" : "Genome-wide analysis of long noncoding RNA expression profile in spontaneously hypertensive rat treated by Ganoderma lingzhi oligopeptide", "dateAssigned" : "2020-07-16T00:00:00.000-05:00", "summary" : "Angiotensin I-converting enzyme (ACE) plays a vital role in cardiovascular disease (CVD). Natural ACE inhibitory peptides from Ganoderma lingzhi (G. lingzhi) showed potential vasodilatation in vitro or in vivo. Recent studies have shown that long non-coding (lncRNA) plays critical roles in biological processes and human diseases, since the roles of lncRNA in CVD remain unclear. Our findings indicate that the expression profiles of lncRNAs has changed in spontaneously hypertensive rats (SHRs) treated by the G. lingzhi peptide, compared with untreatedt groups. It is expected to provide novel insight into the underlying molecular mechanism and potential targets for hypertention therapy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154616" }, "primaryId" : "GEO:GSE154616", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154616" } ] }, "title" : "Mammalian circRNA Atlas", "dateAssigned" : "2020-07-16T00:00:00.000-05:00", "summary" : "We developed a new pipeline for accurate circRNA detection. We build a new atlas for characterizing circRNA in human, monkey, mouse, rat and drosophila brain. Our approach allows full annotation of circRNAs with fewer false positives and negatives than any individual pipeline or combination of them. Moreover, our approach is more sensitive than any individual pipeline and allows more accurate quantification and larger number of differentially expressed circRNAs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34556162" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154653" }, "primaryId" : "GEO:GSE154653", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154653" } ] }, "title" : "Integrated lncRNAs and mRNAs sequencing reveals lncRNAs regulatory network associated with lung injury in LPS-induced septic shock rats", "dateAssigned" : "2020-07-17T00:00:00.000-05:00", "summary" : "Sepsis is associated with increased morbidity and mortality. Long non-coding RNAs (lncRNAs) have been associated with human diseases. Here, we used a microarray to analyze lncRNAs and mRNAs expression and functional network of lung injury in lipopolysaccharide (LPS)-induced septic shock rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154701" }, "primaryId" : "GEO:GSE154701", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154701" } ] }, "title" : "SUV39H2 CONTROLS TROPHOBLAST STEM CELL FATE", "dateAssigned" : "2020-07-20T00:00:00.000-05:00", "summary" : "The placenta is constructed through the orchestration of trophoblast stem (TS) cell expansion and differentiation along a multi-lineage pathway. Dynamic regulation of histone H3K9 methylation is pivotal to cell differentiation for many cell lineages, but little is known about its involvement in trophoblast development. Among the twelve-known histone H3K9 methyltransferases, only SUV39H2 exhibited robust differential expression in stem versus differentiated rat TS cells. SUV39H2 transcript and protein expression were high in the stem state and rapidly declined as TS cells differentiated. Disruption of SUV39H2 expression in TS cells led to prominent phenotypic changes. Suv39h2-specific shRNA knockdown resulted in an arrest in TS cell proliferation and activation of trophoblast cell differentiation. These observations were reinforced by flow cytometry and transcript profiling. Histone H3K9 methylation status at specific loci exhibiting differentiation-dependent gene expression were regulated by SUV39H2 and also represented sites for SUV39H2 occupancy. Analyses of SUV39H2 on ex vivo rat blastocyst development supported its role in regulating TS cell expansion and differentiation. Finally, we identified SUV39H2 as a downstream target of CDX2, a master regulator of trophoblast lineage development. In summary, our findings indicate that SUV39H2 contributes to the maintenance of the TS cell stem state and restrains trophoblast cell differentiation and thus serves as a contributor to the epigenetic regulation of hemochorial placental development.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154799" }, "primaryId" : "GEO:GSE154799", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154799" } ] }, "title" : "Cell type-specific changes in transcriptomic profiles of endothelial cells, iPSC-derived neurons and astrocytes cultured on microfluidic chips", "dateAssigned" : "2020-07-20T00:00:00.000-05:00", "summary" : "In vitro neuronal models are essential for studying neurological physiology, disease mechanisms and potential treatments. Most in vitro models lack controlled vasculature, despite its necessity in brain physiology and disease. Organ-on-chip models offer microfluidic culture systems with dedicated micro-compartments for neurons and vascular cells. Such multi-cell type organs-on-chips can emulate neurovascular unit (NVU) physiology, however there is a lack of systematic data on how individual cell types are affected by culturing on microfluidic systems versus conventional culture plates. This information can provide perspective on initial findings of studies using organs-on-chip models, and further optimizes these models in terms of cellular maturity and neurovascular physiology. Here, we analysed the transcriptomic profiles of co-cultures of human induced pluripotent stem cell (hiPSC)-derived neurons and rat astrocytes, as well as one-day monocultures of human endothelial cells, cultured on microfluidic chips. For each cell type, large gene expression changes were observed when cultured on microfluidic chips compared to conventional culture plates. Endothelial cells showed decreased cell division, neurons and astrocytes exhibited increased cell adhesion, and neurons showed increased maturity when cultured on a microfluidic chip. Our results demonstrate that culturing NVU cell types on microfluidic chips changes their gene expression profiles, presumably due to distinct surface-to-volume ratios and substrate materials. These findings inform further NVU organ-on-chip model optimization and support their future application in disease studies and drug testing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33500551" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154884" }, "primaryId" : "GEO:GSE154884", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154884" } ] }, "title" : "The single-cellsequencing of purified wild type rat intervertebral disc (IVD) cells", "dateAssigned" : "2020-07-22T00:00:00.000-05:00", "summary" : "IVDs are composed of heterogeneous cell groups, a further understanding of marker genes and cell phenotypes of healthy mature IVD cells is essential.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154912" }, "primaryId" : "GEO:GSE154912", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154912" } ] }, "title" : "Expression data from PBDE-47 treated rats at PND4", "dateAssigned" : "2020-07-22T00:00:00.000-05:00", "summary" : "A total of 7, 50, and 149 gene transcripts were differentially expressed between control samples and 0.1, 15, and 50 mg/kg PBDE-47 (using a false discovery rate (FDR) threshold of 0.05). These transcripts were mapped to 2, 40, and 139 genes using Ingenuity Pathway Analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31826744" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154913" }, "primaryId" : "GEO:GSE154913", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154913" } ] }, "title" : "Expression data from DE-71 treated rats at PND4", "dateAssigned" : "2020-07-22T00:00:00.000-05:00", "summary" : "A total of 0, 15, and 162 gene transcripts were differentially expressed between control samples and 0.1, 15, and 50 mg/kg DE-71, respectively (using a false discovery rate (FDR) threshold of 0.05). These transcripts were mapped to 0, 13, and 161 genes using Ingenuity Pathway Analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31826744" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154990" }, "primaryId" : "GEO:GSE154990", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE154990" } ] }, "title" : "microRNA expression profiling of the response of the dorsal motor nucleus of the vagus to physiological perturbations and cardiac injury", "dateAssigned" : "2020-07-23T00:00:00.000-05:00", "summary" : "We developed microRNA expression profiling data from the dorsal motor nucleus of the vagus (DMV) neurons under homeostasis and following physiological perturbations of remote ischemic preconditioning and cardiac ischemia. Male Sprague-Dawley rats were subjected to remote ischemia preconditioning (rIPC), ligation of the left anterior descending artery (LAD), or rIPC with LAD following two hours later (rIPC 2h/LAD). All samples were collected 24 hours after LAD.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155047" }, "primaryId" : "GEO:GSE155047", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155047" } ] }, "title" : "Single cell gene expression profiling of the response of the dorsal motor nucleus of the vagus neurons to remote ischemic preconditioning [DMV_RIPC_RT-PCR]", "dateAssigned" : "2020-07-24T00:00:00.000-05:00", "summary" : "We developed a mesoscale single cell transcriptomics data from hundreds of the dorsal motor nucleus of the vagus (DMV) neurons under homeostasis and following physiological perturbations. Our results revealed that homeostatic DMV neuronal states can be organized into distinguishable input-output signal processing units. Remote ischemic preconditioning induced a distinctive shift in the neuronal states towards diminishing the role of inhibitory inputs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155049" }, "primaryId" : "GEO:GSE155049", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155049" } ] }, "title" : "Single cell gene expression profiling of the response of the dorsal motor nucleus of the vagus neurons to cardiac ischemia [DMV_Cardiac-Ischemia_RT-PCR]", "dateAssigned" : "2020-07-24T00:00:00.000-05:00", "summary" : "We developed a mesoscale single cell transcriptomics data from hundreds of the dorsal motor nucleus of the vagus (DMV) neurons under homeostasis and following physiological perturbations. Our results revealed that homeostatic DMV neuronal states can be organized into distinguishable input-output signal processing units. Chronic cardiac ischemic injury resulted in a dramatic shift in DMV neuronal states suggestive of enhanced neurosecretory function.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155059" }, "primaryId" : "GEO:GSE155059", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155059" } ] }, "title" : "Characterization of lncRNA and mRNA Profiles in Rats With Diabetic Macroangiopathy", "dateAssigned" : "2020-07-24T00:00:00.000-05:00", "summary" : "Diabetic macroangiopathy is one of the most common serious complications of diabetes. Previous studies indicate that lncRNAs involved in the process of diabetes and another vascular disease. However, their detailed mechanism of the lncRNAs involved in diabetic macroangiopathy has not been well characterized. In the present study, we generated rat models of diabetic macroangiopathy induced by High fat. A total of 15 GK rats was constructed as a test group, along with 15 Wistar rats set as a control group, and thoracic aorta tissue from each group was collected. Whole genomic RNA sequencing was performed on thoracic aorta tissue;3223 novel lncRNAs and 20367 annotated lncRNAs were identified in thoracic aorta samples, and 864 lncRNAs were expressed differently in the test and control groups. Gene ontology term enrichment showed the apparent enrichment of inflammatory response and cell apoptosis, which consistent with the results of H&E Staining, TUNEL Assay, and ELISA; Extensive literature reveals inflammatory response and cell apoptosis play an important role in the process of diabetic macroangiopathy.The results of the present study indicated that lncRNAs, especiallyNrep.bSep08,Col5a1,aSep0,soygee.aSep08-unspliced,NONRATT013247.2,votar.aSep08-unspliced,etc,both participate in and mediate the process of inflammatory response,cell apoptosis.What’s more, Our research provides further insights into the understanding of the basic molecular mechanisms underlying diabetic macroangiopathy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155221" }, "primaryId" : "GEO:GSE155221", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155221" } ] }, "title" : "Transcriptome profile of INS-1E Ctrl and hTFEB OE cells", "dateAssigned" : "2020-07-27T00:00:00.000-05:00", "summary" : "To analyse gene expression differences between the human TFEB overexpressing cells vs. Controls, under growing conditions (GC) vs. Fasting conditions (Fast)", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155230" }, "primaryId" : "GEO:GSE155230", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155230" } ] }, "title" : "Comparative analysis of skeletal muscle transcriptional signatures associated with aerobic exercise capacity or response to training in humans and rats", "dateAssigned" : "2020-07-27T00:00:00.000-05:00", "summary" : "In this study, we set out to dissect the intrinsic and response components of aerobic exercise at the transcriptional level in the skeletal muscle.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33193103" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155393" }, "primaryId" : "GEO:GSE155393", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155393" } ] }, "title" : "Blast-related mild TBI alters anxiety-like behavior and transcriptional signatures in the rat amygdala", "dateAssigned" : "2020-07-29T00:00:00.000-05:00", "summary" : "Male Long Evans rats aging 10-12 weeks were exposed to repeated blast overpressure and then went through behavioral tests for anxiety and fear conditioning. After 1-1.5 months (sub-acute) or 12-13 months (chronic), amygdala tissue specimens from all animals were collected. RNA-seq was used to measure transcriptome-wide gene expression of sham and blast animals at different timepoints. The study identified changes in the amygdalar transcriptome and associated anxiety-related phenotypic outcomes related to both blast exposure and aging, which may play a role in the long-term pathological consequences of mTBI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33192359" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155540" }, "primaryId" : "GEO:GSE155540", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155540" } ] }, "title" : "Compartment-specific regulation of gene expression orchestrates homeostatic synaptic scaling", "dateAssigned" : "2020-08-02T00:00:00.000-05:00", "summary" : "Synaptic scaling is a form of homeostatic plasticity which allows neurons to reduce their action potential firing rate in response to chronic alterations in neural activity. Synaptic scaling requires profound changes in gene expression, but the relative contribution of local and cell-wide mechanisms to synaptic scaling is controversial. Here we performed a comprehensive multi-omics characterization of the somatic and process compartments of primary rat hippocampal neurons during synaptic scaling. Thereby, we uncovered highly compartment-specific and correlated changes in the neuronal transcriptome and proteome. Specifically, we identified highly compartment-specific downregulation of crucial regulators of neuronal excitability and excitatory synapse structure. Motif analysis further suggests an important role for trans-acting post-transcriptional regulators, including RNA-binding proteins and microRNAs, in the local regulation of the corresponding mRNAs. Altogether, our study indicates that compartmentalized gene expression changes are widespread in synaptic scaling and might co-exist with neuron-wide mechanism to allow synaptic computation and homeostasis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34396684" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155589" }, "primaryId" : "GEO:GSE155589", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155589" } ] }, "title" : "MethylC-capture sequencing of control, osteoporotic, and Astragalus polysaccharides (APS)-treated osteoporotic SD rats", "dateAssigned" : "2020-08-03T00:00:00.000-05:00", "summary" : "SD rats were intramuscular injected with dexamethasone to induce osteoporosis, and treated with APS. Then, colonic epithelia of control, osteoporotic and APS-treated osteoporotic rats were collected for MethylC-capture sequencing .", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155610" }, "primaryId" : "GEO:GSE155610", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155610" } ] }, "title" : "Transcriptome of Subcortical White Matter and Spinal Cord After Spinal Injury and Cortical Stimulation", "dateAssigned" : "2020-08-03T00:00:00.000-05:00", "summary" : "Spinal cord injury disrupts ascending and descending neural signals causing sensory and motor dysfunction below the injury. Neuromodulation with electrical stimulation is used in both clinical and research settings to induce neural plasticity and improve functional recovery following injury. However, the mechanisms by which electrical stimulation affects recovery remain unclear. In this study we examined the effects of cortical electrical stimulation following injury on transcription at several levels of the central nervous system. We performed a unilateral cervical spinal contusion injury in rats and delivered stimulation for one week to the contralesional motor cortex to activate a descending motor tract.RNA was purified from bilateral subcortical white matter, and 3 levels of the spinal cord. Here we provide the complete data set in the hope that it will be useful for researchers studying electrical stimulation as a therapy to improve recovery from the deficits associated with spinal cord injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34267212" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155699" }, "primaryId" : "GEO:GSE155699", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155699" } ] }, "title" : "Transient ACE Inhibition Suppresses Future Fibrogenic Capacity and Heterogeneity of Cardiac Fibroblast Subpopulations", "dateAssigned" : "2020-08-04T00:00:00.000-05:00", "summary" : "Transient angiotensin converting enzyme (ACE) inhibition in spontaneously hypertensive rats (SHR) protects against future injury-induced cardiac inflammation, fibrosis, and dysfunction. Here, we used single cell RNA sequencing (scRNA-Seq) to test the hypothesis that transient ACE inhibitor treatment would induce a persistent shift in hypertensive cardiac fibroblast subpopulations. Adult male SHRs (11 weeks old) were treated for 2 weeks with an ACE inhibitor, enalapril (30mg/kg/day, p.o.), or water (control) followed by a 2-week washout period (n=7/group). Cardiac fibroblasts were isolated from the left ventricle and subjected to scRNA-Seq. Nine clusters of fibroblasts (numbered 0-8) were identified with 98% of cells clustering into subsets 0-6. Transient treatment produced significant changes within and across clusters. Cluster 1 depicted the highly fibrogenic gene profile, with cluster 6 serving as a gateway to cluster 1. Transient ACE inhibition depleted the gateway and expanded cluster 0, which was the least fibrogenic profile. Moreover, within cluster 1 fibroblasts, ACE inhibition reduced expression of individual fibrosis genes (e.g. COL1A1, COL3A1, and FN1; all p<0.05). Clusters 2-5 reflected proliferative, moderately fibrogenic, translationally active, and lowly inflammatory subsets of fibroblasts, all of which exhibit attenuated fibrogenic gene expression after transient ACE inhibition. In conclusion, transient ACE inhibition shifts cardiac fibroblast subpopulations and degree of activation resulting in an overall reduced fibrogenic phenotype.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33486989" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155709" }, "primaryId" : "GEO:GSE155709", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155709" } ] }, "title" : "A Long Non-Coding RNA (Lrap) Modulates Brain Gene Expression and Levels of Alcohol Consumption in Rats", "dateAssigned" : "2020-08-04T00:00:00.000-05:00", "summary" : "LncRNAs are important regulators of quantitative and qualitative features of the transcriptome. We have used QTL and other statistical analyses to identify a gene coexpression module associated with the phenotype of alcohol consumption. The “hub gene” of this module, Lrap (Long non-coding RNA for alcohol preference), was an unannotated transcript resembling a lncRNA. We used partial correlation analyses to establish that Lrap is a major contributor to the integrity of the coexpression module. Using CRISPR/Cas9 technology, we disrupted an exon of Lrap in Wistar rats. The genetically modified rats were assessed for alcohol consumption and brain RNA expression levels were evaluated using RNASeq. Measures of alcohol consumption in wild type, heterozygous and knockout rats demonstrated that disruption of Lrap produced increases in alcohol consumption/alcohol preference. The disruption of Lrap also produced changes in expression of over 700 other transcripts. Furthermore, it became apparent that Lrap may have a function in alternative splicing of the affected transcripts. More than 20% of the differentially expressed isoforms exhibited evidence for novel alternative splicing between Lrap+/+ and Lrap-/- rats. The GO category of “Response to Ethanol” emerged as one of the top candidates in an enrichment analysis of the differentially expressed transcripts. We validate the role of Lrap as a mediator of alcohol consumption by rats, and also implicate Lrap as a modifier of the expression and splicing of a large number of brain transcripts. A defined subset of these transcripts significantly impacts alcohol consumption by rats (and possibly humans).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155743" }, "primaryId" : "GEO:GSE155743", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155743" } ] }, "title" : "Next generation sequencing analysis of primary rat lung fibroblast, primary rat lung alveolar type 2 cell and a novel 10-4A rat lung cell line transcriptomes", "dateAssigned" : "2020-08-05T00:00:00.000-05:00", "summary" : "Purpose: We report the application of single-molecule-based sequencing technology for high-throughput profiling of a novel 10-4A rat lung fibroblast cell line and compared the transcriptome to freshly isolated primary rat lung fibroblasts and freshly isolated primary rat lung alveolar type 2 cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33162897" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155768" }, "primaryId" : "GEO:GSE155768", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155768" } ] }, "title" : "Effect of HectD3 overexpression on gene expression in neonatal rat cardiomyocytes", "dateAssigned" : "2020-08-05T00:00:00.000-05:00", "summary" : "The present study focuses on the identification of the gene expression profile of neonatal rat cardiomyocytes (NRVCMs) after overexpressing HectD3, an E3 ligase, through Illumina RNA-sequencing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33037313" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155793" }, "primaryId" : "GEO:GSE155793", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155793" } ] }, "title" : "Real-time quantitative PCR analysis of rat aorta samples after stent deployment", "dateAssigned" : "2020-08-06T00:00:00.000-05:00", "summary" : "Bare Metal Stents (BMS), Drug Eluting Stent (DES) and Exosomes Eluting Stent (EES) were placed in rat abdominal aorta for one week. Then total RNA of aortas was extracted. We used ScienCell's GeneQuery Rat Macrophage Polarization Markers qPCR Array Kit to quantitate gene expression of macrophage relevant genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155862" }, "primaryId" : "GEO:GSE155862", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155862" } ] }, "title" : "b-catenin Signaling Dynamics Regulate Cell Fate in Differentiating Neural Stem Cells", "dateAssigned" : "2020-08-07T00:00:00.000-05:00", "summary" : "Stem cells undergo differentiation in complex and dynamic environments wherein instructive signals fluctuate on various timescales. Thus, cells must be equipped to properly respond to the timing of signals, for example to distinguish sustained signaling from transient noise. However, how stem cells respond to dynamic variations in differentiation cues is not well characterized. Here, we use optogenetic activation of b-catenin signaling to probe the dynamic responses of differentiating adult neural stem cells (NSCs). We discover that while elevated, sustained b-catenin activation sequentially promotes proliferation and differentiation, transient b-catenin induces apoptosis. Genetic perturbations revealed that the neurogenic/apoptotic fate-switch was mediated through cell cycle regulation by Growth Arrest and DNA Damage 45 gamma (Gadd45g). Our results thus reveal a role for b-catenin dynamics in NSC fate decisions and may suggest a novel role for signal timing to minimize cell fate errors, analogous to kinetic proofreading of stem cell differentiation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155866" }, "primaryId" : "GEO:GSE155866", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155866" } ] }, "title" : "Transcriptional heterogeneity between primary adult grey and white matter astrocytes underlie differences in modulation of in vitro myelination", "dateAssigned" : "2020-08-07T00:00:00.000-05:00", "summary" : "Conclusions: Primary adult gmASTRs and wmASTRs are heterogeneous at the transcriptional level, differed in their support of in vitro myelination, and their pre-existing phenotype determined TLR3 agonist responses. These findings point to a role of ASTR heterogeneity in regional differences in remyelination efficiency between GM and WM lesions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33308248" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155899" }, "primaryId" : "GEO:GSE155899", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155899" } ] }, "title" : "The translational landscape of phenylephrine-treated neonatal rat cardiomyocytes [Ribo-seq]", "dateAssigned" : "2020-08-07T00:00:00.000-05:00", "summary" : "In this study, we generated nucleotide-resolution translatome as well as transcriptome data of isolated primary cardiomyocytes undergoing hypertrophy. More than 10,000 open reading frames (ORF) were detected from the deep sequencing of ribosome protected fragments orchestrating the shift of translatome in hypertrophied cardiomyocytes.We further identified more than 100 potential micropeptides encoded by uncharacterized small open reading frames (sORFs) in the long noncoding RNA genes. Over two-thirds of these micropeptide candidates were experimentally validated in a random test with three micropeptides showing regulatory function in cardiomyocyte hypertrophy via modulating the activities of Oxidative phosphorylation, Calcium signaling pathway, and MAPK signaling pathway.Our study provided a genome-wide overview of the translational controls of cardiomyocyte hypertrophy and demonstrated an unrecognized role of micropeptides in cardiomyocyte biology.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33677093" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155912" }, "primaryId" : "GEO:GSE155912", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155912" } ] }, "title" : "The translational landscape of phenylephrine-treated neonatal rat cardiomyocytes [nsRNA-seq]", "dateAssigned" : "2020-08-08T00:00:00.000-05:00", "summary" : "In this study, we generated nucleotide-resolution translatome as well as transcriptome data of isolated primary cardiomyocytes undergoing hypertrophy. More than 10,000 open reading frames (ORF) were detected from the deep sequencing of ribosome protected fragments orchestrating the shift of translatome in hypertrophied cardiomyocytes.We further identified more than 100 potential micropeptides encoded by uncharacterized small open reading frames (sORFs) in the long noncoding RNA genes. Over two-thirds of these micropeptide candidates were experimentally validated in a random test with three micropeptides showing regulatory function in cardiomyocyte hypertrophy via modulating the activities of Oxidative phosphorylation, Calcium signaling pathway, and MAPK signaling pathway.Our study provided a genome-wide overview of the translational controls of cardiomyocyte hypertrophy and demonstrated an unrecognized role of micropeptides in cardiomyocyte biology.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33677093" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155913" }, "primaryId" : "GEO:GSE155913", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155913" } ] }, "title" : "The translational landscape of phenylephrine-treated neonatal rat cardiomyocytes [ssRNA-seq]", "dateAssigned" : "2020-08-08T00:00:00.000-05:00", "summary" : "In this study, we generated nucleotide-resolution translatome as well as transcriptome data of isolated primary cardiomyocytes undergoing hypertrophy. More than 10,000 open reading frames (ORF) were detected from the deep sequencing of ribosome protected fragments orchestrating the shift of translatome in hypertrophied cardiomyocytes.We further identified more than 100 potential micropeptides encoded by uncharacterized small open reading frames (sORFs) in the long noncoding RNA genes. Over two-thirds of these micropeptide candidates were experimentally validated in a random test with three micropeptides showing regulatory function in cardiomyocyte hypertrophy via modulating the activities of Oxidative phosphorylation, Calcium signaling pathway, and MAPK signaling pathway.Our study provided a genome-wide overview of the translational controls of cardiomyocyte hypertrophy and demonstrated an unrecognized role of micropeptides in cardiomyocyte biology.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33677093" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155922" }, "primaryId" : "GEO:GSE155922", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155922" } ] }, "title" : "Epigenome-Wide Association Study for Transgenerational Disease Epimutation Sperm Biomarkers following Ancestral Exposure to Jet Fuel Hydrocarbons", "dateAssigned" : "2020-08-08T00:00:00.000-05:00", "summary" : "Jet fuel hydrocarbons is the generic name for aviation fuels used in gas-turbine engine powered aircrafts. Due to the widespread use of jet fuel hydrocarbons, this compound has been recognized as the single largest chemical exposure for military personnel. Previous animal studies have demonstrated the ability of jet fuel (JP-8) exposure to promote the epigenetic transgenerational inheritance of disease susceptibility in subsequent generations. The diseases observed include late puberty, kidney, obesity and multiple disease pathologies. The current study was designed to identify potential sperm DNA methylation biomarkers for specific transgenerational diseases. Observations identify few disease specific differential DNA methylation regions (DMRs) called epimutations in the transgenerational F3 generation great-grand-offspring rats ancestrally exposed to jet fuel. The potential epigenetic DMRs were identified for late puberty, kidney, obesity, and multiple diseases, and found to be predominantly disease specific. These disease specific DMRs have associated genes previously shown to be linked with each of these specific diseases. Therefore, the germline (i.e. sperm) has environmentally induced ancestrally derived epimutations that have the potential to transgenerationally transmit disease susceptibilities to subsequent generations. Epigenetic biomarkers for specific diseases could be developed as medical diagnostics to facilitate clinical management of disease and allow preventative medicine therapeutics.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35440735" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155924" }, "primaryId" : "GEO:GSE155924", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE155924" } ] }, "title" : "Effect of tobacco smoke exposure cessation on lung response to crystalline silica exposure in rats", "dateAssigned" : "2020-08-08T00:00:00.000-05:00", "summary" : "Our previous studies have shown that tobacco smoke exposure exacerbated the lung response to crystalline silica exposure in rats. The objective of the present study, a follow-up to our previous study, was to determine the effect of tobacco smoke exposure cessation on the lung response to crystalline silica exposure in the rats. Rats were exposed to air, crystalline silica (1 week followed by a 1 year progression/recovery period with no exposure), tobacco smoke (6 months of exposure followed by 6 months of recovery with no exposure), or crystalline silica (1 week) plus tobacco smoke (6 months of exposure followed by 6 months of recovery with no exposure). Lung toxicity was determined at the end of the 1-year progression/recovery period in all 4 groups of the rats. Silica exposure resulted in significant lung toxicity which was further exacerbated by tobacco smoke exposure in the rats. Cessation of cigarette smoke exposure did not result in reversal of the silica-induced lung toxicity despite exacerbation of the toxicity by tobacco smoke.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156188" }, "primaryId" : "GEO:GSE156188", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156188" } ] }, "title" : "Gene expression analysis of rat macrophages", "dateAssigned" : "2020-08-13T00:00:00.000-05:00", "summary" : "We used microarray to compare gene expression between bone marrow-derived (BMDM), monocyte-derived (MDM), alveolar (AM), peritoneal (PM) and embryonic stem cell (ESC) derived rat macrophages. The expression of liver macrophages (Kupffer cells) were inferred by analysis of whole livers from Csf1r deficient rats. The transcriptional response of BMDM to LPS was also examined.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33633725" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156442" }, "primaryId" : "GEO:GSE156442", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156442" } ] }, "title" : "The validation case study of read-across based on IATA for hepatotoxicity of Naphthalene and its structurally similar analogs", "dateAssigned" : "2020-08-18T00:00:00.000-05:00", "summary" : "Comparing biological similarity with in vitro test is expected to improve the reliability of read-across for systemic toxicity without animal test. However, because of few case studies, it was hindered to use of this concept for regulatory context. Thus, we compared biological similarity with in vitro test for structurally similar chemicals to demonstrate its validity for grouping chemicals and extract key considerations in read-across. In this study, we selected the hepatotoxicity of Naphthalene and its structurally similar analogs which have 90-day repeated dose toxicity data including 2,7-Naphthalenediol, 1,5-Naphthalenediol, and 1-Naphthol. To elucidate the potential mechanisms and compared them, we conducted in vitro microarray analysis with rat primary hepatocytes", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156457" }, "primaryId" : "GEO:GSE156457", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156457" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to Printex90 (ALI)", "dateAssigned" : "2020-08-19T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 0.9 cm²/cm² through an Air Liquid Interface (ALI) of Printex90 (ALI). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156458" }, "primaryId" : "GEO:GSE156458", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156458" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells in control condition (DMEM culture medium supplemented with 10% of fetal bovine serum)", "dateAssigned" : "2020-08-19T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages: here is the control for Air Liquid Interface (ALI) in DMEM culture medium supplemented with fetal bovine serum (FBS). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156489" }, "primaryId" : "GEO:GSE156489", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156489" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells in control condition (water, H2O)", "dateAssigned" : "2020-08-19T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages: here is the control for Air Liquid Interface (ALI) in water (H2O). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156493" }, "primaryId" : "GEO:GSE156493", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156493" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells in submerged condition (control)", "dateAssigned" : "2020-08-19T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages: here is the control for submerged condition. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156509" }, "primaryId" : "GEO:GSE156509", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156509" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to TiO2 (NM105, p25 anatase/rutile)", "dateAssigned" : "2020-08-19T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 3 cm²/cm² of TiO2 (NM105, p25 anatase/rutile). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156511" }, "primaryId" : "GEO:GSE156511", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156511" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to NM403 carbon nanotubes", "dateAssigned" : "2020-08-19T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 0.8 cm²/cm² of NM403. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156530" }, "primaryId" : "GEO:GSE156530", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156530" } ] }, "title" : "Epigenome-Wide Association Study for Atrazine Induced Transgenerational Histone Retention Sperm Epigenetic Biomarkers for Disease", "dateAssigned" : "2020-08-20T00:00:00.000-05:00", "summary" : "Atrazine is a common agricultural herbicide previously shown to promote epigenetic transgenerational inheritance of disease to subsequent generations. The current study was designed as an epigenome-wide association study (EWAS) to identify transgenerational sperm disease associated differential histone retention regions (DHRs). Gestating female F0 generation rats were transiently exposed to atrazine during the period of embryonic gonadal sex determination, and then subsequent F1, F2, and F3 generations obtained in the absence of any continued exposure. The transgenerational F3 generation males were assessed for disease and sperm collected for epigenetic analysis. Pathology was observed in late pubertal onset and for testis disease, prostate disease, kidney disease, lean pathology, and multiple disease. For these pathologies, sufficient numbers of individual males with only a single specific disease were identified. The sperm DNA and chromatin were isolated from adult one-year animals with the specific diseases and analyzed for DHRs with histone chromatin immunoprecipitation (ChIP) sequencing. Transgenerational F3 generation males with or without disease were compared to identify the disease specific epimutation biomarkers. No common DHRs were found among all the pathologies. Epimutation gene associations were identified and found to correlate to previously known disease linked genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33326428" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156564" }, "primaryId" : "GEO:GSE156564", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156564" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to TiO2 (NRCWE001)", "dateAssigned" : "2020-08-20T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 3 cm²/cm² of rutile TiO2 (NRCWE001). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156571" }, "primaryId" : "GEO:GSE156571", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156571" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to multi-walled carbon nanotubes (NRCWE006)", "dateAssigned" : "2020-08-20T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 1 cm²/cm² of multi-walled carbon nanotubes (NRCWE006 - Mitsui-7). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156573" }, "primaryId" : "GEO:GSE156573", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156573" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to NiZnFe2O4", "dateAssigned" : "2020-08-20T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 9.25 µg/mL of NiZnFe2O4. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156579" }, "primaryId" : "GEO:GSE156579", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156579" } ] }, "title" : "Effect of the acute and chronic administration of Lupinus albus β-conglutin on glycaemia, circulating cholesterol, and liver gene expression profile", "dateAssigned" : "2020-08-20T00:00:00.000-05:00", "summary" : "Constituents of lupin seeds, like γ-conglutin and lupanine, have gained attention as potential complementary treatments for the management of dysglycaemia. Notwithstanding, the effect of other lupin components on carbohydrate metabolism, including β-conglutin protein, has received little attention. Here, we investigated the influence of the acute and chronic administration of β-conglutin on glycaemia modulation in normal and streptozotocin induced-to-diabetes rats. To identify potential molecular targets and pathways involved in this biological response, we analysed the liver transcriptome modulation exerted by β-conglutin in diabetes-induced rats using DNA microarrays. The acute administration of β-conglutin reduced the incremental area under the curve of glycaemia in normal and diabetes-induced animals. In a seven-day study with diabetic animals, glycaemia increased significantly in non-treated animals but remained unchanged in animals treated with a daily dose of β-conglutin. Noteworthy, total cholesterol was significantly lower at the end of the experimental period (−21.8%, p = 0.039). Results of the microarray test and gene ontology analyses revealed several targets and pathways modulated after β-conglutin treatment, including a down-regulation of Jun kinase activity. Moreover, our data indicate that targets related to oxidative stress, inflammation, and estrogenic activity might orchestrate these metabolic effects. In conclusion, our findings show that β-conglutin may be useful to manage postprandial glycaemia and reduce cholesterol levels under the dysglycaemia stage. We identified and proposed new potential molecular targets for further research related to the mechanism of action of β-conglutin.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33166762" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156580" }, "primaryId" : "GEO:GSE156580", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156580" } ] }, "title" : "Intersectional analysis of chronic mild stress-induced lncRNA-mRNA interaction networks in rat hippocampus reveals potential anti-depression/anxiety drug targets", "dateAssigned" : "2020-08-20T00:00:00.000-05:00", "summary" : "Despite studies providing insight into the neurobiology of chronic stress, depression and anxiety, long noncoding RNA (lncRNA)-mediated mechanisms underlying the common and distinct pathophysiology of these stress-induced disorders remain nonconclusive. In a previous study, we used the chronic mild stress paradigm to separate depression-susceptible, anxiety-susceptible and insusceptible rat subpopulations. In the current study, lncRNA and messenger RNA (mRNA) expression was comparatively profiled in the hippocampus of the three stress groups using microarray technology. Groupwise comparisons identified distinct sets of lncRNAs and mRNAs associated with the three different behavioral phenotypes of the stressed rats. To investigate the regulatory roles of the dysregulated lncRNAs upon mRNA expression, correlations between the differential lncRNAs and mRNAs were first analyzed by combined use of weighted gene coexpression network analysis and ceRNA theory-based methods. Subsequent functional analysis of strongly correlated mRNAs indicated that the dysregulated lncRNAs were involved in various biological pathways and processes to specifically induce rat susceptibility or resiliency to depression or anxiety. Further intersectional analysis of phenotype-associated and drug-associated lncRNA-mRNA networks and subnetworks assisted in identifying 16 hub lncRNAs as potential targets of anti-depression/anxiety drugs. Collectively, our study established the molecular basis for understanding the similarities and differences in pathophysiological mechanisms underlying stress-induced depression or anxiety and stress resiliency, revealing several important lncRNAs that represent potentially new therapeutic drug targets for depression and anxiety disorders.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156587" }, "primaryId" : "GEO:GSE156587", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156587" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to Fe2O3 (NRCWE018)", "dateAssigned" : "2020-08-20T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 2 µg/mL of Fe2O3 (NRCWE018). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156590" }, "primaryId" : "GEO:GSE156590", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156590" } ] }, "title" : "Urinary miRNA biomarkers of the rat kidney nephron", "dateAssigned" : "2020-08-20T00:00:00.000-05:00", "summary" : "The Health and Environmental Sciences Institute initiated a cross-laboratory program to identify and characterize microRNA (miRNA) patterns reflecting nephron-specific localization in naïve adult male Sprague-Dawley rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33367795" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156659" }, "primaryId" : "GEO:GSE156659", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156659" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to zinc iron oxide (ZnFe2O4, NRCWE021)", "dateAssigned" : "2020-08-21T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 17 µg/mL of zinc iron oxide (ZnFe2O4, NRCWE021). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156660" }, "primaryId" : "GEO:GSE156660", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156660" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to COOH-functionalized carbon nanotubes (NRCWE042)", "dateAssigned" : "2020-08-21T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 6.8 cm²/cm² of COOH-functionalized carbon nanotubes (NRCWE042). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156666" }, "primaryId" : "GEO:GSE156666", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156666" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to NH2-functionalized carbon nanotubes (NRCWE049)", "dateAssigned" : "2020-08-21T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 1.2 cm²/cm² of NH2-functionalized carbon nanotubes (NRCWE049). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156691" }, "primaryId" : "GEO:GSE156691", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156691" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to pristine single-walled carbon nanotubes (NRCWE055)", "dateAssigned" : "2020-08-23T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 11 cm²/cm² of pristine single-walled carbon nanotubes (NRCWE055). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156694" }, "primaryId" : "GEO:GSE156694", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156694" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to carbon black (Printex 90)", "dateAssigned" : "2020-08-23T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 0.9 cm²/cm² of carbon black (Printex 90). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156695" }, "primaryId" : "GEO:GSE156695", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156695" } ] }, "title" : "Transcriptomic study of NR8383 rat macrophages cells following exposure to ZnO 4 µg/mL and ZnO 16 µg/mL", "dateAssigned" : "2020-08-23T00:00:00.000-05:00", "summary" : "To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 4 µg/mL and 16 µg/mL of ZnO. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156724" }, "primaryId" : "GEO:GSE156724", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156724" } ] }, "title" : "Low responders to endurance training exhibit impaired hypertrophy and divergent biological process responses in skeletal muscle", "dateAssigned" : "2020-08-24T00:00:00.000-05:00", "summary" : "Divergent skeletal muscle phenotypes result from chronic resistance-type- versus endurance-type contraction, reflecting the principle of training specificity. However, it is unclear whether there is a common set of genetic factors that influence skeletal muscle adaptation to different modes of training. Female rats were obtained from out-bred lines selectively bred from high responders to endurance training (HRT) or low responders to endurance training (LRT; n=6/group; generation 19). Both groups underwent 14 d of synergist ablation to induce functional overload of the plantaris muscle prior to comparison to non-overload controls of the same genotype. RNA sequencing was performed to identify Gene Ontology Biological Processes with differential (LRT vs HRT) gene set enrichment. Running distance, determined well in advance of synergist ablation, increased in response to aerobic training in HRT but not LRT (65 ±26% versus -6 ±18%, respectively, mean ±SD, p<0.0001). The hypertrophy response to functional overload was attenuated in LRT versus HRT (20.1 ±5.6% versus 41.6 ±16.1%, respectively, P = 0.015). There were between-group differences in the magnitude of response of 96 upregulated- and 101 downregulated pathways. A further 27 pathways showed contrasting upregulation or downregulation in LRT versus HRT in response to functional overload. In conclusion, low responders to aerobic endurance training were also low responders for compensatory hypertrophy, and attenuated hypertrophy was associated with differential gene expression. Thus, our findings suggest that genetic factors that underpin aerobic training maladaptation may also dysregulate the transcriptional activity of biological processes that contribute to adaptation to mechanical overload.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33486778" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156758" }, "primaryId" : "GEO:GSE156758", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156758" } ] }, "title" : "Transcriptional profile changes in retinal pigment epithelial cell culture after treatment with an α7 nicotinic acetylcholine receptor agonist", "dateAssigned" : "2020-08-24T00:00:00.000-05:00", "summary" : "Conclusions: PNU-282987 activation of RPE causes signficant transcript profile changes in RPE-J cell culture that leads to significant differentially expressed genes as seen in RNA-seq profiles and validated with qRT-PCR. Further, several genes identified in the RNA-seq were found to be necessary for the neurogenic response as seen with generation of KO lines of RPE. Our study is the first to show that activaiton of the α7 nAChR on RPE leads to genetic changes sufficient to induce adult mammalian neurogenesis in the rodent retina and that several novel genes are invovled in this pathway in mammals as compared to other vertebrate models of retinal regeneration.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156859" }, "primaryId" : "GEO:GSE156859", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156859" } ] }, "title" : "Sexually dimorphic ozone-induced changes in fetal rat hypothalamus", "dateAssigned" : "2020-08-25T00:00:00.000-05:00", "summary" : "IUGR is associated with an increased risk of obesity in offspring, which is likely driven in part by reprogramming of the hypothalamus due to suboptimal nutrition and hypoxia during development. As such, we performed mRNA-seq on whole hypothalamic tissue to identify altered expression of genes in our model of IUGR and to identify major pathways that could be associated with fetal undernutrition near term.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33031959" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156908" }, "primaryId" : "GEO:GSE156908", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156908" } ] }, "title" : "Reducing NADPH synthesis counteracts diabetic nephropathy through restoration of AMPK activity", "dateAssigned" : "2020-08-26T00:00:00.000-05:00", "summary" : "Wei et al. performed microarray analysis to explore the metabolism change in diabetes and RYGB surgery treated rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156999" }, "primaryId" : "GEO:GSE156999", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE156999" } ] }, "title" : "Circular RNAs expression profiles and potential key molecules incompletely transected spinal cord injury.", "dateAssigned" : "2020-08-27T00:00:00.000-05:00", "summary" : "Circular RNA is implicated in numerous diseases and conditions, including traumatic injury to the central nervoussystem. However, we know little regarding their role in completely transected spinal cord injury (SCI). Our studyused high-throughput sequencing to analyze circular RNA expression in rats after experimental completetransection of spinal cord. We found differential expression in 400 circular RNAs after SCI, with 249 significantlyup-regulated and 151 significantly down-regulated. We then selected five circular RNAs for qRT-PCR validation,and the results were in agreement with RNA sequencing. Additionally, we predicted the function of circular RNAin SCI through GO and KEGG analyses, as well as the construction of circRNA/microRNA interaction networks.Furthermore, we identified circular RNA chr9:1829226-1834212 and mRNA Hdac11 as key molecules after SCI.In conclusion, this study is the first to characterize circular RNA function in rats after completely transected SCI,through identifying their differential expression. Our results provide insight into the mechanism and therapeutictargets of SCI.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157112" }, "primaryId" : "GEO:GSE157112", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157112" } ] }, "title" : "Transcriptional profiling of whisker follicles and of the striatum in methamphetamine self-administered rats", "dateAssigned" : "2020-08-29T00:00:00.000-05:00", "summary" : "This study provides the first data on gene expression levels in whisker follicles and in the striatum in relation to MA reward and thereby may accelerate the research on the whisker follicle as an alternative source of biomarkers for the diagnosis of MA use disorder.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33238484" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157204" }, "primaryId" : "GEO:GSE157204", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157204" } ] }, "title" : "Subcellular Single Cell Sequencing: mRNA Diversity of Individual Glutamatergic and GABAergic Hippocampal Neurons and their Dendrites.", "dateAssigned" : "2020-08-31T00:00:00.000-05:00", "summary" : "Neurons transport a variety of mRNAs to their dendritic and axonal compartments where they are locally translated. These processes are essential for the functional specialization of these cellular structures. To explore both the intercellular variability and intracellular dynamics of neuronal compartments we characterized the somatic and dendritic transcriptome of single neurons. We used Laser Capture Microdissection to isolate the dendrites and soma of individual neurons from primary hippocampal cultures, followed by scRNA-seq to profile the mRNA content of these compartments. In total, we sequence 276 dendrites and their respective somata, 227 somata without the dendrites, and 16 negative controls (LCM cuts of areas without cellular content). We observed less cell-type specific differences in the dendritic transcriptome than in the somatic transcriptome. However, the dendritic localization of a subset of mRNAs does vary in a cell-type specific manner. Furthermore, we observed that the relation between somatic and dendritic abundance varies according to gene and is strongly influenced by cellular function. This study provides a framework for the regulation of the dendritic transcriptome within and across individual neurons.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33404500" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157348" }, "primaryId" : "GEO:GSE157348", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157348" } ] }, "title" : "Characterization of the intergenerational impact of in utero and postnatal oxycodone exposure", "dateAssigned" : "2020-09-02T00:00:00.000-05:00", "summary" : "Based on the significant physical attributes observed at P14 in the F1 and F2 generations exposed to oxycodone in utero (IUO) and postnatally (PNO), we performed RNA-Seq analysis on the nucleus accumbens (NAc). The NAc was chosen given its association with the reward pathway. RNA-Seq analysis showed several up-and down-regulated genes among the IUO, PNO, and saline groups in both the F1 and F2 generations", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:32968044" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157412" }, "primaryId" : "GEO:GSE157412", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157412" } ] }, "title" : "Acute Ozone-Induced Changes in Metabolic Processes and Liver Gene Expression: The Impact of Hepatic Vagotomy", "dateAssigned" : "2020-09-03T00:00:00.000-05:00", "summary" : "The effects of ozone exposure were examined in rats that have undergone sham surgery or hepatic vagotomy", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157426" }, "primaryId" : "GEO:GSE157426", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157426" } ] }, "title" : "RNA-sequencing in liver of rats exposed to glyphosate, MON 52276, and a mixture of pesticides", "dateAssigned" : "2020-09-03T00:00:00.000-05:00", "summary" : "Human health effects from chronic exposure to pesticide residues are little investigated. We compared standard histopathology and serum biochemistry measures and multi-omics analyses in an in vivo subchronic toxicity test of a glyphosate, its formulated product MON 52276, and mixture of six pesticide active ingredients frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole). Sprague-Dawley rats were administered with the pesticide mixture with each ingredient at its regulatory permitted acceptable daily intake.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34850229" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157441" }, "primaryId" : "GEO:GSE157441", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157441" } ] }, "title" : "Targeting IRF7 asthma phenotypes through immuno-modulation therapy", "dateAssigned" : "2020-09-03T00:00:00.000-05:00", "summary" : "Viral-induced severe asthma exacerbations in children are characterized by IRF7hi and IRF7lo molecular phenotypes. We have developed an experimental animal model that mirrors these response patterns in asthma-resistant PVG and asthma-susceptible BN rats respectively. We aimed to i) characterize the immunological and molecular hallmarks of PVG and BN responses to virus/allergen exposure, and (ii) evaluate the utility of innate immune training with the bacterial lysate OM85 to attenuate ensuing inflammation. Animals were sensitized to OVA/alum, inoculated with murine-adapted Rhinovirus model (vMC0), and challenged with OVA 24h later. RNA-seq was performed on lung and bone marrow at several time points post virus/allergen exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34367159" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157487" }, "primaryId" : "GEO:GSE157487", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157487" } ] }, "title" : "Monocytic ontogeny of regenerated macrophages characterizes the mesotheliomagenic responses to carbon nanotubes", "dateAssigned" : "2020-09-04T00:00:00.000-05:00", "summary" : "Macrophages not only derive from circulating blood monocytes, but also originate from embryonic progenitors that can proliferate. This dichotomic origin has an impact on macrophage functions in steady state and pathological conditions. Long needle-like carbon nanotubes (CNT) damage serous membranes and induce mesothelioma like asbestos fibers. Macrophages predominantly infiltrate CNT-induced injured tissue and contribute to cancer development. Here, we revealed the exact ontogeny of macrophage populations after CNT exposure by comparing the response to needle-like mesotheliomagenic CNT-7 with tangled-like non-mesotheliomagenic CNT-T. In a rat peritoneal cavity model, both CNT induced a rapid and complete depletion of MHCIIlow resident macrophages generating an empty niche available for macrophage repopulation. Macrophage disappearance after mesotheliomagenic CNT-7 was followed by a substantial inflammatory reaction, and macrophage replenishment completed after 7 days. Fifteen days after non-mesotheliomagenic CNT-T, macrophage repopulation was incomplete and accompanied by a limited inflammatory reaction. Cell depletion experiments, flow cytometry and RNA-seq analysis demonstrated that, after CNT-7, resident macrophages were mainly replaced by an influx of monocytes, which differentiated locally into MHCIIhigh inflammatory macrophages. In contrast, the low inflammatory response induced by CNT-T was linked to the activation of self-renewing MHCIIlow macrophages. In conclusion, the mesotheliomagenic response to CNT specifically relies on macrophage niche recolonization by monocytic progenitors. The homeostasis returns after exposure to non mesotheliomagenic CNT-T involves, in contrast, a macrophage maintenance by proliferation. Macrophage depletion and repopulation are thus decisive events characterizing the carcinogenic activity of fibrous particles.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157491" }, "primaryId" : "GEO:GSE157491", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157491" } ] }, "title" : "Influence of dietary whole egg on the transcriptome in Zucker Diabetic Fatty rats", "dateAssigned" : "2020-09-04T00:00:00.000-05:00", "summary" : "Here we analyzed how whole egg consumption in Zucker Diabetic Fatty (ZDF) rats alters microRNA and mRNA expression across the adipose, liver, kidney, and prefrontal cortex tissue. Male ZDF(fa/fa) rats (n= 12) and their lean controls (fa/+) (n= 12) were obtained at 6 wk of age. Rats had ad libitum access to water and were randomly assigned to a modified semi-purified AIN93G casein-based diet or a whole egg-based diet, both providing 20% protein (w/w). TotalRNA libraries were prepared using QuantSeq 3' mRNA-Seq and Lexogen smallRNA library prep kits and were further sequenced on an Illumina HighSeq3000. Differential gene expression was conducted using DESeq2 in R and Benjamini-Hochberg adjusted P- values controlling for false discovery rate at 5%.We identified 9 microRNAs and 583 genes that were differentially expressed in response to 8 wk of consuming whole egg-based diets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33141822" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157498" }, "primaryId" : "GEO:GSE157498", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157498" } ] }, "title" : "Developmental Reprogramming of Myometrial Stem Cells by Endocrine Disruptor Linking to Risk of Uterine Fibroids [ChIP-Seq]", "dateAssigned" : "2020-09-04T00:00:00.000-05:00", "summary" : "We report that developmental exposure to the endocrine disrupting chemical (EDC) diethylstilbestrol increases the estrogen action in myometrial stem cells (MMSCs), the origin from which UFs originate. The expression of reprogrammed estrogen responsive genes (ERGs) is driven by activated mixed lineage leukemia protein-1 (MLL1) in MMSCs. Deactivation of MLL1 reverses reprogramming of ERG expression. In addition, upregulation of ERGs occurs via DNA hypomethylation mechanism. Furthermore, the secretome of reprogrammed MMSCs enhances the proliferation of differentiated myometrial cells through activation of β-catenin signaling. This work identifies epigenetic mechanisms of MLL1/DNA methyltransferase- mediated MMSC reprogramming, and EDC exposure epigenetically targets MMSCs and imparts a hormonal imprint on the ERGs resulting in a \"hyper-estrogenized\" phenotype and increased hormone-dependent risk of UFs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37333266" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157500" }, "primaryId" : "GEO:GSE157500", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157500" } ] }, "title" : "Developmental Reprogramming of Myometrial Stem Cells by Endocrine Disruptor Linking to Risk of Uterine Fibroids [RNA-Seq]", "dateAssigned" : "2020-09-04T00:00:00.000-05:00", "summary" : "We report that developmental exposure to the endocrine disrupting chemical (EDC) diethylstilbestrol increases the estrogen action in myometrial stem cells (MMSCs), the origin from which UFs originate. The expression of reprogrammed estrogen responsive genes (ERGs) is driven by activated mixed lineage leukemia protein-1 (MLL1) in MMSCs. Deactivation of MLL1 reverses reprogramming of ERG expression. In addition, upregulation of ERGs occurs via DNA hypomethylation mechanism. Furthermore, the secretome of reprogrammed MMSCs enhances the proliferation of differentiated myometrial cells through activation of β-catenin signaling. This work identifies epigenetic mechanisms of MLL1/DNA methyltransferase- mediated MMSC reprogramming, and EDC exposure epigenetically targets MMSCs and imparts a hormonal imprint on the ERGs resulting in a “hyper-estrogenized” phenotype and increased hormone-dependent risk of UFs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37333266" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157502" }, "primaryId" : "GEO:GSE157502", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157502" } ] }, "title" : "Developmental Reprogramming of Myometrial Stem Cells by Endocrine Disruptor Linking to Risk of Uterine Fibroids [RRBS]", "dateAssigned" : "2020-09-04T00:00:00.000-05:00", "summary" : "We report that developmental exposure to the endocrine disrupting chemical (EDC) diethylstilbestrol increases the estrogen action in myometrial stem cells (MMSCs), the origin from which UFs originate. The expression of reprogrammed estrogen responsive genes (ERGs) is driven by activated mixed lineage leukemia protein-1 (MLL1) in MMSCs. Deactivation of MLL1 reverses reprogramming of ERG expression. In addition, upregulation of ERGs occurs via DNA hypomethylation mechanism. Furthermore, the secretome of reprogrammed MMSCs enhances the proliferation of differentiated myometrial cells through activation of β-catenin signaling. This work identifies epigenetic mechanisms of MLL1/DNA methyltransferase- mediated MMSC reprogramming, and EDC exposure epigenetically targets MMSCs and imparts a hormonal imprint on the ERGs resulting in a “hyper-estrogenized” phenotype and increased hormone-dependent risk of UFs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37333266" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157539" }, "primaryId" : "GEO:GSE157539", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157539" } ] }, "title" : "Transgenerational Disease Specific Epigenetic Sperm Biomarkers after Ancestral Exposure to Dioxin", "dateAssigned" : "2020-09-04T00:00:00.000-05:00", "summary" : "Dioxin is one of the most common historic industrial contaminants with several major industry and government accidents having exposed large numbers of the worldwide population over the past century. Previous rat studies have demonstrated the ability of dioxin (2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)) exposure to promote the epigenetic transgenerational inheritance of disease susceptibility in subsequent generations. The types of disease observed include testis, ovary, kidney, prostate and obesity pathologies. The current study was designed to use an epigenome-wide association study (EWAS) to identify potential sperm DNA methylation biomarkers for specific transgenerational diseases. The transgenerational F3 generation dioxin lineage male rats with and without a specific disease were compared to identify differential DNA methylation regions (DMRs). The genomic features of the DMRs are characterized. Observations demonstrate that disease specific epimutation DMRs exist for the transgenerational dioxin lineage rats that can potentially be used as epigenetic biomarkers for testis, ovary, kidney, prostate and obesity diseases. These disease specific DMRs were associated with genes that have previously been shown to be linked with these diseases. This EWAS for transgenerational disease identified epigenetic biomarkers and provides the proof of concept of the potential to develop similar biomarkers for humans to diagnose disease susceptibilities and facilitate preventative medicine.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35440735" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157551" }, "primaryId" : "GEO:GSE157551", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157551" } ] }, "title" : "Reduced representation bisulfite sequencing in liver of rats exposed to glyphosate, MON 52276, and a mixture of pesticides", "dateAssigned" : "2020-09-05T00:00:00.000-05:00", "summary" : "Human health effects from chronic exposure to pesticide residues are little investigated. We compared standard histopathology and serum biochemistry measures and multi-omics analyses in an in vivo subchronic toxicity test of a glyphosate, its formulated product MON 52276, and mixture of six pesticide active ingredients frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole). Sprague-Dawley rats were administered with the pesticide mixture with each ingredient at its regulatory permitted acceptable daily intake.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34850229" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157683" }, "primaryId" : "GEO:GSE157683", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157683" } ] }, "title" : "Sex-specific transcriptomic profiles and imprinting drive nicotine self-administration in rats and inform the genetic basis of human smoking behavior", "dateAssigned" : "2020-09-08T00:00:00.000-05:00", "summary" : "Tobacco cigarette smoking, with nicotine (NIC) as the addictive component, is a large risk factor for human mortality. In animals, repeated NIC exposure leads to sensitization (SST) and enhances self-administration (SA) of NIC. However, the molecular basis of SST and SA and their genetic relevance to smoking behavior are poorly understood. Using F1 progeny of inbred Envigo rats (F344/BN), we carried out a transcriptional profiling of NIC SST and SA in ventral tegmental area (VTA), nucleus accumbens core (Nac) and shell (Nash). We observed male-specific NIC SST and a parental effect of NIC with SA only present in paternal F344 crosses. Gene differential expression (DE) analysis revealed sex and brain region-specific transcriptomic signatures of SST and SA, with genes downregulated in male VTA associated with both SST and SA, while genes upregulated in male Nac were associated with SA. DE genes associated with SST and SA are enriched for those related to synaptic processes, myelin sheath, and tobacco use disorder or chemdependency. Interestingly, we found that for SST the downregulated genes in the male VTA tended to be upregulated in female VTA, and the overlapping genes were strongly enriched for smoking genome-wide association study (GWAS) risk variants, which may thus explain male-specific SST. To gain mechanistic insight on the observed parental effect of SA, we analyzed the allelic imbalance of expression (AIE) in reciprocally crossed F1 rats that exhibited differential tendency of SA and found widespread region-specific AIE. For the SA-inclined rats, the genes showing AIE bias towards paternal F344 alleles in Nac were strongly enriched for genes upregulated in Nac DE—the gene set most relevant to NIC SA—and also for GWAS risk variants of smoking initiation. These findings show a prominent role for sex and region-specific gene expression and imprinting in NIC SST and SA, and suggest a mechanistic link between genes underlying these processes and human NIC addiction. This study provides a resource for understanding the biology underlying the genetic findings on human smoking phenotypes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34007041" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157726" }, "primaryId" : "GEO:GSE157726", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157726" } ] }, "title" : "Sex-specific transcriptomic profiles of nicotine sensitization in rats inform the genetic basis of human smoking behavior", "dateAssigned" : "2020-09-09T00:00:00.000-05:00", "summary" : "Tobacco cigarette smoking, with nicotine (NIC) as the addictive component, is a large risk factor for human mortality. In animals, repeated NIC exposure leads to sensitization (SST) and enhances self-administration (SA) of NIC. However, the molecular basis of SST and SA and their genetic relevance to smoking behavior are poorly understood. Using F1 progeny of inbred Envigo rats (F344/BN), we carried out a transcriptional profiling of NIC SST and SA in ventral tegmental area (VTA), nucleus accumbens core (Nac) and shell (Nash). We observed male-specific NIC SST and a parental effect of NIC with SA only present in paternal F344 crosses. Gene differential expression (DE) analysis revealed sex and brain region-specific transcriptomic signatures of SST and SA, with genes downregulated in male VTA associated with both SST and SA, while genes upregulated in male Nac were associated with SA. DE genes associated with SST and SA are enriched for those related to synaptic processes, myelin sheath, and tobacco use disorder or chemdependency. Interestingly, we found that for SST the downregulated genes in the male VTA tended to be upregulated in female VTA, and the overlapping genes were strongly enriched for smoking genome-wide association study (GWAS) risk variants, which may thus explain male-specific SST. To gain mechanistic insight on the observed parental effect of SA, we analyzed the allelic imbalance of expression (AIE) in reciprocally crossed F1 rats that exhibited differential tendency of SA and found widespread region-specific AIE. For the SA-inclined rats, the genes showing AIE bias towards paternal F344 alleles in Nac were strongly enriched for genes upregulated in Nac DE—the gene set most relevant to NIC SA—and also for GWAS risk variants of smoking initiation. These findings show a prominent role for sex and region-specific gene expression and imprinting in NIC SST and SA, and suggest a mechanistic link between genes underlying these processes and human NIC addiction. This study provides a resource for understanding the biology underlying the genetic findings on human smoking phenotypes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34007041" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157736" }, "primaryId" : "GEO:GSE157736", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157736" } ] }, "title" : "Cranial manipulation modulates cholinergic pathway gene expression in an animal model of age-related cognitive decline", "dateAssigned" : "2020-09-09T00:00:00.000-05:00", "summary" : "In this study, we examine the effect of cranial osteopathic manipulation (COM) on gene expression, in an animal model for age-related cognitive decline (aged rats). We found that COM significantly affected the expression of 36 genes in the neuronal pathway (False Discovery Rate (FDR) < 0.004). The top five neuronal genes with the largest fold-change (Slc5a7, Chat, Slc18a3, Adcy5 and Cacna2d2, >2-fold change, FDR<0.004) are part of the cholinergic neurotransmission mechanism, which is known to affect cognitive function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34995434" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157919" }, "primaryId" : "GEO:GSE157919", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157919" } ] }, "title" : "Captopril treatment in rats with DEN-induced cirrhosis and hepatocellular carcinoma", "dateAssigned" : "2020-09-14T00:00:00.000-05:00", "summary" : "Hepatocellular carcinoma (HCC) is one of the leading cause of cancer-related mortality worldwide. Liver cirrhosis is well-established risk factor of HCC development, although prevention of HCC in cirrhosis patients is challenging. By utilizing bioinformatic compound screening based on a clinical HCC-risk-predicitve gene signature, we identified captopril as a potential HCC chemoprevention agent. We tested the drug in rats with diethylnitrosamine (DEN)-induced cirrhosis and HCC, and confirmed its HCC-preventive effect.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35801591" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157921" }, "primaryId" : "GEO:GSE157921", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157921" } ] }, "title" : "Time course analysis of the effect of embedded metal on skeletal muscle gene expression [Array]", "dateAssigned" : "2020-09-14T00:00:00.000-05:00", "summary" : "As a consequence of military operations, many veterans suffer from penetrating wounds and long-term retention of military grade heavy metal fragments. Fragments vary in size and location, and complete surgical removal may not be feasible or beneficial in all cases. Increasing evidence suggests retention of heavy metal fragments may have serious biological implications, including increased risks for malignant transformation. Previous studies assessed the tumorigenic effects of metal alloys in rats, demonstrating combinations of metals are sufficient to induce tumor formation after prolonged retention in skeletal muscle tissue. In this study, we analyzed transcriptional changes in skeletal muscle tissue in response to eight different military-relevant pure metals over 12 months. We found that most transcriptional changes occur at 1 and 3 months after metal pellets are embedded in skeletal muscle and these effects resolve at 6 and 12 months. We also report significant immunogenic effects of nickel and cobalt and suppressive effects of lead and depleted uranium on gene expression. Overall, skeletal muscle exhibits a remarkable capacity to adapt to and recover from internalized metal fragments; however, the cellular response to chronic exposure may be restricted to the metal-tissue interface. This data suggests that unless affected regions are specifically captured by biopsy, it would be difficult to reliably detect changes in muscle gene expression that would be indicative of long-term adverse health outcomes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33017228" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157924" }, "primaryId" : "GEO:GSE157924", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157924" } ] }, "title" : "Regulation of acupuncture on genes in brain stem", "dateAssigned" : "2020-09-14T00:00:00.000-05:00", "summary" : "We used microarray to detail the expression of wake-up related genes in brainstem", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157929" }, "primaryId" : "GEO:GSE157929", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE157929" } ] }, "title" : "Time course analysis of the effect of embedded metal on skeletal muscle gene expression [RNA-seq]", "dateAssigned" : "2020-09-14T00:00:00.000-05:00", "summary" : "As a consequence of military operations, many veterans suffer from penetrating wounds and long-term retention of military grade heavy metal fragments. Fragments vary in size and location, and complete surgical removal may not be feasible or beneficial in all cases. Increasing evidence suggests retention of heavy metal fragments may have serious biological implications, including increased risks for malignant transformation. Previous studies assessed the tumorigenic effects of metal alloys in rats, demonstrating combinations of metals are sufficient to induce tumor formation after prolonged retention in skeletal muscle tissue. In this study, we analyzed transcriptional changes in skeletal muscle tissue in response to eight different military-relevant pure metals over 12 months. We found that most transcriptional changes occur at 1 and 3 months after metal pellets are embedded in skeletal muscle and these effects resolve at 6 and 12 months. We also report significant immunogenic effects of nickel and cobalt and suppressive effects of lead and depleted uranium on gene expression. Overall, skeletal muscle exhibits a remarkable capacity to adapt to and recover from internalized metal fragments; however, the cellular response to chronic exposure may be restricted to the metal-tissue interface. This data suggests that unless affected regions are specifically captured by biopsy, it would be difficult to reliably detect changes in muscle gene expression that would be indicative of long-term adverse health outcomes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33017228" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158086" }, "primaryId" : "GEO:GSE158086", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158086" } ] }, "title" : "Epigenome-Wide Association Study (EWAS) Identifies Transgenerational Disease Biomarkers in Sperm Following Ancestral Exposure to the Pesticide Methoxychlor", "dateAssigned" : "2020-09-16T00:00:00.000-05:00", "summary" : "Environmental exposures such as chemical toxicants can alter gene expression and disease susceptibility through epigenetic processes. Epigenetic changes can be passed to future generations through germ cells through epigenetic transgenerational inheritance of increased disease susceptibility. The current study used an epigenome-wide association study (EWAS) to investigate whether specific transgenerational epigenetic signatures of differential DNA methylation regions (DMRs) exist that are associated with particular disease states in the F3 generation great-grand offspring of F0 generation rats exposed during gestation to the agricultural pesticide methoxychlor. The transgenerational epigenetic profile of sperm from F3 generation methoxychlor lineage rats that have only one disease state was compared to those that have no disease. Observations identify disease specific patterns of DMRs for these transgenerational rats that can potentially serve as epigenetic biomarkers for prostate disease, kidney disease, obesity, and the presence of multiple diseases. The chromosomal locations, genomic features, and gene associations of the DMRs are characterized. Disease specific DMR sets contained DMR associated genes that have previously been shown to be associated with that specific disease. Future epigenetic biomarkers could potentially be developed and validated for humans as a disease susceptibility diagnostic tool to facilitate preventative medicine and management of disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35440735" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158170" }, "primaryId" : "GEO:GSE158170", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158170" } ] }, "title" : "Maternal high-fat-diet alters lactation-specific miRNA expression and programs the DNA methylome in female offspring", "dateAssigned" : "2020-09-17T00:00:00.000-05:00", "summary" : "Reduced representation bisulfite sequencing was used to explore differentially methylated regions and sites within the amygdala of female rat offspring during earlylife and adulthood, in response to maternal high fat diet exposure. DMRs shared across early life and adulthood included pathways involved in neurodevelopment and genes regulating the DNMT machinery and protein function. To our knowledge, this is the first study to identify persistent genome-wide DNA methylation modifications associated with mHFD exposure in offspring from early life to adulthood.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158188" }, "primaryId" : "GEO:GSE158188", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158188" } ] }, "title" : "Gene expression in the nucleus accumbens shell of adult rats of both sexes after chronic exposure to delta9-tetrahydrocannabinol during adolescence", "dateAssigned" : "2020-09-18T00:00:00.000-05:00", "summary" : "Canabinoid exposure during adolescence alters the rewarding properties of drugs of abuse by mechanisms that are not fully understood. The nucleus accumbens is a key node of the circuit mediating the rewarding effects of most drugs. Here, we present data on the differential gene expression in the nucleus accumbens shell in male and female Wistar rats (postnatal day 90) after exposure to THC (3 mg/kg i.p.) or vehicle (ethanol:cremophor:saline; 1:1:18; 2 mL/kg i.p.) during adolescence (postnatal day 28 to postnatal day 44; injections on alternate days). There were 96 DEGs in THC-males compared to VEH-males and 87 DEGs in the females’ comparison. Only nine of these DEGs were present in both the THC vs. VEH comparison in both sexes. Our results suggest that THC exposure during adolescence affects several families of genes that have important functions for brain development, behavior and synaptic plasticity and could explain, at least in part, the complex behavioral phenotype observed in adult individuals with exposure to cannabinoids during adolescence.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34436576" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158251" }, "primaryId" : "GEO:GSE158251", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158251" } ] }, "title" : "Transcript changes in primary Leydig cells treated with Sertoli cell released exosomes", "dateAssigned" : "2020-09-20T00:00:00.000-05:00", "summary" : "In this study, we aim to figure out if Sertoli cells released exosomes can regulate the survival and steroidogenesis of Leydig cells. We found Sertoli cells released exosomes can cross the blood-testis barrier, deliver their contents into the Leydig cells, and promote the survival of Leydig cells through CCL20.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158254" }, "primaryId" : "GEO:GSE158254", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158254" } ] }, "title" : "Epigenome-Wide Association Study for Pesticide (Permethrin and DEET) Induced DNA Methylation Epimutation Biomarkers for Specific Transgenerational Disease", "dateAssigned" : "2020-09-20T00:00:00.000-05:00", "summary" : "Permethrin and N,N-diethyl-meta-toluamide (DEET) are the pesticides and insect repellent most commonly used by humans. These pesticides have been shown to promote the epigenetic transgenerational inheritance of disease in rats. The current study was designed as an epigenome-wide association study (EWAS) to identify potential sperm differential DNA methylation regions (DMRs) for specific transgenerational disease. Outbred Sprague Dawley gestating female rats (F0) were exposed to the pesticide combination including Permethrin and DEET. Their great-grand offspring (F3) were only transgenerationally exposed to pesticides. The transgenerational adult male rat sperm were collected from individuals with single and multiple diseases and compared to non-diseased animals to identify DMRs associated with transgenerational disease transmission. The exposure of gestating female rats to a permethrin and DEET pesticide combination promoted testis disease, prostate disease, kidney disease, and the presence of multiple disease in the subsequent great-grand offspring F3 generation. Interestingly, the majority of the disease specific sperm DMR associated genes were previously found to be linked to relevant disease specific genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35440735" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158342" }, "primaryId" : "GEO:GSE158342", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158342" } ] }, "title" : "Functional regeneration and repair of tendons using biomimetic scaffolds loaded with recombinant Periostin", "dateAssigned" : "2020-09-22T00:00:00.000-05:00", "summary" : "For molecular profiling of tendon maturation, we performed mRNA microarray analyses of total rat tendon tissue harvested from normal neonatal and 6-8w Achilles’ tendons and identified meaningful genes in down-regulated group", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158509" }, "primaryId" : "GEO:GSE158509", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158509" } ] }, "title" : "Exosomes derived from hypertrophic cardiomyocytes induce inflammation in macrophages via miR-155 mediated MAPK pathway.", "dateAssigned" : "2020-09-24T00:00:00.000-05:00", "summary" : "We report the application of RNA sequencing technology for high-throughput profiling of normal cardiomyocytes-derived and hypertrophic cardiomyocytes- derived exosomes. The miRNA expression profiles were determined by high throughput miRNA sequencing, and 635 differentially expressed miRNAs were found. However, compared with the control group, 7 miRNAs were significantly differentially expressed in exosomes released from Ang II-treated cardiomyocytes. A total of 4 miRNAs were upregulated while 3 were downregulated. We used qRT-PCR to characterize relative expression levels of miR-155 and miR-212-3p to validate the data obtained through miRNA sequencing. The results obtained through qRT-PCR and miRNA sequencing were essentially identical. To elucidate the potential role of miRNAs in hypertrophic cardiomyocytes, the prediction of miRNA targets was performed and 11,637 genes were obtained. To reduce the false positives rate of target gene prediction, only the predicted targets within the 3 databases described above were further analyzed. Finally, 5,477 predicted target genes were selected for further investigation. Our results support the concept that exosomal microRNAs have emerged as important inflammatory response modulators regulating the cardiac hypertrophy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33613526" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158553" }, "primaryId" : "GEO:GSE158553", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158553" } ] }, "title" : "Long-Term Soy Protein Isolate Intake Reduces Liver Steatosis through Changes in Global Gene Expression in Obese Zucker Rats", "dateAssigned" : "2020-09-25T00:00:00.000-05:00", "summary" : "To understand how soy protein isolate (SPI) reduced liver steatosis in male obese Zucker rats, we conducted global gene expression (RNAseq) analysis on liver samples of male rats fed either the SPI or a control casein (CAS)-based diet (n=8 per group) for 16 wks. Bioinformatics was conducted using Ingenuity Pathway Analysis (IPA) software (Qiagen, CA) with P < 0.05 and 1.3 fold differential expression cutoff values.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34262928" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158560" }, "primaryId" : "GEO:GSE158560", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158560" } ] }, "title" : "Electroacupuncture alleviates mechanical allodynia of a rat model of CRPS-I and modulates gene expression profiles in dorsal root ganglia", "dateAssigned" : "2020-09-25T00:00:00.000-05:00", "summary" : "Complex regional pain syndrome type-I (CRPS-I) is chronic neurological disorder accompanied with devastating pain. Most conventional medical treatments lack effectiveness, making CRPS-I a challenging clinical condition. Electroacupuncture (EA) showed effectiveness in alleviating the pain symptoms of CRPS-I patients. However, the molecular mechanisms underlying EA’s therapeutic effect are still not well understood. Here, we established the rat chronic post-ischemic pain (CPIP) model to mimic CRPS-I and performed repetitive EA on bilateral hind limbs of the CPIP model rats. We then performed RNA-sequencing (RNA-Seq) to study the differences in gene expression, gene networks and molecular pathways in ipsilateral DRGs innervating the hind limb of the CPIP model rats with and without repetitive EA treatment. Our results found that repetitive EA treatment significantly alleviated mechanical allodynia in bilateral hind limbs of CPIP model rats. RNA-Seq analysis indicated that EA modulated the expression of multiple genes and gene networks in the DRGs of CPIP model rats. Further bioinformatics analysis identified the up-regulation of an array of genes involved in biological process such as neutrophil chemotaxis and immune response in the DRGs of CPIP model rats after EA treatment. Thus, these results suggest that EA may alleviate pain response in CPIP model rats via regulating multiple genes. Our work may help to further advance the understandings of the molecular mechanisms underlying EA’s therapeutic effects on CRPS-I and help to identify novel targets for CRPS-I treatment", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158655" }, "primaryId" : "GEO:GSE158655", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158655" } ] }, "title" : "Methamphetamine Induces Sex-Dependent Changes in Gene Expression in Male and Female Hearts", "dateAssigned" : "2020-09-28T00:00:00.000-05:00", "summary" : "Male and female rats received daily injections of saline or methamphetamine for 10 days. Changes in gene expression were assessed by RNA sequencing either 24 hours or 30 days following the last injection. Methamphetamine induced changes in the myocardial transcriptome were significantly greater in female hearts than male hearts both in terms of the number of genes affected and the magnitude of the changes. The largest changes in female hearts involved genes that regulate the circadian clock (Dbp, Per3, Per2, BMal1, and Npas2) which is known to impact myocardial sensitivity to ischemia. These genes were unaffected by methamphetamine in male hearts. All changes in gene expression identified at day 11 returned to baseline by day 30. These data demonstrate that female rats are more sensitive than males to methamphetamine-induced changes in the myocardial transcriptome and that methamphetamine does not induce changes in myocardial transcription that persist long term after exposure to the drug has been discontinued.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33845768" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158658" }, "primaryId" : "GEO:GSE158658", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158658" } ] }, "title" : "Expression data from proliferating and quiescent adult hippocampal neural stem and progenitor cells", "dateAssigned" : "2020-09-28T00:00:00.000-05:00", "summary" : "We have characterized the transcriptome of adult rat hippocampal neural stem and progenitor cell (NSPC) cultures. The NSPCs cultures can be reversibly arrested by the quiescence-promoting signal BMP4. We provide expression data from NSPCs grown as neurospheres for 4 days in vitro in the presence of FGF2 (proliferating NSPCs) or FGF2+BMP4 (quiescent NSPCs) showing that entry into quiescence involves major changes in the transcriptional profile of the cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158697" }, "primaryId" : "GEO:GSE158697", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158697" } ] }, "title" : "Keystone genes for tooth development [Rat RNA-Seq]", "dateAssigned" : "2020-09-28T00:00:00.000-05:00", "summary" : "5 samples each from embryonic day 15.5, and 17.5 of rat developing molar tooth.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34506480" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158760" }, "primaryId" : "GEO:GSE158760", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158760" } ] }, "title" : "ChIP-seq data from pika Epas1 knock in MAF and RNA-seq data from mouse, rat, rabbit and Tibetan pika fibroblasts", "dateAssigned" : "2020-09-29T00:00:00.000-05:00", "summary" : "MAF from pika Epas1-3FLAG knock-in mice were extracted and immortalized. After 12h DMOG treatment, cells were conducted for the ChIP-seq (Bmal1,Flag). We found that in knock-in mice fibroblasts, EPAS1-3FLAG can bind to similar E-box locus compared with BMAL1. Fibroblasts from mouse, rat, rabbit and Tibetan pika were extracted (and Tibetan pika fibroblasts were immortalized). RNA was extracted at 90% confluency. We found that Per2 mRNA level was significantly lower in Tibetan pika fibroblasts compared with other species.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158781" }, "primaryId" : "GEO:GSE158781", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158781" } ] }, "title" : "Differential expression profiles of tsRNAs in myocardial ischemic rats with/without caloric restriction", "dateAssigned" : "2020-09-30T00:00:00.000-05:00", "summary" : "We report the application of high-throughput RNA sequencing technology to examine expression profiling of transfer RNA (tRNA)-derived small RNAs (tsRNAs) in a normal control group (Norm group), isoproterenol (ISO)-induced myocardial ischemic group (MI group), and CR-pretreatment plus ISO-induced myocardial ischemic group (CR+MI group). A total of 714 precisely matched tsRNAs were identified in the myocardial tissues from the three groups of rats (701 in Norm, 708 in MI, and 712 in CR+MI). We find that 302 tsRNAs were identified to be notably dysregulated in the MI group: 166 tsRNAs were upregulated while 136 tsRNAs were downregulated compared with those in the Norm group. After CR pretreatment, we identified 136 tsRNAs that were significantly altered compared with those in the MI group: 45 were upregulated while 91 were downregulated. This study provides new ideas for future research on elucidating the mechanisms of CR pretreatment through regulating tsRNAs levels in myocardial ischemic injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158831" }, "primaryId" : "GEO:GSE158831", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158831" } ] }, "title" : "Organ-, sex-, and age-dependent patterns of endogenous LINE-1 mRNA expression at a single locus resolution", "dateAssigned" : "2020-09-30T00:00:00.000-05:00", "summary" : "Expression of full-length LINE-1 mRNA, the first step in the L1 copy-and-paste amplification cycle, is a prerequisite for L1-associated genomic instability resulting from DNA damage and insertional mutagenesis. We used our stringent bioinformatics method to parse L1 mRNA transcripts and measure the level of full-length L1 mRNA expressed in mouse and rat organs at a locus-specific resolution. We find that expression of L1 loci in rodents exhibits striking organ specificity with less than 0.8% of loci shared between different organs of the same organism. This organ specificity in L1 mRNA expression is preserved in male and female mice and across different age groups. Unexpectedly, we discovered notable differences in L1 mRNA expression between sexes with only 5% of expressed L1 loci shared between male and female mice. Moreover, we report that the levels of total L1 mRNA expression and the number and spectrum of expressed L1 loci fluctuate with age as independent variables, demonstrating different patterns in different organs and sexes. Overall, our comparisons between organs and sexes and across ages ranging from 2 to 22 months establish previously unforeseen dynamic changes in L1 mRNA expression in vivo. These milestone findings establish a previously lacking atlas of endogenous L1 mRNA expression across a broad range of biological variables that will guide future studies addressing the understanding of mechanisms that govern expression of a limited number of L1 loci in any given organ and the impact of environmental and genetic perturbations on L1 mRNA expression and its involvement in disease initiation and progression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34023901" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158832" }, "primaryId" : "GEO:GSE158832", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158832" } ] }, "title" : "Lung transcriptome sequencing anlysis in Male Sprague-Dawley rats", "dateAssigned" : "2020-09-30T00:00:00.000-05:00", "summary" : "we dissected the chemical components of MXSG by liquid chromatography-mass spectrometry (LC-ESI-MS/MS) and analyzed the intervention pathways of MXSG based on components detected through network pharmacology. At the same time, the therapeutic effect of MXSG on COVID-19 was explained through published articles, and the relevant regulatory mechanism was proposed. Then, in this study, the regulatory effect of MXSG on inflammatory lung injury was explorated through transcriptome results.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33324213" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158900" }, "primaryId" : "GEO:GSE158900", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158900" } ] }, "title" : "Similar pulmonary toxicity and gene expression changes after short-term inhalation exposure to surface-modified copper oxide nanoparticles", "dateAssigned" : "2020-10-01T00:00:00.000-05:00", "summary" : "This study investigated the pulmonary toxicity of Copper oxide nanoparticles (CuO NPs) surface modified with polyethylenimine (PEI) or ascorbate (ASC), was investigated. Rats were exposed nose-only to a fixed exposure concentration of ASC or PEI coated CuO NPs for 5 consecutive days. On day 6 and day 27 post-exposure, pulmonary toxicity markers in bronchoalveolar lavage fluid (BALF) were analyzed and histopathological evaluation of the lungs was performed, along with microarray analyses on whole lung tissue samples.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158903" }, "primaryId" : "GEO:GSE158903", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158903" } ] }, "title" : "Gene expression modification in lungs of rats exposed to DQ-12 by endotracheal instillation", "dateAssigned" : "2020-10-01T00:00:00.000-05:00", "summary" : "In this work we study the pulmonary toxicological properties of cristalline silica DQ-12 using molecular toxicological approache. For this, we exposed Sprague Dawley rats by endotracheal instillation. Lung samples have been collected up to 180 days after the end of exposure and transcriptomics analysis were performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37446067" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158943" }, "primaryId" : "GEO:GSE158943", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158943" } ] }, "title" : "Genome-wide identification of altered m6A-related transcript profiles for vascular tissue in septic rats", "dateAssigned" : "2020-10-02T00:00:00.000-05:00", "summary" : "Sepsis is the leading cause of death in hospital intensive care units. Recent studies have shown that N6-methyladenosine (m6A) modification promotes the inflammatory response, and we evaluated the effect of lipopolysaccharide (LPS) on aortic m6A modifications in mRNAs and lncRNAs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34507301" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158991" }, "primaryId" : "GEO:GSE158991", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE158991" } ] }, "title" : "Chronic Colitis Impairs Cardiac Function by Suppressing Brain-Derived Neurotrophic Factor in the Adult Heart", "dateAssigned" : "2020-10-04T00:00:00.000-05:00", "summary" : "Inflammatory bowel disease (IBD) represents a spectrum of chronic inflammatory mediated conditions with known extraintestinal complications. The interplay between patients with heart failure (HF) and IBD has previously been noted, but the mechanisms driving these changes have not been well elucidated. We elucidated mechanisms in which chronic colitis can impair cardiac function via alteration of miRNA expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34543287" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159009" }, "primaryId" : "GEO:GSE159009", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159009" } ] }, "title" : "Genetic differences in estrous cycle effects on the rat brain transcriptome", "dateAssigned" : "2020-10-05T00:00:00.000-05:00", "summary" : "Males and females often differ on propensity for a substance use disorder (SUD), etiology and clinical manifestation of SUD, and response to SUD treatment strategies (Riley et al 2018). The fluctuation of sex-related hormones in the brain and/or circulation may contribute to some of these differences. For example, estradiol activity has been associated with sensitivity to drugs of abuse (Tonn Eisinger et al 2018) and vulnerability to SUD (Anker and Carroll 2011). In particular, estrogen can affect the dopamine system in brain and this may contribute to differences in the etiology and the clinical manifestation of SUD (Bobzean et al 2014). Without direct association with SUD, others have shown that stage of the estrous cycle influences RNA transcription levels and splicing in particular brain regions (Duclot and Kabbaj 2015; DiCarlo et al 2017). What has not been thoroughly explored is whether genetic factors can modify the effect of estrous cycle on RNA transcript and ultimately, whether the interaction of these two factors can influence the sex-related differences in SUD vulnerability.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159011" }, "primaryId" : "GEO:GSE159011", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159011" } ] }, "title" : "Plasma miR-9-3p and miR-136-3p levels as novel diagnostic biomarkers for mild traumatic brain injury", "dateAssigned" : "2020-10-05T00:00:00.000-05:00", "summary" : "Conclusions: Elevated plasma miRNA signature of miR-9a-3p, miR-136-3p and miR-434-3p distinguishes rats with mTBI from the naive, in the lateral FPI model of TBI. Further, all these miRNAs exhibit a dose-dependent increase in plasma levels with increase in injury severities.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33557217" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159039" }, "primaryId" : "GEO:GSE159039", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159039" } ] }, "title" : "Bulk RNA-seq analysis of the effects of ECHS1 knockdown on cardiomyocyte transcriptome", "dateAssigned" : "2020-10-05T00:00:00.000-05:00", "summary" : "Short-Chain Enoyl-CoA Hydratase Mediates Histone Crotonylation and Contributes to Cardiac Homeostasis", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33683949" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159058" }, "primaryId" : "GEO:GSE159058", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159058" } ] }, "title" : "Integrated metabolomic and transcriptomic analysis reveals metabolic adaptation of rats to Abcg2/Abcb1a knockout", "dateAssigned" : "2020-10-05T00:00:00.000-05:00", "summary" : "Breast Cancer Resistance Protein (Bcrp) and P-glycoprotein (Pgp) are xenobiotic efflux transporters that limit permeability of their substrates in the gastrointestinal system and brain, and increase drug clearance in liver and kidney. Bcrp and Pgp are also known to transport different endogenous metabolites such as riboflavin, urate, sulfated steroids and glucocorticoids. However, a systemic approach to understand the endogenous substrates and function of these transporters is still lacking. We hypothesized that Bcrp and Pgp have important endogenous functions and play a crucial role in maintaining metabolomic homeostasis in the biological system. To understand the impact of Bcrp and Pgp on endogenous metabolome, we performed untargeted metabolomics of CSF and plasma of male Sprague Dawley (SD) rats (WT) and SD rats lacking both Bcrp and Pgp (double knock-out, dKO rats) (n= 8 per genotype). In addition, we performed genome-wide microarray analysis of brain frontal cortex, kidney and liver from the same animals to analyze changes in gene expression (n=5 per genotype). Our results indicate distinct differences in metabolites and gene expression between WT and dKO rats. Rank order based on both fold change (>1.5 or <0.67) and significance (p <0.05) identified 29 metabolites in CSF and 47 metabolites in plasma as most significantly altered between WT and dKO rats, which includes, among other biochemicals, known substrates of Bcrp e.g., riboflavin, urate, daidzein and its metabolites. Significantly altered metabolites in plasma as well as CSF showed signatures of altered fatty acid metabolism and oxidative stress, which was further supported by the pathway analysis of significantly altered genes. These findings may lead to new insights in understanding the endogenous function of Bcrp and Pgp transporters and identification of functional biomarkers of these transporters", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34255797" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159136" }, "primaryId" : "GEO:GSE159136", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159136" } ] }, "title" : "Alcohol dependence in rats is associated with global changes in gene expression in the central amygdala", "dateAssigned" : "2020-10-06T00:00:00.000-05:00", "summary" : "Over-representation analysis of cell types; functional groups and molecular pathways revealed biological categories potentially important for the development of alcohol dependence in our model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34573170" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159168" }, "primaryId" : "GEO:GSE159168", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159168" } ] }, "title" : "miRNA profiling of Wild Type Wistar rat in postanatal retinal development", "dateAssigned" : "2020-10-07T00:00:00.000-05:00", "summary" : "Methods : Wistar WU rats ranging in age from P1 to P21 were anesthetized by inhalation using Forane prior to sacrifice at the same hour to avoid circadian variation. Total RNA was extracted from the retinal tissues of various developmental stages using NucleoSpin miRNA kit (Macherey–Nagel, Düren, Germany) following manufacturer's instructions. The miRNA concentration was assessed using Qubit microRNA Assay Kit (ThermoFisher Scientific, MA, USA). The RNA integrity number (RIN), an algorithm for judging the integrity of RNA samples, were evaluated using Agilent 2100 Bioanalyzer (Agilent Technologies, USA) following the manufacturing instruction of the RNA 6000 Nano kit and RIN>7 was considered acceptable. MicroRNAs was also determined using the Agilent Small RNA Kit to have deeper view in the 10 to 40-nucleotide size range. Small RNA library construction from pooled retinal samples (N=3, in each age-group) were carried out according to the Ion Total RNA-Seq Kit v2 protocol (Revision E) with slight modification. Enzymatic reaction was performed in half reaction volume, while cleaning procedures were executed with the accurate final volume according to the protocol. The Ion 316 or 318 ™ Chip v2 was used for sequencing on the Ion Torrent PGM™ instrument according to the protocol of Ion PGM™ Hi-Q View Sequencing Kit. To assess reliability of miRNA workflow solution in 316 v2 chip, two independent P7 samples were assayed (biological replicates) and P21 sample were sequenced as technical replicates in every sequencing procedure. Some samples were also sequenced in 318 v2 chip (P3, P5, P10, P15 and P21) as biological replicate. Ion Torrent Suite Platform was used to trim the raw sequence data and remove any residual sequencing adapter fragments that remained on the 5′ or 3′ ends. Reads were mapped to the non-coding RNAs from ENSEMBL [Rnor_6.0 (GCA_000001895.4)] using TMAP algorithm. These aligned BAM (Binary Alignment Map) files were further processed in Galaxy Web-based platform (Afgan, 2018) via Cufflinks, Cuffmerge and Cuffdiff (Version 2.2.1.3) application (Trapnell, 2010). Further analysis and visualising of the datasets was carried out in R Studio Software environment. qRT–PCR validation was performed using TaqMan assays.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37084144" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159200" }, "primaryId" : "GEO:GSE159200", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159200" } ] }, "title" : "Identification of translational microRNA biomarker candidates for ketoconazole-induced liver injury using next-generation sequencing", "dateAssigned" : "2020-10-07T00:00:00.000-05:00", "summary" : "Drug induced liver injury (DILI) is a leading cause of acute liver failure. Reliable and translational biomarkers are needed for early detection of DILI. microRNAs (miRNAs) have received wide attention as a novel class of potential DILI biomarkers. However, it is unclear how DILI drugs other than acetaminophen may influence miRNA expression or which miRNAs could serve as useful biomarkers in humans. We selected ketoconazole (KCZ), a classic hepatotoxin, to study miRNA biomarkers for DILI as a proof-of-concept for a workflow that integrated in vivo, in vitro, and bioinformatics analyses. We examined hepatic miRNA expression in KCZ-treated rats at multiple doses and durations using miRNA-sequencing and correlated our results with conventional DILI biomarkers such as liver histology. Significant dysregulation of rno-miR-34a-5p, rno-miR-331-3p, rno-miR-15b-3p, and rno-miR-676 was associated with cytoplasmic vacuolization, a phenotype in rat livers with KCZ-induced injury, which preceded the elevation of serum liver transaminases (ALT and AST). Between rats and humans, miR-34a-5p, miR-331-3p, and miR-15b-3p were evolutionarily conserved with identical sequences, whereas miR-676 showed 73% sequence similarity. Using quantitative PCR, we found that the levels of hsa-miR-34a-5p, hsa-miR-331-3p, and hsa-miR-15b-3p were significantly elevated in the culture media of HepaRG cells treated with 100 mM KCZ (a concentration that could induce cytotoxicity). Additionally, we computationally characterized the miRNA candidates for their gene targeting, target functions, and miRNA/target evolutionary conservation. In conclusion, we identified miR-34a-5p, miR-331-3p, and miR-15b-3p as translational biomarker candidates for early detection of KCZ-induced liver injury with a workflow applicable to computational toxicology studies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33078836" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159228" }, "primaryId" : "GEO:GSE159228", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159228" } ] }, "title" : "Cyclo (His-Pro) is an effective treatment for the AKI-to-CKD Transition", "dateAssigned" : "2020-10-08T00:00:00.000-05:00", "summary" : "Results: Cyclo (His-Pro) is an effective treatment for the AKI-to-CKD Transition", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159265" }, "primaryId" : "GEO:GSE159265", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159265" } ] }, "title" : "H2AK119ub1 ChIP-seq in rat peripheral nerve", "dateAssigned" : "2020-10-08T00:00:00.000-05:00", "summary" : "ChIP-seq of H2AK119ub1 in sham and injured rat peripheral nerve.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34090875" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159306" }, "primaryId" : "GEO:GSE159306", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159306" } ] }, "title" : "Expression data of circRNAs from the fetal rats with anorectal malformations", "dateAssigned" : "2020-10-09T00:00:00.000-05:00", "summary" : "Anorectal malformations (ARMs) are among the most common congenital terminal digestive tract malformations. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs, play roles in the development of the digestive system; however, their contributions to the pathogenesis of ARMs are not well-established. Many dysregulated circRNAs as the primary factor could play an important role in the development of anorectum. We used high-throughput sequencing to reveal the regulatory mechanism of gene expression underlying the development of anorectal malformations. These results provide original insight into the roles of circRNAs in ARMs and provide a valuable resource for further analyses of molecular mechanisms and signaling networks.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33927745" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159309" }, "primaryId" : "GEO:GSE159309", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159309" } ] }, "title" : "Lipopolysaccharide Alters the m6A Epitranscriptomic Tagging of RNAs in Cardiac Tissue", "dateAssigned" : "2020-10-09T00:00:00.000-05:00", "summary" : "N6-methyladenosine (m6A) modification plays important roles in the pathology of a variety of diseases. However, the roles of m6A modification in sepsis-induced myocardial dysfunction are not well defined.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34395520" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159438" }, "primaryId" : "GEO:GSE159438", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159438" } ] }, "title" : "MethylC-capture sequencing and RNA sequencing of control (CTL), chronic nonbacterial prostatitis (CNP) and polysaccharide (PPs)-treated SD rats [RNA-Seq]", "dateAssigned" : "2020-10-13T00:00:00.000-05:00", "summary" : "SD rats were intramuscular injected with dexamethasone to induce osteCPorosis, and treated with APS. Then, colonic epithelia of control, osteCPorotic and APS-treated osteCPorotic rats were collected for MethylC-capture sequencing .", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159439" }, "primaryId" : "GEO:GSE159439", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159439" } ] }, "title" : "MethylC-capture sequencing and RNA sequencing of control (CTL), chronic nonbacterial prostatitis (CNP) and polysaccharide (PPs)-treated SD rats [Bisulfite-Seq]", "dateAssigned" : "2020-10-13T00:00:00.000-05:00", "summary" : "SD rats were intramuscular injected with dexamethasone to induce osteCPorosis, and treated with APS. Then, colonic epithelia of control, osteCPorotic and APS-treated osteCPorotic rats were collected for MethylC-capture sequencing .", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159452" }, "primaryId" : "GEO:GSE159452", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159452" } ] }, "title" : "scRNAseq analysis from mixed cell culture from rat optic nerve", "dateAssigned" : "2020-10-13T00:00:00.000-05:00", "summary" : "scRNAseq analysis from mixed cell culture from rat optic nerve", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33627831" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159453" }, "primaryId" : "GEO:GSE159453", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159453" } ] }, "title" : "Therapeutic use of R-spondins to augment the cerebrovascular and neuronal Wnt signaling and improve stroke outcome in mice [neuron RNA-Seq]", "dateAssigned" : "2020-10-13T00:00:00.000-05:00", "summary" : "Although Wnt signaling is critical for blood-brain barrier function, neuronal survival and adult neurogenesis, Wnt proteins are poorly suited as therapeutics for stroke given production and pharmacokinetic challenges. Here, we show that R-spondins (RSPOs), a family of easily produced secreted proteins that robustly augment Wnt signaling, were widely expressed in adult mouse brain and upregulated upon ischemia and reperfusion injury. Neutralizing endogenous RSPOs with their membrane receptor LGR5 and ZNRF3/RNF43 soluble ectodomains increased cerebral infarction in a murine stroke model. Conversely, systemic administration of RSPOs substantially reduced cerebral infarction and improved neurological outcomes. The neuroprotective effects of RSPOs were dependent on LGR4/ZNRF3-mediated canonical Wnt/-catenin signaling in the endothelia, neuronal cells and neural stem/progenitor cells, all of which contributed synergistically to reduce cerebral ischemia/reperfusion injury. Thus, we identified a previously unknown neuroprotective mechanism and the therapeutic potential of recombinant RSPOs in ischemic stroke.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159555" }, "primaryId" : "GEO:GSE159555", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159555" } ] }, "title" : "Identification of regulated genes associated with ketogenic diet treatment following SCI", "dateAssigned" : "2020-10-19T00:00:00.000-05:00", "summary" : "To evaluate the changes in gene expression after spinal cord injury (SCI) and treatment with a Ketogenic Diet or a Control Diet (Refs., CD: F5960, Bioserv®; KD: F5848, Bioserv®), gene expression was studied 7 days after SCI surgery in rats. A total of 8 adult male Sprague-Dawley rats (~300 g at time of injury; Harlan Breeding Laboratory) were group-housed (21°C; 12 h: 12 h light:dark cycle). After a unilateral C5 laminectomy -dorsal processes of C4-C6 were held with a clamp and fixed in a frame tilted at a 22.5° angle and the cord was consutesd with a force of 150 Kdynes using the Infinite Horizon impactor- the animals were given ad libitum access to the 2 diets. Total RNA was isolated from 5-mm segment centered on the site of impact.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34381166" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159563" }, "primaryId" : "GEO:GSE159563", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159563" } ] }, "title" : "A holistic systems approach to characterize the impact of pre- and post-natal oxycodone exposure on neurodevelopment and behavior", "dateAssigned" : "2020-10-19T00:00:00.000-05:00", "summary" : "RNA-sequencing of total RNA isolated from P14 PFC tissues of animals exposed to oxycodone or saline revealed alterations in the expression of key genes associated with synaptic transmission, neurodevelopment, mood disorders, and addiction in the treatment groups.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33490084" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159668" }, "primaryId" : "GEO:GSE159668", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159668" } ] }, "title" : "Whole transcriptome analysis of hypoxic pulmonary hypertension", "dateAssigned" : "2020-10-20T00:00:00.000-05:00", "summary" : "Non-coding RNA plays an important regulatory role in the occurrence and development of hypoxic pulmonary hypertension (HPH). Therefore, we use high-throughput RNA sequence and bioinformatics methods to analyze the whole transcriptome HPH rats in lung tissue.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34374413" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159722" }, "primaryId" : "GEO:GSE159722", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159722" } ] }, "title" : "Transcriptome analysis reveals downregulation of urocortin expression in the hypothalamo-neurohypophysial system of Spontaneously Hypertensive rats", "dateAssigned" : "2020-10-21T00:00:00.000-05:00", "summary" : "Tissue extracted from the Supraoptic nucleus (SON), paraventricular nucleus (PVN) to determine gene expression differences as a consequence of hypertension within these structures", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33815127" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159815" }, "primaryId" : "GEO:GSE159815", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159815" } ] }, "title" : "The Regulatory Evolution of the Primate Fine-Motor System", "dateAssigned" : "2020-10-21T00:00:00.000-05:00", "summary" : "In mammals, fine motor control is essential for skilled behavior, and is subserved by specialized subdivisions of the primary motor cortex (M1) and other components of the brain’s motor circuitry. We profiled the epigenomic state of several components of the Rhesus macaque motor system, including subdivisions of M1 corresponding to hand and orofacial control. We compared this to open chromatin data from M1 in rat, mouse, and human. We found broad similarities as well as unique specializations in open chromatin regions (OCRs) between M1 subdivisions and other brain regions, as well as species- and lineage-specific differences reflecting their evolutionary histories. By distinguishing shared mammalian M1 OCRs from primate- and human-specific specializations, we highlight gene regulatory programs that could subserve the evolution of skilled motor behaviors such as speech and tool use. Further, in order to predict candidate enhancers in additional species for which primary data was not available, we developed machine learning models trained on genome sequence across species.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35410163" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159861" }, "primaryId" : "GEO:GSE159861", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE159861" } ] }, "title" : "Low responders to endurance training exhibit greater atrophy", "dateAssigned" : "2020-10-22T00:00:00.000-05:00", "summary" : "Divergent skeletal muscle phenotypes result from chronic resistance-type versus endurance-type contraction, reflecting the principle of training specificity. However, it is unclear whether there is a common set of genetic factors that influence skeletal muscle adaptation to disuse. Female rats were obtained from out-bred lines selectively bred from high responders to endurance training (HRT) or low responders to endurance training (LRT; n=6/group; generation 19). Both groups underwent 3 d of hindlimb immobilization to induce atrophy of the plantaris and soleus muscles prior to comparison to non-immobilization controls of the same genotype. RNA sequencing was performed to identify Gene Ontology Biological Processes with differential (LRT vs HRT) gene set enrichment. Running distance, determined well in advance of hindlimb immobilization, increased in response to aerobic training in HRT but not LRT. The atrophy response to hindlimb immobilization was exaggerated in LRT versus HRT. There were between-group differences for 140 processes in plantaris muscle and 118 processes in soleus muscle. In conclusion, low responders to aerobic endurance training exhibited exaggerated atrophy, and this was associated with differential gene expression. Thus, our findings suggest that genetic factors that underpin aerobic training maladaptation may also dysregulate the transcriptional activity of biological processes that contribute to adaptation to hindlimb immobilization.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35025912" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160025" }, "primaryId" : "GEO:GSE160025", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160025" } ] }, "title" : "Cytoplasmic cleavage of IMPA1 3’UTR is necessary for maintaining axon integrity.", "dateAssigned" : "2020-10-25T00:00:00.000-05:00", "summary" : "The 3’ untranslated regions (3’UTRs) of messenger RNAs (mRNA) are non-coding sequences involved in many aspects of mRNA metabolism, including intracellular localisation and translation. Incorrect processing and delivery of mRNA causes severe developmental defects and has been implicated in many neurological disorders. Here, we use deep sequencing to show that in sympathetic neuron axons, the 3’UTRs of many transcripts undergo cleavage, generating isoforms that express the coding sequence with a short 3’UTR, and stable 3’UTR-derived fragments of unknown function. Cleavage of the long 3’UTR of Inositol Monophosphatase 1 ( IMPA1 ), mediated by a protein complex containing the endonuclease Ago2 and the RNA binding protein HuD, generates a translatable isoform that is necessary for maintaining the integrity of sympathetic neuron axons. Thus, our study provides a new mechanism of mRNA metabolism that simultaneously regulates local protein synthesis and generates a yet undescribed class of non-coding RNAs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33626357" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160069" }, "primaryId" : "GEO:GSE160069", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160069" } ] }, "title" : "Direct RNA-RNA interaction between Neat1 and RNA targets, as a mechanism for RNAs paraspeckle retention", "dateAssigned" : "2020-10-25T00:00:00.000-05:00", "summary" : "The goal of this study was to determine if the lncRNA Neat1, in addition to its structural role, may also be directly involved in the binding by base pairing of RNAs and consequently in their retention in paraspeckles", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33573434" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160117" }, "primaryId" : "GEO:GSE160117", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160117" } ] }, "title" : "Gene expression modification in lungs of rats exposed to TiO2 by inhalation", "dateAssigned" : "2020-10-26T00:00:00.000-05:00", "summary" : "In this work we study the pulmonary toxicological properties of titanium dioxide using molecular toxicological approache. For this, we exposed Sprague Dawley rats by inhalation. Lung samples have been collected up to 180 days after the end of exposure and transcriptomics analysis were performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37446067" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160153" }, "primaryId" : "GEO:GSE160153", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160153" } ] }, "title" : "Liver sexual dimorphism in key signaling pathways across the rat life course", "dateAssigned" : "2020-10-26T00:00:00.000-05:00", "summary" : "Introduction: At the molecular level, cellular aging involves changes in multiple gene pathways, which can produce many aging phenotypes. In the liver, senescence changes lead to impaired hepatic function. We hypothesized that the natural hepatic aging process is driven by sex-dependent mechanisms. Purpose: We studied our well-established model of aging in which we have previously determined aging of metabolism, reproduction and endocrine systems. We performed liver transcriptomics (RNA-seq) on male and female rats at 110 and 650 days (d) fed with normal rat chow to determine changes key signaling pathways related to senescence processes. Methods: To identify the functional F1 liver changes due to natural aging processes, we evaluated the differentially expressed genes (DEGs) between 650d and 110d in males and females, with separate pairwise comparisons due to the marked differences. Genes were filtered based on ?1.4 fold change (FC) and nominal P value <0.05 (Studentｴs t-test). Results: We found that the natural liver aging process shows sex-differences. RNA-seq revealed more male (3,967) than female (283) differentially expressed genes (DEG) and pathways over the 110d to 650d period studied. Cell cycle pathway signaling in males was accompanied by decreased protein and gene expression of key genes (CDK2, CDK4, Cycd and PCNA) and an increase of p57 at 650d vs. 110d. In females, protein and gene expression of cell growth regulators such as p15 and p21, that inhibit cell cycle G1 progression were increased. Moreover, additionally the cell senescence pathway showed sexual dimorphism in liver gene regulation. Conclusions: Our results demonstrate how the natural aging process affects the liver transcriptome signature in a sex-dependent manner, specifically in cell cycle and cell senescence pathways, pathways that contribute in a major fashion to the development of aging-induced liver diseases. Understanding cellular senescence pathways involved in the natural aging process will aid evaluation of mechanisms associated with altered aging and frailty trajectories.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34387378" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160155" }, "primaryId" : "GEO:GSE160155", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160155" } ] }, "title" : "Gene expression modification in lungs of rats exposed to carbon black by inhalation", "dateAssigned" : "2020-10-26T00:00:00.000-05:00", "summary" : "In this work we study the pulmonary toxicological properties of Printex using molecular toxicological approache. For this, we exposed Sprague Dawley rats by inhalation. Lung samples have been collected up to 180 days after the end of exposure and transcriptomics analysis were performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37446067" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160175" }, "primaryId" : "GEO:GSE160175", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160175" } ] }, "title" : "Gene expression modification in lungs of rats exposed to carbon nanotube by inhalation [Mitsui]", "dateAssigned" : "2020-10-26T00:00:00.000-05:00", "summary" : "In this work we study the pulmonary toxicological properties of Mitsui using molecular toxicological approache. For this, we exposed Sprague Dawley rats by inhalation. Lung samples have been collected up to 180 days after the end of exposure and transcriptomics analysis were performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37446067" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160361" }, "primaryId" : "GEO:GSE160361", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160361" } ] }, "title" : "System genetics in rat HXB/BXH reference population identifies Tti2 as a pleiotropic quantitative trait gene for adult hippocampal neurogenesis and serum glucose", "dateAssigned" : "2020-10-28T00:00:00.000-05:00", "summary" : "Neurogenesis in the adult hippocampus contributes to learning and memory in the healthy brain and is dysregulated in metabolic and neurodegenerative diseases, but the molecular relationships between neural stem cells activity, adult neurogenesis and global metabolism are largely unknown. We applied unbiased systems genetics to reveal genetic correlations between adult neurogenesis and metabolism of peripheral tissues in a genetic reference population of 30 HXB/BXH recombinant inbred (RI) strains, derived from a cross between spontaneously hypertensive (SHR/OlaIpcv) and Brown Norway (BN-Lx/Cub) rats. We measured the rates of precursor cell proliferation, survival of new neurons, and gene expression profiles in the hippocampi of RI and parental strains and combined them with published metabolic phenotypes to reveal a “neuro-metabolic” quantitative trait locus (QTL) for serum glucose and neuronal survival, which was further narrowed down to the Tti2 (Telo2 interacting protein 2) gene, which is a regulator of activity and stability of PIKK kinases. To validate Tti2 as a causal QTL gene, we generated a targeted frameshift mutation on the SHR/OlaIpcv background. Heterozygous SHR-Tti2+/- rats showed decreased hippocampal neurogenesis and hallmarks of dysglycemia when compared to wild-type littermates. Here we present gene expression profiling of hippocampus, liver, soleus muscle and peritoneal fat in SHR-Tti2 heterozygous rats and wild-type SHR control littermates. Our findings suggest that Tti2 may represent a direct molecular link between glucose metabolism and structural brain plasticity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160418" }, "primaryId" : "GEO:GSE160418", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160418" } ] }, "title" : "DNA copy number alterations in neutron- or gamma-ray-induced rat mammary carcinomas", "dateAssigned" : "2020-10-29T00:00:00.000-05:00", "summary" : "To investigate DNA copy number changes in rat mammary carcinomas induced by neutron or gamma-ray irradiation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:30842142" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160419" }, "primaryId" : "GEO:GSE160419", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160419" } ] }, "title" : "DNA copy number alterations in radiation-induced rat renal carcinomas", "dateAssigned" : "2020-10-29T00:00:00.000-05:00", "summary" : "To investigate DNA copy number changes in rat renal carcinomas induced by ionizing radiation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:31925975" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160433" }, "primaryId" : "GEO:GSE160433", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160433" } ] }, "title" : "Prenatal Alcohol Exposure in Rats Diminish Postnatal Cxcl16 Chemokine Ligand Brain Expression", "dateAssigned" : "2020-10-29T00:00:00.000-05:00", "summary" : "Maternal ethanol consumption during pregnancy is one of the main causes of Neurodevelopmental disorders (NDD). Prenatal alcohol exposure (PAE) produces several adverse manifestations. Even low or moderate intake has been associated with long lasting behavioral and cognitive impairment in offspring. In this study we examined the gene expression profile in the rat nucleus accumbens using microarrays, comparing animals prenatally exposed to ethanol and controls. The microarray gene expression showed an overall downward regulatory effect of PAE. Gene cluster analysis reveals that the main affected gene groups are related to transcription regulation, transcription factors and homeobox genes. We focus on the expression of the C-X-C motif chemokine ligand 16 (Cxcl16) which was differentially expressed. There is a significant reduction in the expression of this chemokine throughout the brain under PAE conditions, evidenced here by qPCR and immunohistochemistry. Chemokines are involved in neuroprotection and implicated in alcohol-induced brain damaged and neuroinflammation in the developing CNS, therefore, the significance of the overall decrease in Cxcl16 expression in the brain as a consequence of PAE, may reflect a reduced ability to neuroprotection against subsequent conditions, such as excitotoxic damage, inflammatory processes or even hypoxic-ischemic insult.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33333834" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160495" }, "primaryId" : "GEO:GSE160495", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160495" } ] }, "title" : "Early life adversity promotes sex-specific resilience to opioid addiction-related phenotypes", "dateAssigned" : "2020-10-30T00:00:00.000-05:00", "summary" : "Early life stress that is not overwhelming can have an “inoculating” effect that promotes resilience in adulthood. However, the mechanisms underlying stress inoculation are unknown and animal models are lacking. Here we used the limited bedding and nesting (LBN) model of adversity to evaluate stress inoculation of addiction-related phenotypes. In LBN, pups from postnatal day 2–9 and their dams were exposed to a low resource environment. In adulthood, they were tested for addiction-like phenotypes and compared to rats raised in standard housing conditions. High levels of impulsivity are associated with substance abuse, but LBN reduced impulsive choice compared to controls in males. LBN males also self-administered less morphine and had a lower breakpoint on a progressive ratio reinforcement schedule than controls. LBN had no effect on addiction-related behavior in females. The nucleus accumbens (NAc) mediates these behaviors, so we tested whether LBN altered NAc physiology in drug-naïve and morphine-exposed rats. LBN reduced sEPSC frequency in males, but not females. Only in males, LBN prevented a morphine-induced increased in the AMPA/NMDA ratio. RNA sequencing and genome-wide assessments of histone modifications were performed to delineate the molecular signature in the NAc associated with LBN-derived phenotypes. LBN produced sex-specific changes in transcription, including in genes related to glutamate transmission. Remodeling of unique histone marks may have contributed to these distinct transcriptional profiles. Collectively, these studies reveal that LBN causes a male-specific stress inoculation effect against addiction-related phenotypes. Identifying factors that promote resilience to addiction may reveal novel treatment options for patients.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33593913" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160500" }, "primaryId" : "GEO:GSE160500", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160500" } ] }, "title" : "Transcriptomic and metabolomic Profiling reveal the protective effect of Acanthopanax senticosus (Rupr. & Maxim.) Harms combined with Gastrodia elata Blume on cerebral ischemia-reperfusion injury", "dateAssigned" : "2020-10-30T00:00:00.000-05:00", "summary" : "In this work, we discussed the effects Acanthopanax senticosus Harms (ASE) combined with Gastrodia elata Blume (GEB) in the treatment of CIR injury. In pharmacodynamic studies, found that co-administration of ASE and GEB may improve neuronal injury and prevent neuronal apoptosis by reducing oxidative stress and inflammation, and also help prevent CIR injury. On the basis of our hypothesis, we combined the results of transcriptomic and metabonomic analyses and found that ASE and GEB could prevent cerebral ischemia-reperfusion injury induced by middle cerebral artery occlusion by targeting phenylalanine, pyrimidine, methionine, and sphingolipid metabolism. This study provides the basis for the compatibility and efficacy of ASE and GEB.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160514" }, "primaryId" : "GEO:GSE160514", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160514" } ] }, "title" : "DNA copy number alterations in radiation-induced rat mammary carcinomas", "dateAssigned" : "2020-10-30T00:00:00.000-05:00", "summary" : "To investigate DNA copy number changes in rat mammary carcinomas induced by ioizing radiation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34388197" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160543" }, "primaryId" : "GEO:GSE160543", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160543" } ] }, "title" : "Comparison of the transcriptional changes in dorsal root ganglion between paclitaxel and oxaliplatin induced peripheral neuropathic pain in rats", "dateAssigned" : "2020-10-30T00:00:00.000-05:00", "summary" : "In this study, we screened the differentially expressed genes (DEGs) in dorsal root ganglion between paclitaxel and oxaliplatin induced peripheral neuropathic pain in rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34808752" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160573" }, "primaryId" : "GEO:GSE160573", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160573" } ] }, "title" : "Bromodomain protein inhibition protects β-cells from cytokine-induced death and dysfunction via antogonism of NF-κB pathway", "dateAssigned" : "2020-10-31T00:00:00.000-05:00", "summary" : "We report that BET inhibitor (I-BET762) protect against cytokine induced pancreatic beta-cell apoptosis and did RNA-Seq to determine global transcriptome changes with the drug.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160806" }, "primaryId" : "GEO:GSE160806", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160806" } ] }, "title" : "Hippocampal GR and pCREB binding analysis of glucocorticoid enhanced memory formation [ChIP-seq]", "dateAssigned" : "2020-11-04T00:00:00.000-06:00", "summary" : "Methods: Adult male rats received 3 minutes of object exploration training or no training either with a 3.0mg.kg post-training corticosterone injection or vehicle injection to study the molecular effects underlying enhanced memory formation. Hippocampi were dissected 45 minutes after injection and snap-frozen. Subsequently, Chromatin ImmunoPrecipitation was performed for GR and pCREB and the ChIP samples were sequenced.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33840130" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160807" }, "primaryId" : "GEO:GSE160807", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160807" } ] }, "title" : "Hippocampal transcriptome analysis of glucocorticoid enhanced memory formation [RNA-seq]", "dateAssigned" : "2020-11-04T00:00:00.000-06:00", "summary" : "Methods: Adult male rats received 3 minutes of object exploration training or no training either with a 3.0mg.kg post-training corticosterone or vehicle injection to study the molecular effects underlying enhanced memory formation. Hippocampi were dissected 3 hours after injection and snap-frozen. Subsequently, total RNA was isolated and send for 100bp paired-end sequencing by BGI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33840130" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160914" }, "primaryId" : "GEO:GSE160914", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160914" } ] }, "title" : "Perirenal Adipose Afferent Nerves Sustain Pathological High Blood Pressure", "dateAssigned" : "2020-11-05T00:00:00.000-06:00", "summary" : "Hypertension is a pathological condition of persistent high blood pressure (BP) of which the underlying mechanisms remain largely obscure. Here, we show that the afferent nerves in perirenal adipose tissue are a regulatory site in triggering and maintaining pathological high BP, without affecting physiological BP. Bilateral perirenal adipose tissue (PRAT) ablation leads to a long-term and effective reduction of BP in spontaneous hypertensive rats (SHR) and high fat and high salt diet fed rats, but has no effect on normal BP in control Wistar-Kyoto or control SD rats. Moreover, gain- and loss-of-function studies show that augmented activities of L1-L2 dorsal root ganglia (DRG) neurons are responsible for hypertension in SHR. Further, L1-L2 DRG neuron transcriptomics uncovers significant changes in neuron development, remodeling, and plasticity. Importantly, calcitonin gene-related peptide (CGRP), a systemic vasodilator, is induced after PRAT ablation. We went on to show that CGRP antagonist blocks the BP-lowering effect of PRAT ablation. CGRP is therefore a key endogenous suppressor of hypertension that is sequestered by anti-hypertensive PRAT in SHRs. Taken together, we identify PRAT afferent nerves as a pathological node of hypertension that sustains high BP via suppressing CGRP, thereby providing a therapeutic target to tackle primary hypertension.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35668093" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160926" }, "primaryId" : "GEO:GSE160926", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE160926" } ] }, "title" : "Intermittent short-duration reoxygenation protects against simulated high altitude-induced pulmonary hypertension in rats", "dateAssigned" : "2020-11-05T00:00:00.000-06:00", "summary" : "High-altitude pulmonary hypertension (HAPH) is a severe and progressive disease caused by chronic hypoxia and subsequent pulmonary vascular remodeling. No cure is currently available owing to an incomplete understanding about vascular remodeling. It is believed that hypoxia-induced diseases can be prevented by treating hypoxia. Thus, this study aimed to determine whether daily short-duration reoxygenation at sea level attenuates pulmonary hypertension under high-altitude hypoxia. To this end, a simulated 5,000-m hypoxia rat model was used to evaluate the effect of short-duration reoxygenation. Results show that intermittent, not continuous, short-duration reoxygenation effectively attenuates hypoxia-induced pulmonary hypertension. The mechanisms underlining the protective effects involved that intermittent, short-duration reoxygenation prevented functional and structural remodeling of pulmonary arteries and proliferation, migration, and phenotypic conversion of pulmonary artery smooth muscle cells under hypoxia. The specific genes or potential molecular pathways responsible for mediating the protective effects were also characterised by RNA sequencing.This study is novel in revealing a new potential method in preventing high-altitude pulmonary hypertension. It gives insights into the selection and optimisation of oxygen supply schemes in high-altitude areas.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161044" }, "primaryId" : "GEO:GSE161044", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161044" } ] }, "title" : "RNA sequencing analysis of rupture-prone intracranial aneurysms and the remaining circle of Willis in rats", "dateAssigned" : "2020-11-08T00:00:00.000-06:00", "summary" : "Comprehensive gene expression profile was obtained by RNA sequencing analysis using total RAN purified from intracranial aneurysm lesions and remaining circle of Willis in rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33203959" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161091" }, "primaryId" : "GEO:GSE161091", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161091" } ] }, "title" : "Potential therapeutic effects of long-term stem cells administration: impact on the gene profile and kidney function of PKD/Mhm (Cy/+) rats [PKD_Dez19]", "dateAssigned" : "2020-11-09T00:00:00.000-06:00", "summary" : "Cystic kidney disease (CKD) is a heterogeneous group of genetic disorders and one of the most common causes of end-stage renal disease. Here, we investigate the potential effects of long-term human stem cells treatment on kidney function and the gene expression profile of PKD/Mhm (Cy/+) rats. Human adipose derived stromal cells (ASC) and human skin-derived ABCB5+ stromal cells (2x106) were monthly, over a period of 6 months, infused intravenously or injected intraperitoneally. Additionally, ASC and ABCB5+ derived conditioned media were administrated intraperitoneally. Gene expression profile results showed a significant reprogramming of metabolism related pathways along with the down-regulation of cAMP, NF-B and apoptosis pathways. During the experimental period, the principal renal parameters as well as renal function using an innovative non-invasive transcutaneous device were measured. All together, these analyses show a moderate amelioration of the renal function in ABCB5+ and ASC treated groups. Additionally, ABCB5+ and ASC derived conditioned media treatments lead to milder, but still promising improvements. Cell-based therapy may constitute a novel therapeutic approach in CKD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35566725" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161092" }, "primaryId" : "GEO:GSE161092", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161092" } ] }, "title" : "Potential therapeutic effects of long-term stem cells administration: impact on the gene profile and kidney function of PKD/Mhm (Cy/+) rats [PKD_Jan19]", "dateAssigned" : "2020-11-09T00:00:00.000-06:00", "summary" : "Cystic kidney disease (CKD) is a heterogeneous group of genetic disorders and one of the most common causes of end-stage renal disease. Here, we investigate the potential effects of long-term human stem cells treatment on kidney function and the gene expression profile of PKD/Mhm (Cy/+) rats. Human adipose derived stromal cells (ASC) and human skin-derived ABCB5+ stromal cells (2x106) were monthly, over a period of 6 months, infused intravenously or injected intraperitoneally. Additionally, ASC and ABCB5+ derived conditioned media were administrated intraperitoneally. Gene expression profile results showed a significant reprogramming of metabolism related pathways along with the down-regulation of cAMP, NF-B and apoptosis pathways. During the experimental period, the principal renal parameters as well as renal function using an innovative non-invasive transcutaneous device were measured. All together, these analyses show a moderate amelioration of the renal function in ABCB5+ and ASC treated groups. Additionally, ABCB5+ and ASC derived conditioned media treatments lead to milder, but still promising improvements. Cell-based therapy may constitute a novel therapeutic approach in CKD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35566725" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161122" }, "primaryId" : "GEO:GSE161122", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161122" } ] }, "title" : "Cortical transcriptomic changes in the newborn rat brain after exposure to surgery and anesthesia in the third trimester", "dateAssigned" : "2020-11-09T00:00:00.000-06:00", "summary" : "We report changes in the cortical transcriptome of newborn rat pups after exposure to anesthesia and surgery in the third trimester using unbiased RNA-seq analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35210555" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161141" }, "primaryId" : "GEO:GSE161141", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161141" } ] }, "title" : "A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin-associated histone modifications", "dateAssigned" : "2020-11-09T00:00:00.000-06:00", "summary" : "Aging has been shown to be a strong driver of DNA methylation changes, leading to the development of robust biomarkers in humans and more recently, in mice. This study aimed to generate a novel epigenetic clock in rats—a model with unique physical, physiological, and biochemical advantages for studying mammalian aging. Additionally, we incorporated behavioral data, unsupervised machine learning, and network analysis to identify epigenetic signals that not only track with age, but also relate to phenotypic aging and reflect higher-order molecular aging changes. We used DNAm data from reduced representation bisulfite sequencing (RRBS) to train an epigenetic age (DNAmAge) measure in Fischer 344 CDF (F344) rats. In an independent sample of n=32 F344 rats, we found that this measure correlated with age at (r=0.93), and related to physical functioning (5.9e-3), after adjusting for age and differential cell counts. DNAmAge was also found to correlate with age in C57BL/6 mice (r=0.79), and was decreased in response to caloric restriction (CR), such that the longer the animal was on a CR diet, the greater the decrease in DNAm. We also observed resetting of DNAm when kidney and lung fibroblasts when converted to induced pluripotent stem cells (iPSCs). Using weighted gene correlation network analysis (WGCNA) we identified two modules that appeared to drive our DNAmAge measure. These two modules contained CpGs in intergenic regions that showed substantial overlap with histone marks H3K9me3, H3K27me3, and E2F1 transcriptional factor binding. In moving forward, our ability to unravel the complex signals linking DNA methylation changes to functional aging would require experimental studies in model systems in which longitudinal epigenetic changes can be related to other molecular and physiological hallmarks of aging.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33179594" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161142" }, "primaryId" : "GEO:GSE161142", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161142" } ] }, "title" : "Emergence of Dynamic Neuro-Immune Profile During Mid-life Aging in the Female Brain: Implications for Alzheimer’s Disease Risk [P3]", "dateAssigned" : "2020-11-09T00:00:00.000-06:00", "summary" : "Aging and endocrine transition states can significantly impact inflammation across organ systems. Neuroinflammation is a well-documented feature in Alzheimer’s disease (AD). Herein, we investigated neuro-inflammation that emerges during mid-life aging, chronological and endocrinological, in the female brain as an early initiating mechanism driving AD risk later in life. Analyses were conducted in a translational rodent model of mid-life chronological and endocrinological aging followed by validation in transcriptomic profiles from women versus age-matched men. In the translational model, the neuroinflammatory profile of mid-life aging in females was endocrine and chronological state specific, dynamic, anatomically distributed and persistent. Microarray dataset analyses of aging human hippocampus indicated a sex difference in neuroinflammatory profile in which women exhibited a profile comparable to the pattern discovered in our translational rodent model, whereas age-matched men exhibited a profile consistent with low neuro-immune activation. Translationally, these findings have implications for therapeutic interventions during mid-life to decrease late-onset AD risk.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33319170" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161212" }, "primaryId" : "GEO:GSE161212", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161212" } ] }, "title" : "microRNA expression signatures for rat oscc", "dateAssigned" : "2020-11-10T00:00:00.000-06:00", "summary" : "miRNA expression profiles in SD rat HNSCC", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161233" }, "primaryId" : "GEO:GSE161233", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161233" } ] }, "title" : "Emergence of Dynamic Neuro-Immune Profile During Mid-life Aging in the Female Brain: Implications for Alzheimer’s Disease Risk [Hot flash]", "dateAssigned" : "2020-11-10T00:00:00.000-06:00", "summary" : "Aging and endocrine transition states can significantly impact inflammation across organ systems. Neuroinflammation is a well-documented feature in Alzheimer’s disease (AD). Herein, we investigated neuro-inflammation that emerges during mid-life aging, chronological and endocrinological, in the female brain as an early initiating mechanism driving AD risk later in life. Analyses were conducted in a translational rodent model of mid-life chronological and endocrinological aging followed by validation in transcriptomic profiles from women versus age-matched men. In the translational model, the neuroinflammatory profile of mid-life aging in females was endocrine and chronological state specific, dynamic, anatomically distributed and persistent. Microarray dataset analyses of aging human hippocampus indicated a sex difference in neuroinflammatory profile in which women exhibited a profile comparable to the pattern discovered in our translational rodent model, whereas age-matched men exhibited a profile consistent with low neuro-immune activation. Translationally, these findings have implications for therapeutic interventions during mid-life to decrease late-onset AD risk.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33319170" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161240" }, "primaryId" : "GEO:GSE161240", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161240" } ] }, "title" : "MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity [Rat_Neurons_RNAseq]", "dateAssigned" : "2020-11-11T00:00:00.000-06:00", "summary" : "Neuron-enriched microRNAs (miRNAs), miR-9/9* and miR-124 (miR-9/9*-124), direct cell fate switching of human fibroblasts to neurons when ectopically expressed by repressing anti-neurogenic genes. How these miRNAs function after the onset of the transcriptome switch to a neuronal fate remains unclear. Here, we identified direct targets of miRNAs by Argonaute (AGO) HITS-CLIP as reprogramming cells activate the neuronal program and reveal the role of miR-124 that directly promotes the expression of its target genes associated with neuronal development and function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34031238" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161261" }, "primaryId" : "GEO:GSE161261", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161261" } ] }, "title" : "Transcriptomic analysis of mRNA of inguinal white adipose tissues from ZSF1 lean and obese rats, ZSF1 obese rats under calorie restriction, as well as ZSF1 obese rats dosed with Cmpd1.", "dateAssigned" : "2020-11-11T00:00:00.000-06:00", "summary" : "The analysis is performed to understand the role of Cmpd1 in modulating transcritomic profiles in the inguinal white adipose tissues of ZSF1 rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161312" }, "primaryId" : "GEO:GSE161312", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161312" } ] }, "title" : "Multi-omics analysis to examine gene expression and metabolites from multisite adipose-derived mesenchymal stem cells", "dateAssigned" : "2020-11-11T00:00:00.000-06:00", "summary" : "The aim of this study was to explore the gene expression and metabolites among multisite adipose-derived mesenchymal stem cells, and investigate the metabolic pathway of multisite adipose-derived mesenchymal stem cells using a multi-omics analysis. Subcutaneous adipose-derived mesenchymal stem cells (SASCs), perirenal adipose-derived mesenchymal stem cells (PASCs), and epididymal adipose-derived mesenchymal stem cells (EASCs) were isolated from Sprague Dawley rats. RNA and metabolites were extracted and sequenced using transcriptomics and metabolomics analyses, respectively. There were 720 differentially expressed genes (DEGs) in EASCs and 688 DEGs in PASCs compared with SASCs; there were 166 unique DEGs in EASCs, 134 unique DEGs in PASCs, and 554 common DEGs between EASCs and PASCs. Furthermore, there were 220 differential metabolites in EASCs, 249 differential metabolites in PASCs, 83 unique differential metabolites in EASCs, 112 unique differential metabolites in PASCs, and 137 common differential metabolites between EASCs and PASCs. The transcriptomics and metabolomics analyses identified four hub genes, one in EASCs and three in PASCs. There are functional differences among multisite adipose-derived mesenchymal stem cells that may be related to the hub genes Atac2, Rrm1, Rrm2, and Gla. The relevant signaling pathways are the Ras signaling pathway, HIF-1 signaling pathway, and the p53 signaling pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33679891" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161315" }, "primaryId" : "GEO:GSE161315", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161315" } ] }, "title" : "Fracture Hematoma Micro-Architecture Plays a Crucial Role in Determining Bone Healing Outcomes", "dateAssigned" : "2020-11-12T00:00:00.000-06:00", "summary" : "The fracture hematoma that forms between the broken fragments of bone serves as a natural fibrin scaffold. However, there is no data regarding the differences between the micro-architectural and biological properties of hematomas formed in normally healing, delayed healing, and non-healing bone defects. Mimicking these three conditions in the rat femur, we demonstrate clear differences in fibrin clot morphology, which directly affect the gene expression pattern. Specifically, RNA-sequencing reveals that the expression of essential osteogenic genes in normally healing defects are significantly up-regulated, whereas in delayed and non-healing defects they are down-regulated. Surprisingly, there were no substantial differences between delayed and non-healing defects. Most importantly, this study demonstrates that the healing outcome has already been determined at the earliest stage of bone healing. These findings could be used to develop biomaterial scaffolds mimicking the micro-architectural properties of normally healing fracture hematoma as a treatment strategy for bone defects. The hypothesis of this study was that the micro-architectural properties of the initially formed hematoma has a significant effect on the regulation of the biological process at the fracture site, which ultimately determines the outcome of bone healing. Three different healing models were investigated - normally healing, delayed healing, and non-healing defects. The results demonstrated that the intrinsic micro-architectural properties of hematomas between those groups varied distinctly in terms of fiber diameter, porosity, and density of the formed fibrin network. Those differences influenced biological responses, as evidenced by a higher expression of osteogenic genes in normally healing compared to delayed and non-healing defects, and the failed activation of BMP-2 in non-healing defects. More importantly, our results demonstrate healing outcomes are already determined at the initial (hematoma) stage of bone healing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35882120" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161317" }, "primaryId" : "GEO:GSE161317", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161317" } ] }, "title" : "T-5224, a selective inhibitor of c-Fos/AP-1, suppresses IgE-mediated mast cell activation†", "dateAssigned" : "2020-11-12T00:00:00.000-06:00", "summary" : "Conclusions:Our study represents the first detailed analysis of RBL-2H3 transcriptomes, with biologic replicates, generated by RNA-seq technology.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34130714" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161404" }, "primaryId" : "GEO:GSE161404", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161404" } ] }, "title" : "Otsuka Long-Evans Tokushima fatty rats with Roux-en-Y gastric bypass surgery", "dateAssigned" : "2020-11-13T00:00:00.000-06:00", "summary" : "Objective: The mechanisms underlying type 2 diabetes resolution after Roux-en-Y gastric bypass (RYGB) are unclear. We previously observed temporal migrations in small intestinal glycolysis, suggesting that glucose excretion may contribute to glucose homeostasis. This study aimed to evaluate the mechanisms underlying serum glucose excretion and its contribution to glucose homeostasis by using 2-deoxy-2-[18F]-fluoro-D-glucose (FDG) positron emission tomography. Design: FDG distribution in reconstructed intestinal limbs of sham- or RYGB-operated obese rats was identified. RNA sequencing was performed in areas of high or low FDG uptake.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161498" }, "primaryId" : "GEO:GSE161498", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161498" } ] }, "title" : "Transcriptional effect of early-life adversity in adult hippocampus", "dateAssigned" : "2020-11-15T00:00:00.000-06:00", "summary" : "Early-life adversity (ELA) is associated with lifelong memory deficits, yet the responsible mechanisms remain unclear. We imposed ELA by rearing rat pups in simulated poverty, assessed hippocampal memory, and probed changes in gene expression, their transcriptional regulation and the consequent changes in hippocampal neuronal structure. ELA rats had poor hippocampal memory and stunted hippocampal pyramidal neurons, associated with ~140 differentially expressed genes. Upstream regulators of the altered genes included glucocorticoid receptor and, unexpectedly, the transcription factor neuron-restrictive silencer factor (NRSF/REST). NRSF contributed critically to the memory deficits because blocking its function transiently following ELA rescued spatial memory and restored the dendritic arborization of hippocampal pyramidal neurons in ELA rats. Blocking NRSF function in vitro augmented dendritic complexity of developing hippocampal neurons, suggesting that NRSF represses genes involved in neuronal maturation. These findings establish important, surprising contributions of NRSF to ELA-induced transcriptional programming that disrupts hippocampal maturation and memory function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33326786" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161520" }, "primaryId" : "GEO:GSE161520", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161520" } ] }, "title" : "Novel role of miR-18a-5p and Galanin in rat lung ischemia-reperfusion mediated response", "dateAssigned" : "2020-11-16T00:00:00.000-06:00", "summary" : "Lung ischemia-reperfusion (IR) is known to occur after lung transplantation or cardiac bypass. IR leads to tissue inflammation and damage, is also associated with increased morbidity and mortality. Various receptors are known to partake in activation of innate immune system, but the downstream mechanism of tissue damage and inflammation is yet unknown. MicroRNAs (miRNA) are in the forefront in regulating ischemia reperfusion injury and are involved in inflammatory response. Here, we have identified by high throughput approach and evaluated distinct set of miRNAs that may play a role in response to IR in rat lung tissue. Top three differentially expressed miRNAs were validated through quantitative PCRs in the IR rat lung model and an in vitro model of IR of hypoxia and reoxygenation exposed type II alveolar cells. Among the miRNAs, miR-18a-5p showed consistent downregulation in both the model systems on IR. Cellular and molecular analysis brought to light a crucial role of this miRNA in ischemia reperfusion. MiR-18a-5p plays a role in IR mediated apoptosis, ROS production and regulates the expression of neuropeptide Galanin. It also influences the nuclear localization of transcription factor: Nuclear factor-erythroid 2 related factor (Nrf2) which in turn may regulate the expression of miR-18a gene. Thus, we have not only established a rat model for lung IR and enumerate the important miRNAs involved in IR but have also extensively characterized the role of miR-18a-5p in the same. This study will have important clinical and therapeutic implications for and during transplantation procedures.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34497682" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161540" }, "primaryId" : "GEO:GSE161540", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161540" } ] }, "title" : "Astrocyte-secreted IL-33 mediates homeostatic synaptic plasticity in the adult hippocampus", "dateAssigned" : "2020-11-16T00:00:00.000-06:00", "summary" : "Hippocampal synaptic plasticity is important for learning and memory formation. Homeostatic synaptic plasticity is a specific form of synaptic plasticity that is induced upon prolonged changes in neuronal activity to maintain network homeostasis. While astrocytes are important regulators of synaptic transmission and plasticity, it is largely unclear how they interact with neurons to regulate synaptic plasticity at the circuit level. Here, we show that neuronal activity blockade selectively increases the expression and secretion of IL-33 (interleukin-33) by astrocytes in the hippocampal cornu ammonis 1 (CA1) subregion. This IL-33 stimulates an increase in excitatory synapses and neurotransmission through the activation of neuronal IL-33 receptor complex and synaptic recruitment of the scaffold protein PSD-95. We found that acute administration of tetrodotoxin in hippocampal slices or inhibition of hippocampal CA1 excitatory neurons by optogenetic manipulation increases IL-33 expression in CA1 astrocytes. Furthermore, IL-33 administration in vivo promotes the formation of functional excitatory synapses in hippocampal CA1 neurons, whereas conditional knockout of IL-33 in CA1 astrocytes decreases the number of excitatory synapses therein. Importantly, blockade of IL-33 and its receptor signaling in vivo by intracerebroventricular administration of its decoy receptor inhibits homeostatic synaptic plasticity in CA1 pyramidal neurons and impairs spatial memory formation in mice. These results collectively reveal an important role of astrocytic IL-33 in mediating the negative-feedback signaling mechanism in homeostatic synaptic plasticity, providing insights into how astrocytes maintain hippocampal network homeostasis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33443211" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161611" }, "primaryId" : "GEO:GSE161611", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161611" } ] }, "title" : "circRNAs, miRNAs and mRNAs expression profiling in rBMSCs affected by Ta-modified Ti surface or simple Ti surface", "dateAssigned" : "2020-11-17T00:00:00.000-06:00", "summary" : "We have employed circRNAs, miRNAs and mRNAs expression profiling as a discovery platform to identify genes with the potential to distinguish rBMSCs affected by Ta-modified Ti surface or simple Ti surface", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161798" }, "primaryId" : "GEO:GSE161798", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161798" } ] }, "title" : "Macrophage derived-inflammation for confitioning of mesenchymal stromal cells", "dateAssigned" : "2020-11-19T00:00:00.000-06:00", "summary" : "Conclusions: We found that macrophage-derived inflammation induces a transcriptomic makeover on MSC, enhancing their reparative potential. These results reveal the possibility to use inflammation as a priming method for MSC before transplantation, which could potentiate the transplant's efficacy. Further pre-clinical studies are necessary to determine the effects of the beneficial outcomes in tissue, as well as the implications of compromised viability and motility.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33466704" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161836" }, "primaryId" : "GEO:GSE161836", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161836" } ] }, "title" : "Pulmonary immune cell transcriptome changes in double-hit model of BPD induced by chorioamnionitis and postnatal hyperoxia", "dateAssigned" : "2020-11-19T00:00:00.000-06:00", "summary" : "Preterm infants with bronchopulmonary dysplasia (BPD) have lifelong increased risk of respiratory morbidities associated with environmental pathogen exposure and underlying mechanisms are poorly understood. The resident immune cells of the lung play vital roles in host defense. However, the effect of perinatal events associated with BPD on pulmonary-specific immune cells is not well understood. We used a double-hit model of BPD induced by prenatal chorioamnionitis followed by postnatal hyperoxia, and performed global transcriptome analysis of all resident pulmonary immune cells. This is the first comprehensive report delineating transcriptomic changes in resident immune cells of the lung in a translationally relevant double-hit model of BPD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33446917" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161954" }, "primaryId" : "GEO:GSE161954", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE161954" } ] }, "title" : "High (5X) 5-methyltetrahydrofolate (MTHF) vs folic acid (FA) pregnancy diets on hypothalamic gene expression of Wistar rat dams upon birth.", "dateAssigned" : "2020-11-22T00:00:00.000-06:00", "summary" : "Conclusion: This study provides novel insight towards the differential effects of folate form during pregnancy on regulating dynamic changes in gene expression of the maternal brain upon birth. The results of our study may led to hypothesis testing to identify novel candidate genes and pathways targeted by folate during pregnancy that have a role in disease on-set and/or prevention.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33375730" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162001" }, "primaryId" : "GEO:GSE162001", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162001" } ] }, "title" : "Rat lung cancer model induced with smoky coal", "dateAssigned" : "2020-11-23T00:00:00.000-06:00", "summary" : "The Xuanwei area is a hot spot of lung adenocarcinoma in females in China, which is strongly associated with the consumption of local smoky coal. Comprehensive characterization of its genomic and immunological landscapes is crucial for cancer prevention and the development of precision therapy. Here, we report extensive genomic, transcriptomic, and immunological profiles of 117 Xuanwei female lung adenocarcinoma (XWFA), comprising 112 pairs of tumour-normal whole-exon sequencing (WES) profiles and 33 normal and 115 tumour mRNA-seq profiles.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34987843" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162013" }, "primaryId" : "GEO:GSE162013", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162013" } ] }, "title" : "Next generation sequencing of circular RNAs in diabetes mellitus rats after sleeve gastrectomy", "dateAssigned" : "2020-11-23T00:00:00.000-06:00", "summary" : "Sleeve gastrectomy (SG) can improve diabetes mellitus dramatically. However, the mechanisms remain largely undetermined. With the advancement of in-depth bioinformatic analysis, non-coding RNAs especially circular RNAs(circRNAs), have been implicated in many biological processes. To explore whether circRNAs mediate the amelioration of diabetes mellitus after SG, we subjected liver samples of diabetic rats after SG and shame operations for RNA sequencing. Through RNA sequencing, we identified a dramatically differentially expressed profile of 107 circRNAs. Some of these specific circRNAs were only expressed in diabetic rats after SG, which may be promising biological markers of SG prognosis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162018" }, "primaryId" : "GEO:GSE162018", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162018" } ] }, "title" : "Next generation sequencing of long non-coding RNAs in diabetes mellitus rats after sleeve gastrectomy", "dateAssigned" : "2020-11-23T00:00:00.000-06:00", "summary" : "Sleeve gastrectomy (SG) could improve diabetes mellitus dramatically. However, the mechanisms remain largely undetermined. With the advancement of in-depth bioinformatic analysis, non-coding RNAs especially long non-coding RNAs(lncRNAs), have been implicated in many biological processes. To explore whether lncRNAs mediate the amelioration of diabetes mellitus condition after SG, we subjected liver samples of diabetic rats after SG and shame operations for RNA sequencing. Further, interaction network between lncRNAs and mRNAs/microRNAs(miRNAs) were constructed to infer the function of lncRNAs in diabetic remission, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Through RNA sequencing, we identified more than 9000 lncRNAs with a dramatically differentially expressed profile of 147 lncRNAs. Some of these specific lncRNAs were only expressed in diabetic rats after SG, which may be promising biological markers of diabetic remission and SG prognosis. Through co-analysis between lncRNAs and mRNAs, 20 potential target genes of lncRNAs were screened out. Further bioinformatic analysis indicated the differentially expressed lncRNAs harbored various miRNAs binding sites and three representative lncRNA-miRNA networks of lnc50 and lnc136 were constructed. The KEGG analysis revealed that differential expressed lncRNAs were mainly related to mitogen-activated protein kinase (MAPK) pathway. These results demonstrated that SG dramatically altered expression profile of lncRNAs on diabetes mellitus, and altered lncRNAs expression may contribute to the improvement on diabetic remission through MAPK pathway by interaction with mRNA/miRNA. Our findings provide valuable resources for molecular mechanism of diabetic remission after SG and is benefit for development of lncRNAs-based diagnostic and therapeutic interventions of diabetes mellitus.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162072" }, "primaryId" : "GEO:GSE162072", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162072" } ] }, "title" : "Transcriptome profiling following focal ischemic stroke in female rats", "dateAssigned" : "2020-11-24T00:00:00.000-06:00", "summary" : "Background. Women account for 60% of all stroke deaths and are more often permanently disabled than men, despite their higher observed stroke incidence. Considering the clinical population affected by stroke, an obvious drawback is that many pre-clinical and clinical studies only investigate young males. To improve therapeutic translation from bench to bedside, we believe that it is advantageous to include both sexes in experimental models of stroke. The aims of this study were to identify early cerebral vascular responses to ischemic stroke in females, compare the differential gene expression patterns with those seen in males, and identify potential new therapeutic targets. Results. Transient middle cerebral artery occlusion (tMCAO) was used to induce stroke in both female and male rats, the middle cerebral arteries (MCAs) were isolated 3 hours post reperfusion and RNA was extracted. Affymetrix whole transcriptome expression profiling was performed on female (n = 12) MCAs to reveal differentially expressed genes. In total, 1076 genes had an increased expression and 879 genes a decreased expression in the occluded MCAs as compared with the control MCAs from female rats. An enrichment of genes related to apoptosis, regulation of transcription, protein autophosphorylation, inflammation, oxidative stress, and tissue repair and recovery were seen in the occluded MCA. The high expression genes chosen for qPCR verification (Adamts4, Olr1, JunB, Fosl1, Serpine1, S1pr3, Ccl2 and Socs3) were all shown to be upregulated in the same manner in both females and males after tMCAO (p < 0.05; n = 23). When comparing the differentially expressed genes in female MCAs (occluded and non-occluded) with our previous findings in males after tMCAO, a total of 297 genes overlapped (all groups had 32 genes in common). Conclusions. The cascades of processes initiated in the vasculature following reperfusion are complex. Dynamic gene expression alterations were observed in the occluded MCAs, and to a less pronounced degree in the non-occluded MCAs. Dysregulation of inflammation and blood-brain barrier breakdown are possible pharmacological targets. The sample of genes (<1% of differentially expressed genes) validated for this microarray did not reveal any sex differences.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33297959" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162140" }, "primaryId" : "GEO:GSE162140", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162140" } ] }, "title" : "A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [non-human Hi-C]", "dateAssigned" : "2020-11-25T00:00:00.000-06:00", "summary" : "Comprehensive transcriptomic survey of the pig (Sus scrofa) may lead to a better understanding of mechanisms of tissue specialization that underlie economic traits of this species and accelerate its use as a biomedical model. Here, we characterized four distinct transcript types (lncRNAs, TUCPs, miRNAs and circRNAs) in 31 adult pig tissues and two cell lines, together with protein-coding genes. We dissected their distinct structural and transcriptional features and uncovered transcriptome variability as related to tissue physiology. We discovered extraordinary diversity among 47 anatomically distinct skeletal muscle types, as well as among six adipose depots, which are linked to their diverse origins, metabolic features, cell composition, physical activity and mitochondrial pathways. In particular, transcription of HOX genes across skeletal muscles exhibited a position-dominant pattern, revealing a similar developmental history of these tissues within the same body part. Transcriptional patterns across adipose depots demonstrated a metabolically protective role of subcutaneous adipose tissue and the association of visceral adipose tissue with metabolic dysfunction. Comparative analysis of the transcriptomes of seven tissues of the pig and nine other vertebrates revealed insights into evolutionary divergence of transcription that contributes to lineage-specific tissue biology. We also analyzed long-range regulation of promoters by their enhancers with downstream transcription in subcutaneous adipose tissues of six mammals, showing that evolutionary stability of transcription can mainly be attributed to multiple enhancers buffering gene expression patterns against genetic perturbations, thereby conferring robustness during speciation. Collectively, this study offers a resource for the accelerated use of the pig as a biomedical model for human biology and disease and uncovers molecular bases of its diverse economic traits.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34140474" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162142" }, "primaryId" : "GEO:GSE162142", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162142" } ] }, "title" : "A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [RNA-Seq across species]", "dateAssigned" : "2020-11-25T00:00:00.000-06:00", "summary" : "Comprehensive transcriptomic survey of the pig (Sus scrofa) may lead to a better understanding of mechanisms of tissue specialization that underlie economic traits of this species and accelerate its use as a biomedical model. Here, we characterized four distinct transcript types (lncRNAs, TUCPs, miRNAs and circRNAs) in 31 adult pig tissues and two cell lines, together with protein-coding genes. We dissected their distinct structural and transcriptional features and uncovered transcriptome variability as related to tissue physiology. We discovered extraordinary diversity among 47 anatomically distinct skeletal muscle types, as well as among six adipose depots, which are linked to their diverse origins, metabolic features, cell composition, physical activity and mitochondrial pathways. In particular, transcription of HOX genes across skeletal muscles exhibited a position-dominant pattern, revealing a similar developmental history of these tissues within the same body part. Transcriptional patterns across adipose depots demonstrated a metabolically protective role of subcutaneous adipose tissue and the association of visceral adipose tissue with metabolic dysfunction. Comparative analysis of the transcriptomes of seven tissues of the pig and nine other vertebrates revealed insights into evolutionary divergence of transcription that contributes to lineage-specific tissue biology. We also analyzed long-range regulation of promoters by their enhancers with downstream transcription in subcutaneous adipose tissues of six mammals, showing that evolutionary stability of transcription can mainly be attributed to multiple enhancers buffering gene expression patterns against genetic perturbations, thereby conferring robustness during speciation. Collectively, this study offers a resource for the accelerated use of the pig as a biomedical model for human biology and disease and uncovers molecular bases of its diverse economic traits.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34140474" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162144" }, "primaryId" : "GEO:GSE162144", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162144" } ] }, "title" : "Genome-wide occupancy of linker histone variant H1T2 in round/elongating spermatids of rats", "dateAssigned" : "2020-11-25T00:00:00.000-06:00", "summary" : "Conclusion: Present study revealed that H1T2 is preferentially associated with the intergenic loci(majorly LINE L1 elements).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162146" }, "primaryId" : "GEO:GSE162146", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162146" } ] }, "title" : "A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [RNA-Seq for pig and rat]", "dateAssigned" : "2020-11-25T00:00:00.000-06:00", "summary" : "Comprehensive transcriptomic survey of the pig (Sus scrofa) may lead to a better understanding of mechanisms of tissue specialization that underlie economic traits of this species and accelerate its use as a biomedical model. Here, we characterized four distinct transcript types (lncRNAs, TUCPs, miRNAs and circRNAs) in 31 adult pig tissues and two cell lines, together with protein-coding genes. We dissected their distinct structural and transcriptional features and uncovered transcriptome variability as related to tissue physiology. We discovered extraordinary diversity among 47 anatomically distinct skeletal muscle types, as well as among six adipose depots, which are linked to their diverse origins, metabolic features, cell composition, physical activity and mitochondrial pathways. In particular, transcription of HOX genes across skeletal muscles exhibited a position-dominant pattern, revealing a similar developmental history of these tissues within the same body part. Transcriptional patterns across adipose depots demonstrated a metabolically protective role of subcutaneous adipose tissue and the association of visceral adipose tissue with metabolic dysfunction. Comparative analysis of the transcriptomes of seven tissues of the pig and nine other vertebrates revealed insights into evolutionary divergence of transcription that contributes to lineage-specific tissue biology. We also analyzed long-range regulation of promoters by their enhancers with downstream transcription in subcutaneous adipose tissues of six mammals, showing that evolutionary stability of transcription can mainly be attributed to multiple enhancers buffering gene expression patterns against genetic perturbations, thereby conferring robustness during speciation. Collectively, this study offers a resource for the accelerated use of the pig as a biomedical model for human biology and disease and uncovers molecular bases of its diverse economic traits.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34140474" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162152" }, "primaryId" : "GEO:GSE162152", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162152" } ] }, "title" : "Identification and evolutionary comparison of circular RNAs in five mammalian species and three organs.", "dateAssigned" : "2020-11-25T00:00:00.000-06:00", "summary" : "Our analyses of circRNA repertoires across five species representing three mammalian lineages (marsupials, eutherians: rodents, primates) reveal that surprisingly few circRNAs arise from orthologous genes from different species. Even the circRNAs from shared loci are associated with young, recently active and species-specific transposable elements, rather than with common, ancient transposon integration events. These observations suggest that many circRNAs emerged convergently during evolution – as a byproduct of splicing in orthologs prone to transposable element insertion. Overall, our findings argue against widespread functional circRNA conservation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34542406" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162237" }, "primaryId" : "GEO:GSE162237", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162237" } ] }, "title" : "Aryl hydrocarbon receptor is essential for the pathogenesis of pulmonary arterial hypertension [ChIP-Seq]", "dateAssigned" : "2020-11-27T00:00:00.000-06:00", "summary" : "Pulmonary arterial hypertension (PAH) is a devastating disease characterized by arteriopathy in the small to medium-sized distal pulmonary arteries, often accompanied by infiltration of inflammatory cells. Aryl hydrocarbon receptor (AHR), a nuclear receptor/transcription factor, detoxifies xenobiotics and regulates the differentiation and function of various immune cells. However, the role of AHR in the pathogenesis of PAH is largely unknown. Here, we explore the role of AHR in the pathogenesis of PAH. AHR agonistic activity in serum was significantly higher in PAH patients than in healthy volunteer and was associated with poor prognosis of PAH. Sprague-Dawley (SD) rats treated with the potent endogenous AHR agonist, 6-formylindolo[3,2-b]carbazole in combination with hypoxia develop severe pulmonary hypertension (PH) with plexiform-like lesions, whereas SD rats treated with the potent vascular endothelial growth factor receptor 2 inhibitors did not. Ahr-knockout (Ahr-/-) rats generated using the CRISPR/Cas9 system did not develop PH in the SU5416/hypoxia model. A diet containing Qing-Dai, a Chinese herbal drug, in combination with hypoxia led to development of PH in Ahr+/+ rats, but not in Ahr-/- rats. RNA-seq analysis, ChIP-seq analysis, immunohistochemical analysis, and bone marrow transplantation experiments shows that activation of several inflammatory signaling pathways were upregulated in endothelial cells and peripheral blood mononuclear cells, which led to infiltration of CD4+ IL-21+ T cells and MRC1+ macrophages into vascular lesions in an AHR-dependent manner. Taken together, AHR plays crucial roles in the development and progression of PAH and the AHR signaling pathway represents a promising novel therapeutic target for PAH", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33836606" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162239" }, "primaryId" : "GEO:GSE162239", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162239" } ] }, "title" : "Aryl hydrocarbon receptor is essential for the pathogenesis of pulmonary arterial hypertension [day 4 RNA-Seq]", "dateAssigned" : "2020-11-27T00:00:00.000-06:00", "summary" : "Pulmonary arterial hypertension (PAH) is a devastating disease characterized by arteriopathy in the small to medium-sized distal pulmonary arteries, often accompanied by infiltration of inflammatory cells. Aryl hydrocarbon receptor (AHR), a nuclear receptor/transcription factor, detoxifies xenobiotics and regulates the differentiation and function of various immune cells. However, the role of AHR in the pathogenesis of PAH is largely unknown. Here, we explore the role of AHR in the pathogenesis of PAH. AHR agonistic activity in serum was significantly higher in PAH patients than in healthy volunteer and was associated with poor prognosis of PAH. Sprague-Dawley (SD) rats treated with the potent endogenous AHR agonist, 6-formylindolo[3,2-b]carbazole in combination with hypoxia develop severe pulmonary hypertension (PH) with plexiform-like lesions, whereas SD rats treated with the potent vascular endothelial growth factor receptor 2 inhibitors did not. Ahr-knockout (Ahr-/-) rats generated using the CRISPR/Cas9 system did not develop PH in the SU5416/hypoxia model. A diet containing Qing-Dai, a Chinese herbal drug, in combination with hypoxia led to development of PH in Ahr+/+ rats, but not in Ahr-/- rats. RNA-seq analysis, ChIP-seq analysis, immunohistochemical analysis, and bone marrow transplantation experiments shows that activation of several inflammatory signaling pathways were upregulated in endothelial cells and peripheral blood mononuclear cells, which led to infiltration of CD4+ IL-21+ T cells and MRC1+ macrophages into vascular lesions in an AHR-dependent manner. Taken together, AHR plays crucial roles in the development and progression of PAH and the AHR signaling pathway represents a promising novel therapeutic target for PAH", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33836606" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162243" }, "primaryId" : "GEO:GSE162243", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162243" } ] }, "title" : "Aryl hydrocarbon receptor is essential for the pathogenesis of pulmonary arterial hypertension [day56 RNA-Seq]", "dateAssigned" : "2020-11-27T00:00:00.000-06:00", "summary" : "Pulmonary arterial hypertension (PAH) is a devastating disease characterized by arteriopathy in the small to medium-sized distal pulmonary arteries, often accompanied by infiltration of inflammatory cells. Aryl hydrocarbon receptor (AHR), a nuclear receptor/transcription factor, detoxifies xenobiotics and regulates the differentiation and function of various immune cells. However, the role of AHR in the pathogenesis of PAH is largely unknown. Here, we explore the role of AHR in the pathogenesis of PAH. AHR agonistic activity in serum was significantly higher in PAH patients than in healthy volunteer and was associated with poor prognosis of PAH. Sprague-Dawley (SD) rats treated with the potent endogenous AHR agonist, 6-formylindolo[3,2-b]carbazole in combination with hypoxia develop severe pulmonary hypertension (PH) with plexiform-like lesions, whereas SD rats treated with the potent vascular endothelial growth factor receptor 2 inhibitors did not. Ahr-knockout (Ahr-/-) rats generated using the CRISPR/Cas9 system did not develop PH in the SU5416/hypoxia model. A diet containing Qing-Dai, a Chinese herbal drug, in combination with hypoxia led to development of PH in Ahr+/+ rats, but not in Ahr-/- rats. RNA-seq analysis, ChIP-seq analysis, immunohistochemical analysis, and bone marrow transplantation experiments shows that activation of several inflammatory signaling pathways were upregulated in endothelial cells and peripheral blood mononuclear cells, which led to infiltration of CD4+ IL-21+ T cells and MRC1+ macrophages into vascular lesions in an AHR-dependent manner. Taken together, AHR plays crucial roles in the development and progression of PAH and the AHR signaling pathway represents a promising novel therapeutic target for PAH", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33836606" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162244" }, "primaryId" : "GEO:GSE162244", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162244" } ] }, "title" : "Aryl hydrocarbon receptor is essential for the pathogenesis of pulmonary arterial hypertension [PBMC]", "dateAssigned" : "2020-11-27T00:00:00.000-06:00", "summary" : "Pulmonary arterial hypertension (PAH) is a devastating disease characterized by arteriopathy in the small to medium-sized distal pulmonary arteries, often accompanied by infiltration of inflammatory cells. Aryl hydrocarbon receptor (AHR), a nuclear receptor/transcription factor, detoxifies xenobiotics and regulates the differentiation and function of various immune cells. However, the role of AHR in the pathogenesis of PAH is largely unknown. Here, we explore the role of AHR in the pathogenesis of PAH. AHR agonistic activity in serum was significantly higher in PAH patients than in healthy volunteer and was associated with poor prognosis of PAH. Sprague-Dawley (SD) rats treated with the potent endogenous AHR agonist, 6-formylindolo[3,2-b]carbazole in combination with hypoxia develop severe pulmonary hypertension (PH) with plexiform-like lesions, whereas SD rats treated with the potent vascular endothelial growth factor receptor 2 inhibitors did not. Ahr-knockout (Ahr-/-) rats generated using the CRISPR/Cas9 system did not develop PH in the SU5416/hypoxia model. A diet containing Qing-Dai, a Chinese herbal drug, in combination with hypoxia led to development of PH in Ahr+/+ rats, but not in Ahr-/- rats. RNA-seq analysis, ChIP-seq analysis, immunohistochemical analysis, and bone marrow transplantation experiments shows that activation of several inflammatory signaling pathways were upregulated in endothelial cells and peripheral blood mononuclear cells, which led to infiltration of CD4+ IL-21+ T cells and MRC1+ macrophages into vascular lesions in an AHR-dependent manner. Taken together, AHR plays crucial roles in the development and progression of PAH and the AHR signaling pathway represents a promising novel therapeutic target for PAH", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33836606" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162277" }, "primaryId" : "GEO:GSE162277", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162277" } ] }, "title" : "RNA-seq analysis of rat cardiac fibroblast transcriptome at three distinct developmental ages", "dateAssigned" : "2020-11-27T00:00:00.000-06:00", "summary" : "The purpose of this study was to map the cardiac fibroblast transcriptome at three distinct developmental ages to investigate age-dependent gene expression differences in these cells, which are critically important to extracellular matrix turnover and repair, the inflammatory process, and cardiac remodeling after injury. To do so we isolated RNA from Sprague Dawley rats at fetal, neonatal, and adult developmental stages and performed RNA-seq. Overall, we identified an array of transcriptomic differences with respect to developmental age that suggests that CFs increase expression of immune- and inflammation-associated genes with age, with a decrease in cardiac development-associated genes and pathways. These results reinforce established evidence of phenotypic heternogenity of CFs with respect to age.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34281425" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162402" }, "primaryId" : "GEO:GSE162402", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162402" } ] }, "title" : "Expression profiles and their potential roles of tRNA-derived small RNAs in hippocampus of nicotine dependence rat", "dateAssigned" : "2020-12-01T00:00:00.000-06:00", "summary" : "The mechanism of nicotine dependence and nicotine related pain remains unclear. tRNAs, a major source of small noncoding RNAs (ncRNA), are the immediate areas of research focus, which have an important role in many pathophysiological processes. However, the role of tRNAs on nicotine dependence and related pain hasn’t been explored yet. In this study, our results indicated that the expression profiles of tRNAs have changed in nicotine treated rats as compared with normal rats, and among those, some differentially expressed tRNAs might be novel targets for nicotine dependence or nicotine related pain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162419" }, "primaryId" : "GEO:GSE162419", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162419" } ] }, "title" : "Sex specific gene expression patterns in cortico-limbic structures associate with psychiatric disorders", "dateAssigned" : "2020-12-01T00:00:00.000-06:00", "summary" : "In humans there are sex-specific differences in the prevalence and symptomology of psychiatric disorders. However, preclinical animal models have primarily used males. As such, the molecular mechanisms underlying sex-specific differences in mental illness are not well established. In this study, we compared transcriptome-wide gene expression profiles in male and female rats within the corticolimbic system, including the cingulate cortex, nucleus accumbens medial shell (NAcS), ventral dentate gyrus and the basolateral amygdala. We found a considerable number of differentially expressed genes (DEGs) between males and females across all brain regions. However, 84.9% of all DEGs were found in the NAcS (> 5000 genes; p < 0.01, FDR < 0.01). Relating these DEGs to genome wide association studies (GWAS) revealed an enrichment for loci associated with major depressive disorder (Psychiatric Genomics Consortium 2019). We compared the DEGs in the NAcS to an analgous human dataset (Labonte, 2017), and found 587 common DEGs which were enriched for genes associated with both anxiety (neuro genetics study, 2016) and broad depression (UK biobank, 2018). Our data provide comprehensive evidence of sex molecular profiles in the NAcS. Importantly these differences associate with anxiety and depression, suggesting an intrinsic molecular basis for sex-based differences in disease prevalence and presentation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162524" }, "primaryId" : "GEO:GSE162524", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162524" } ] }, "title" : "Differential expression of Dusp1 and immediate early response genes in hippocampus of rats, subjected to forced swimming test", "dateAssigned" : "2020-12-02T00:00:00.000-06:00", "summary" : "This submission contains a result of a study of transcriptional profiles in the brains of rats that were exposed to the FST. RNA-seq is performed on hyppocampus tissues of rats 20 minutes and 24 hours after FST.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37340011" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162545" }, "primaryId" : "GEO:GSE162545", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162545" } ] }, "title" : "Comprehensive analysis of the transcriptome-wide m6A methylome of neonatal heart regeneration via MeRIP sequencing", "dateAssigned" : "2020-12-02T00:00:00.000-06:00", "summary" : "Aim: To systematically classify the profile of the RNA m6A modification landscape of neonatal heart regeneration. Materials and Methods: Cardiomyocyte proliferation markers were detected via immunostaining. The expression of m6A modification regulators was detected using quantitative real-time PCR (qPCR) and Western blotting. Genome-wide profiling of m6A-modified transcripts was conducted with m6A-modified RNA immunoprecipitation sequencing (m6A-RIP-seq) and RNA sequencing (RNA-seq). The Gene Expression Omnibus database (GEO) dataset was used to verify the hub genes. Results: METTL3 and the level of m6A modification in total RNA were lower in P7 rat hearts than in P0 ones. In all, 1637 m6A peaks were differentially expressed using m6A-RIP-seq, with 84 upregulated and 1553 downregulated. Furthermore, conjoint analyses of m6A-RIP-seq, RNA-seq, and GEO data generated eight potential hub genes with differentially expressed hypermethylated or hypomethylated m6A levels. Conclusion: Our data show novel information on m6A modification changes in cardiac regeneration. The modifications made possible by directly modulating m6A may attract future study of cardiac regeneration.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162548" }, "primaryId" : "GEO:GSE162548", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162548" } ] }, "title" : "Integrated analysis of long noncoding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in early stage of post-peripheral nerve injury in Sprague-Dawley rats", "dateAssigned" : "2020-12-02T00:00:00.000-06:00", "summary" : "The regulatory role of lncRNAs in the early stage post peripheral nerve injury (PNI) is not yet clear. In this study, next-generation sequencing was used to perform deep sequencing on normal sciatic nerves (control) and lesional tissues derived on the 4th (D4) and 7th days (D7) after sciatic nerve injury in rats. Time-point unique differentially expressed lncRNAs (DElncRNAs) were analyzed for functional enrichment. The results showed that 776 DElncRNAs were unique to D4, and their functions were mainly enriched in wound healing, phosphatase binding and MAPK signaling pathways; 317 DElncRNAs were unique to D7, and their functions were mainly enriched in ion transmembrane transporter channel activity; 579 DElncRNAs were shared by these two days, and their functions were mainly enriched in axongenesis, the PI3K-Akt signaling pathway and cell cycle. Furthermore, lncRNA-mRNA interaction networks were constructed in functions or pathways with a high enrichment rate. Finally, 3 mRNAs and 4 lncRNAs in the axongenesis interaction network were selected, and their expression levels were verified by RT-qPCR. This study preliminarily revealed the regulatory role of lncRNAs at different time points in the early stage post PNI, which provides potential targets for basic research and clinical treatment of PNI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33971626" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162565" }, "primaryId" : "GEO:GSE162565", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162565" } ] }, "title" : "Gene expression Profiles following mild and severe muslce contusion in rats", "dateAssigned" : "2020-12-02T00:00:00.000-06:00", "summary" : "Animal models of muscle contusion (mild and severe) were developed to investigate the cellular response to mechanical muscle damage", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33398324" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162627" }, "primaryId" : "GEO:GSE162627", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162627" } ] }, "title" : "Merkel Cell Polyomavirus Encodes Circular RNAs (circRNAs) Enabling a Dynamic circRNA/microRNA/mRNA Regulatory Network", "dateAssigned" : "2020-12-03T00:00:00.000-06:00", "summary" : "Viral noncoding RNAs have acquired increasing prominence as important regulators of infection and mediators of pathogenesis. Circular RNAs (circRNAs) generated by backsplicing events have been identified in several oncogenic human DNA viruses. Here, we show that Merkel cell polyomavirus (MCV), the etiologic cause of ~80% of Merkel cell carcinomas (MCCs), also expresses circular RNAs. By RNase R-resistant RNA sequencing, four putative circRNA backsplice junctions (BSJs) were identified from the MCV early region (ER). The most abundantly expressed MCV circRNA, designated circMCVT, is generated through backsplicing of all of ER exon II to form a 762-nucleotide (nt) circular RNA molecule. Curiously, circMCV-T, as well as two other less abundantly expressed putative MCV circRNAs, overlaps in a complementary fashion the MCV microRNA (miRNA) locus that encodes MCV-miR-M1. circMCV-T is consistently detected in concert with linear T antigen transcripts throughout infection, suggesting a crucial role for this RNA molecule in the regulatory functions of the early region, known to be vital for viral replication. Knocking out the hairpin structure of MCV-miR-M1 in genomic early region expression constructs and using a new high-efficiency, recombinase-mediated, recircularized MCV molecular clone demonstrates that circMCV-T levels decrease in the presence of MCV-miR-M1, underscoring the interplay between MCV circRNA and miRNA. Furthermore, circMCV-T partially reverses the known inhibitory effect of MCV-miR-M1 on early gene expression. RNase R-resistant RNA sequencing of lytic rat polyomavirus 2 (RatPyV2) identified an analogously located circRNA, stipulating a crucial, conserved regulatory function of this class of RNA molecules in the family of polyomaviruses.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33323517" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162705" }, "primaryId" : "GEO:GSE162705", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162705" } ] }, "title" : "Impact of short- and long-term extracellular acidosis on gene expression of tumors in vitro and in vivo", "dateAssigned" : "2020-12-04T00:00:00.000-06:00", "summary" : "Results: The analyses revealed that 147 genes were uniformly regulated in both cell lines (in vitro) and 79 genes in both experimental tumors after 24 h at low pH. 265 genes were uniformly regulated during long- and short-term exposure to low pH.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33407762" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162751" }, "primaryId" : "GEO:GSE162751", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162751" } ] }, "title" : "Effect of the deletion of the lncRNA Neat1 on the rhythmic gene expression in the GH4C1 cell line", "dateAssigned" : "2020-12-07T00:00:00.000-06:00", "summary" : "The goal of this study was to determine the effect of the deletion of the lncRNA Neat1 on the rhythmic gene expression in the GH4C1 cell line", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33995907" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162823" }, "primaryId" : "GEO:GSE162823", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162823" } ] }, "title" : "Expression data from mandibular condylar cartilage of rats", "dateAssigned" : "2020-12-07T00:00:00.000-06:00", "summary" : "We used microarrays to obtain new insights into the MCC cells by performing a comprehensive zone-specificgene expression profile analysis for each zone of the MCC isolated from 5-week-old rats using LCM technology and compare it to femoral condylar cartilage (FCC) profiles.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34413358" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162862" }, "primaryId" : "GEO:GSE162862", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162862" } ] }, "title" : "The gene expression profile of humanized rat livers", "dateAssigned" : "2020-12-08T00:00:00.000-06:00", "summary" : "We investigated the transcriptome of repopualted human hepatocytes in humanized rat livers.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34382351" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162970" }, "primaryId" : "GEO:GSE162970", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE162970" } ] }, "title" : "Mutation of the cell cycle regulator p27Kip1 drives pseudohypoxic pheochromocytoma development", "dateAssigned" : "2020-12-10T00:00:00.000-06:00", "summary" : "Background: Pseudohypoxic tumors activate pro-oncogenic pathways typically associated with severe hypoxia even when sufficient oxygen is present, leading to highly aggressive tumors. Prime examples are pseudohypoxic pheochromocytomas and paragangliomas (p-PPGLs), neuroendendocrine tumors currently orphan of effective therapy. Previous attempts to generate mouse models for p-PPGLs all failed. Here, we describe that the rat MENX line, carrying a Cdkn1b (p27) frameshift-mutation, spontaneously develops pseudohypoxic pheochromocytoma (p-PCC). Methods: We compared rat p-PCCs with their cognate human tumors at different levels: histology, immunohistochemistry, catecholamine profiling, electron microscopy, transcriptome and metabolome. Vessels architecture and angiogenic potential of PCCs was analyzed by light-sheet fluorescence microscopy ex vivo and multi-spectral optoacoustic tomography (MSOT) in vivo. Results: Analysis of tissues at various stages, from hyperplasia to advanced grades, allowed us to correlate tumor characteristics with progression. Pathological changes affecting mitochrondrial ultrastructure where present already in hyperplasias. Rat PCCs secreted high levels of norepinephrine and dopamine. Transcriptomic and metabolomic analysis revealed changes in oxidative phosphorylation that aggravated over time, leading to an accumulation of the oncometabolite 2-hydroxyglutarate, and to hypermethylation, evident by loss of the epigenetic mark 5-hmC. While rat PCC xenografts showed high oxygenation, induced by massive neoangiogenesis, rat PCC transcriptomes possessed a pseudohypoxic signature of high Hif2a, Vegfa, and low Pnmt expression, thereby clustering with human p-PPGL. Conclusion: Endogenous rat PCCs recapitulate key phenotypic features of human p-PPGLs. Thus, MENX rats emerge as the best available animal model of these aggressive tumors. Our study provides evidence of a link between cell cycle dysregulation and pseudohypoxia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33401758" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163080" }, "primaryId" : "GEO:GSE163080", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163080" } ] }, "title" : "Based on RNA-SEQ and experimental validation to explore the similarities and differences in catabolism and proliferation of chondrocyte inflammatory models between rats and mice.", "dateAssigned" : "2020-12-11T00:00:00.000-06:00", "summary" : "IL-1β promotes the proliferation of rat chondrocytes and inhibits the proliferation of mouse chondrocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35120538" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163127" }, "primaryId" : "GEO:GSE163127", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163127" } ] }, "title" : "Neuronal activity promotes nuclear proteasome-mediated degradation of PDCD4 to regulate activity-dependent transcription in neurons", "dateAssigned" : "2020-12-14T00:00:00.000-06:00", "summary" : "Activity-dependent gene expression is critical for synapse development and plasticity. To elucidate novel mechanisms linking neuronal activity to changes in transcription, we compared the nuclear proteomes of tetrodotoxin-silenced and bicuculline-stimulated cultured neurons using nuclear-localized APEX2 proximity biotinylation and mass spectrometry. The tumor suppressor protein PDCD4 was enriched in the nuclear proteome of silenced neurons, and PDCD4 levels rapidly decreased in the nucleus and cytoplasm of stimulated neurons. The activity-dependent decrease of PDCD4 was prevented by inhibitors of both PKC and proteasome activity and by a phospho-incompetent mutation of Ser71 in the βTRCP ubiquitin ligase-binding motif of PDCD4. We compared the activity-dependent transcriptomes of neurons expressing wildtype or degradation-resistant (S71A) PDCD4. We identified 91 genes as PDCD4 targets at the transcriptional level, including genes encoding proteins critical for synapse formation, remodeling, and transmission. Our findings indicate that regulated degradation of nuclear PDCD4 facilitates activity-dependent transcription in neurons.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34617965" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163132" }, "primaryId" : "GEO:GSE163132", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163132" } ] }, "title" : "Dynamic gene expression in Schwann cell for regulating myelination", "dateAssigned" : "2020-12-14T00:00:00.000-06:00", "summary" : "To obtain the dynamic gene expression of myelinating Schwann cells, we have employed gene expression profiling microarray as a discovery platform to analyze the gene expression of Schwann cells in different stages of myelination in an DRG neuron and SC co-culture myelinating model. Rat Schwann cells and dorsal root ganglion (DRG) neurons were cocultured and induced myelination in DMEM medium containing 15% FBS, 50 ng/ml NGF and 50 μg/ml L-ascorbic acid for 21d. During the co-cultivation, myelinating SCs at different stages dissected by Laser microdissection (LMD) in myelination model (i.e. co-culture 1d, 3d, 7d, 14d, 21d), the Schwann cells without co-culture as control samples (i.e. co-culture 0d). The results from Euclidean distance matrix, principal component analysis, and hierarchical clustering indicated that 2 nodal transitions in temporal gene expressions could segregate 3 distinct transcriptional phases within the period of DRG/SC co-culture 21 days. The 3 phases were designated as “premyelination”, “myelination”, and “mature phase”, respectively, by referring to morphological observation of post co-culture changes and gene ontology (GO) analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36110998" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163193" }, "primaryId" : "GEO:GSE163193", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163193" } ] }, "title" : "Sprague Dawley Whole Egg MicroRNA & Total RNA Sequencing", "dateAssigned" : "2020-12-14T00:00:00.000-06:00", "summary" : "In order to understand the effects that egg consumption has on tissue-specific microRNA and gene expression, we examined the role of whole egg consumption (20% protein, w/w) on differentially expressed genes (DEGs) between male rat (n =12) transcriptomes in the prefrontal cortex (PFC), liver, kidney and adipose tissue.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34041258" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163226" }, "primaryId" : "GEO:GSE163226", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163226" } ] }, "title" : "Effect of maternal iron deficiency on placental gene expression on gestational day 18.5 in rats", "dateAssigned" : "2020-12-15T00:00:00.000-06:00", "summary" : "Iron deficiency occurs when iron demands chronically exceed intake, and is particularly prevalent in pregnant women. Iron deficiency during pregnancy poses health risks for the baby. The placenta serves as the interface between a pregnant mother and her baby; thus, maternal iron deficiency may indirectly impact fetal growth and development by altering placental function. In this study, pregnant Sprague-Dawley rats were fed either a low-iron or iron-replete diet starting two weeks before mating. On gestational day 18.5, RNA was collected, and a Clariom S microarray was performed to elucidate differences in gene expression between gestaional day 18.5 placentas isolated from dams fed iron replete or iron deficient diets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34647996" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163255" }, "primaryId" : "GEO:GSE163255", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163255" } ] }, "title" : "RNAseq of the retinas of diabetic Goto-Kakizaki (GK) rats treated with spironolactone", "dateAssigned" : "2020-12-15T00:00:00.000-06:00", "summary" : "To identify the transcriptional regulatory mechanisms associated with the biological anti-edematous and anti-inflammatory effect of spironolactone, we performed an analysis of the regulated genes in the neuroretina of GK rats aged 14 months and treated with a formulation of Spironolacton-loaded Microspheres (Sp-MSs) that released spironolactone for at least 2 months (mean size 30µm, 1µg/mg MSs/day). RNA-sequencing was performed on the neural retina and non-loade microspheres (NL-MSs) served as control treatment. The heatmaps of genes differentially regulated by Sp-MSs individuals as compared to NL-MSs showed a clear difference between the two conditions with 114 genes significantly regulated between the two groups, 27 significantly down regulated and 87 significantly up regulated (Log2FC ≥ 0,5, adjusted p<0.05). Pathway enrichment analysis using hallmark gene-set function highlighted 9 significantly regulated pathways: unfolded protein response, UV response, G2M checkpoint, allograft rejection, interferon gamma response, MTORC1 signaling, oxidative phosphorylation, MYC targets and adipogenesis (Figure EV 3B, C). Genes encoding proteins known to intervene in vascular permeability and retinal edema were counter regulated by Sp-MSs including Vldlr, Sesn2, Adcyap1, Dusp8, Pten, Slc7a1, Tjp1, Dlg1, Sema7a, although Vegf was rather up-regulated, suggested an anti-edematous mechanism independent from VEGF. The effect of Sp-MSs was confirmed by quantitative PCR for number of these genes demonstrating that spironolactone acts as a transcriptional regulator to normalize the diabetic retina.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34426510" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163298" }, "primaryId" : "GEO:GSE163298", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163298" } ] }, "title" : "The expression patterns of piRNAs in the CA1 region of the transient Global Cerebral Ischemia rats hippocampus", "dateAssigned" : "2020-12-16T00:00:00.000-06:00", "summary" : "Conclusions: In our study, we identified a cohort of piRNAs in CA1 of rats. Furthermore, we demonstrated directly contrast changes of piRNAs interacted with Piwil2 in CA1 after tGCI, as compared to those in HPC rats. Therefore, this study revealed that PIWI/piRNAs respond to ischemic brain damage and neuroprotection mediated by HPC. To the best of our knowledge, this is the first study ever on piRNAs associated with Piwil2 in cerebral ischemic tolerance.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35794855" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163299" }, "primaryId" : "GEO:GSE163299", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163299" } ] }, "title" : "The piRNAs bounding to Piwil2 in the CA1 region of the transient Global Cerebral Ischemia rats hippocampus", "dateAssigned" : "2020-12-16T00:00:00.000-06:00", "summary" : "Conclusions: In our study, we identified a cohort of piRNAs in CA1 of rats. We demonstrated directly contrast changes of piRNAs interacted with Piwil2 in CA1 after tGCI, as compared to those in HPC rats. The results of the prediction showed that DNMT3A may be a potential common target of the 7 differentially expressed piRNAs interacted with Piwil2. Therefore, we focused on the expression of DNMT3A in CA1 after tGCI with or without HPC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35794855" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163302" }, "primaryId" : "GEO:GSE163302", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163302" } ] }, "title" : "Conserved Spermatogonial Gene Networks Couple to Glutathione and Pentose Phosphate Metabolism but not Cysteine Biosynthesis", "dateAssigned" : "2020-12-16T00:00:00.000-06:00", "summary" : "Here, gene profiles in rat spermatogonial stem cell lines are compared to publicly available mouse, monkey and human spermatogonial gene profiles. Interestingly, rat spermatogonia expressed metabolic control factors Foxa1, Foxa2 and Foxa3. Germline Foxa2 was enriched in Gfra1Hi and Gfra1Low undifferentiated A-single spermatogonia. Foxa2-bound loci in spermatogonial chromatin were over-represented by conserved stemness genes (Dusp6, Gfra1, Etv5, Rest, Nanos2, Foxp1) that intersect bioinformatically with conserved glutathione/pentose phosphate metabolism genes (Tkt, Gss, Gclc, Gclm, Gpx1, Gpx4, Fth), marking elevated spermatogonial GSH:GSSG. Cystine-uptake and intracellular conversion to cysteine typically couple glutathione biosynthesis to pentose phosphate metabolism. Rat spermatogonia, curiously, displayed poor germline stem cell viability in cystine-containing media, and, like primate spermatogonia, exhibited reduced transsulfuration pathway markers. Exogenous cysteine, cysteine-like mercaptans, somatic testis cells and ferroptosis inhibitors counteracted the cysteine starvation-induced spermatogonial death and stimulated spermatogonial growth factor activity in vitro.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33458605" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163374" }, "primaryId" : "GEO:GSE163374", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163374" } ] }, "title" : "Parental (F0) compared to MSC educated (F2) prostate cancer cell lines", "dateAssigned" : "2020-12-16T00:00:00.000-06:00", "summary" : "Our studies demonstrated that bone marrow derived mesenchymal stromal cells (MSCs) drive the emergence of an apoptosis resistant population of prostate cancer cells that are also cross resistant to chemotherapy such as docetaxel. The goals of this RNAQuant study was to determine differential gene expression between the naïve and MSC educated prostate cancer cells in order to better understand the mechanisms underlying apoptosis resistance.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33526787" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163412" }, "primaryId" : "GEO:GSE163412", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163412" } ] }, "title" : "Ancestral Plastics Exposure Induces Transgenerational Disease Specific Sperm Epigenome-Wide Association Biomarkers Methylation Epimutation Biomarkers for Specific Transgenerational Disease", "dateAssigned" : "2020-12-17T00:00:00.000-06:00", "summary" : "Plastic derived compounds are one of the most frequent daily world-wide exposures. Previously a mixture of plastic derived toxicants involving bisphenol A (BPA), Bis(2-ethylhexyl) phthalate (DEHP), and dibutyl phthalate (DBP) at lower dose exposures of a gestating female rat were found to promote the epigenetic transgenerational inheritance of disease to the offspring (F1 generation), grand-offspring (F2 generation) and great-grand-offspring (F3 generation). Epigenetic analysis of the male sperm was found to result in differential DNA methylation regions (DMRs) in the transgenerational F3 generation male sperm. The current study is distinct and was designed to identify potential sperm DNA methylation biomarkers for specific transgenerational diseases. Observations show disease specific DMRs called epimutations in the transgenerational F3 generation great-grand-offspring rats ancestrally exposed to plastics. The epigenetic DMR biomarkers were identified for testis disease, kidney disease, and multiple (≥2) diseases. These disease sperm epimutation biomarkers were found to be predominantly disease specific. The genomic locations and features of these DMRs were identified. Interestingly, the disease specific DMR associated genes were previously shown to be linked with each of the specific diseases. Therefore, the germline has ancestrally derived epimutations that potentially transmit transgenerational disease susceptibilities. Epigenetic biomarkers for specific diseases could be used as diagnostics to facilitate clinical management of disease and preventative medicine.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35440735" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163462" }, "primaryId" : "GEO:GSE163462", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163462" } ] }, "title" : "Expression data from rat hippocampus", "dateAssigned" : "2020-12-18T00:00:00.000-06:00", "summary" : "To explore gene expression changes in the inferior colliculus (IC) after single-sided deafness", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163474" }, "primaryId" : "GEO:GSE163474", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163474" } ] }, "title" : "Rat PRDM9 shapes recombination landscapes, duration of meiosis, gametogenesis, and age of fertility", "dateAssigned" : "2020-12-18T00:00:00.000-06:00", "summary" : "Vertebrate recombination concentrates in meiotic chromatin regions (hotspots) that are opened in some species by the DNA-sequence-specific-binding histone H3 trimethyltransferase PRDM9, while other species recombine in regions with already opened chromatin and other function. Inactivation of the mouse Prdm9 gene induces the shift of hotspots to functional regions, gross fertility reduction in males, and sterility in females. In contrast, the other vertebrate species lacking PRDM9 remain fertile. To resolve this discrepancy, we generated Prdm9 deletions in the Rattus norvegicus genome and generated the first rat genome-wide maps of recombination-initiating double-strand break hotspots. Rat strains carrying the same wild-type Prdm9 allele shared 88% hotspots but strains with different Prdm9 alleles only 3%. After Prdm9 deletion, rat hotspots relocated to functional regions, 40% to positions corresponding to Prdm9-independent mouse hotspots. Despite of hotspot relocation and of decreased fertility, Prdm9-deficient rats of the SHR/OlaIpcv strain produced apparently normal offspring. Rat PRDM9 thus makes recombination landscape unique, but it is unnecessary for recombination. This peculiarity is likely similar for human PRDM9 and may resolve the paradox between the apparently species-specific functions. PRDM9 is known to play a role in speciation, as it causes mouse hybrid sterility via meiotic asynapsis. Besides the expected mild meiotic arrest, we also detected apoptosis of postmeiotic spermatids, suggesting that PRDM9 has an additional role during spermatogenesis and perhaps also in speciation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33910563" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163562" }, "primaryId" : "GEO:GSE163562", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163562" } ] }, "title" : "Genome wide chromatin accessibility analysis reveals a role for CREB in retinal ganglion cells axon growth decline in development and regeneration after optic nerve injury [ATAC-seq]", "dateAssigned" : "2020-12-20T00:00:00.000-06:00", "summary" : "CNS neurons lose their ability to grow and regenerate axons during development. This is the case for Retinal Ganglion Cells (RGCs) in the retina, which transmit visual information to the brain via axons projecting into the optic nerve. RGCs are unable to regenerate their axon after injury, and start a degeneration process that leads to cell death and loss of vision. To identifying molecular mechanisms that increase regeneration of RGC and may offer new treatment strategies for patients with glaucoma or other types of optic neuropathies, we focused on the identification of transcription factors and chromatin accessible sites that are enriched in RGC during developmental stages, in which axon growth capacity is robust. We find that stage-specific gene expression changes are correlated with temporal changes in promoter chromatin accessibility. We also find that Creb binding motifs are enriched in the differentially opened regions of the chromatin at embryonic developmental stage. Overexpression of active Creb promotes axon regeneration after optic nerve injury. Our results provide a map of the chromatin accessibility during RGC development and highlights that manipulating TF associated with developmental stages can stimulate axon growth in adulthood.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34290335" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163563" }, "primaryId" : "GEO:GSE163563", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163563" } ] }, "title" : "Genome wide chromatin accessibility analysis reveals a role for CREB in retinal ganglion cells axon growth decline in development and regeneration after optic nerve injury [RNA-seq]", "dateAssigned" : "2020-12-20T00:00:00.000-06:00", "summary" : "CNS neurons lose their ability to grow and regenerate axons during development. This is the case for Retinal Ganglion Cells (RGCs) in the retina, which transmit visual information to the brain via axons projecting into the optic nerve. RGCs are unable to regenerate their axon after injury, and start a degeneration process that leads to cell death and loss of vision. To identifying molecular mechanisms that increase regeneration of RGC and may offer new treatment strategies for patients with glaucoma or other types of optic neuropathies, we focused on the identification of transcription factors and chromatin accessible sites that are enriched in RGC during developmental stages, in which axon growth capacity is robust. We find that stage-specific gene expression changes are correlated with temporal changes in promoter chromatin accessibility. We also find that Creb binding motifs are enriched in the differentially opened regions of the chromatin at embryonic developmental stage. Overexpression of active Creb promotes axon regeneration after optic nerve injury. Our results provide a map of the chromatin accessibility during RGC development and highlights that manipulating TF associated with developmental stages can stimulate axon growth in adulthood.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34290335" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163582" }, "primaryId" : "GEO:GSE163582", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163582" } ] }, "title" : "tRNA-derived fragments regulate the functional maturation of neonatal β-cells [ncRNA-Seq]", "dateAssigned" : "2020-12-21T00:00:00.000-06:00", "summary" : "Annotation of tRNA fragments relies on the alignment of signals obtained from small RNA-seq on mature tRNA positions and requires the pretreatment of the RNA to remove tRNA modifications that may interfere with sequencing.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163584" }, "primaryId" : "GEO:GSE163584", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163584" } ] }, "title" : "tRNA-derived fragments regulate the functional maturation of neonatal β-cells [RNA-Seq]", "dateAssigned" : "2020-12-21T00:00:00.000-06:00", "summary" : "In neonatal islets from P10 rats, 3 sets of tRNA-derived fragments (tiRNA-5HisGTG/GluCTC/GluTTC) were inhibited with LNA inhibitiors ex vivo and mRNA-seq was performed to potentially identify the gene expression changes upon the inhibition", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163614" }, "primaryId" : "GEO:GSE163614", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163614" } ] }, "title" : "Gene expression profile in cerebral ischemia-reperfusion injury of rat model", "dateAssigned" : "2020-12-21T00:00:00.000-06:00", "summary" : "To reveal the alterations of mRNA profile in cerebral ischemia-reperfusion injury in rat. The SD rats were used to established the middle cerebral artery occlusion and reperfusion (MCAO/R) model. RNA-seq were performed to identify differences in gene expression.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33796004" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163620" }, "primaryId" : "GEO:GSE163620", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163620" } ] }, "title" : "The conservation and divergence of epigenitic reprogramming during mammalian early development", "dateAssigned" : "2020-12-21T00:00:00.000-06:00", "summary" : "To explore how parental epigenetic information is transmitted to the next generation across mammals, we systematically investigated the epigenomes of oocytes and early embryos among human, bovine, porcine, rat, and mouse. This unprecedented dataset revealed strikingly diverse, species-specific innovation of epigenetic transition. In oocytes, DNA methylation is restricted to active gene bodies in rodents, allowing methylation of maternal imprints but not intergenic paternal imprints. Strikingly, hypermethylation also occurs in non-transcribed regions in porcine and bovine, where paternal imprints instead reside in hypomethylated, megabase-long “CpG continents (CGCs)”. Despite the presence of H3K4me3 and H3K27me3 domains in non-human oocytes, only rodent H3K27me3 survives beyond genome activation, supporting H3K27me3-mediated imprinting. Coincidently, regulatory elements are segregated away from H3K27me3 domains, the ectopic invasion of which leads to aberrant embryonic transcription. Finally, human does not fully resemble any of the rest species. Hence, mammals invent diverse epigenetic inheritance and reprogramming which center around a delicate balance in establishing imprints while protecting other regulatory regions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34818044" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163654" }, "primaryId" : "GEO:GSE163654", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163654" } ] }, "title" : "Whole-genome microarrays in the ischemic penumbra of mice and rats 2hrs and 6hrs after permanent middle cerebral artery occlusion (pMCAO)", "dateAssigned" : "2020-12-21T00:00:00.000-06:00", "summary" : "Whole-genome microarrays were used to examine differential gene regulation in the ischemic penumbra of mice and rats 2hrs and 6hrs after permanent middle cerebral artery occlusion (pMCAO). The differentially expressed genes in the ischemic penumbra at each time point were compared between the two species.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163665" }, "primaryId" : "GEO:GSE163665", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163665" } ] }, "title" : "Nicotinamide for the treatment of heart failure with preserved ejection fraction", "dateAssigned" : "2020-12-21T00:00:00.000-06:00", "summary" : "Heart failure with preserved ejection fraction (HFpEF) is a highly prevalent and intractable form of cardiac decompensation commonly associated with diastolic dysfunction. Here, we show that diastolic dysfunction in patients with HFpEF is associated with a cardiac deficit in nicotinamide adenine dinucleotide (NAD+). Elevating NAD+ by oral supplementation of its precursor, nicotinamide, improved diastolic dysfunction induced by aging (in 2-year-old C57BL/6J mice), hypertension (in Dahl salt-sensitive rats) or cardiometabolic syndrome (in ZSF1 obese rats). Mechanistically, this effect was mediated partly through alleviated systemic comorbidities and enhanced myocardial bioenergetics, as evidenced by cardiac trasncriptome and metabolome analyses. Simultaneously, nicotinamide directly improved cardiomyocyte passive stiffness and calcium-dependent active relaxation through increased deacetylation of titin and the sarcoplasmic reticulum calcium ATPase 2a, respectively. In a long-term human cohort study, high dietary intake of naturally occurring NAD+ precursors was associated with lower blood pressure and reduced risk of cardiac mortality. Collectively, these results suggest NAD+ precursors, and especially nicotinamide, as potential therapeutic agents to treat diastolic dysfunction and HFpEF in humans.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33568522" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163758" }, "primaryId" : "GEO:GSE163758", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163758" } ] }, "title" : "Estradiol-dependent gene expression profile in the amygdala of ovariectomized SHRs", "dateAssigned" : "2020-12-23T00:00:00.000-06:00", "summary" : "Pre-menopausal women exhibit a lower arterial pressure (AP), a lower sympathetic outflow and a greater baroreceptor reflex than age-matched men. However, AP and subsequent cardiovascular diseases dramatically increases in post-menopausal women. Estrogen level is believed to play a role in the regulation of the basal blood pressure, emotion and hormonal response in the different periods of life of a woman but the molecular mechanisms are still not well understood. Amygdala is a major nucleus of the limbic system involved in the control of cardiovascular, behavior and hormonal response to stress or fear. Since variations in estrogen level are associated with cardiovascular, behavior, and hormonal response changes, we hypothesized that it could also be associated with different neuronal functions in amygdala, characterized by a differential gene expression profile. Young Female SHRs were ovariectomized (OV) and half of them received an estradiol treatment (OV+E2) for one month. We investigated whether the amygdala of ovariectomized rats exhibit gene expression differences after estradiol treatment by using microarray technique.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35100063" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163763" }, "primaryId" : "GEO:GSE163763", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163763" } ] }, "title" : "Analysis of ctDNA methylation induced by ionizing to different ograns", "dateAssigned" : "2020-12-23T00:00:00.000-06:00", "summary" : "This study aims to compared ctDNA methylation status induced by ionizing to different ograns. SD rats were irradiated with local radaition to brain, lung or skin. Serum was collected and subjiected to ctDNA extraction. ctDNA were then treated by methylation-sensive bisulfite and sequencing.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163966" }, "primaryId" : "GEO:GSE163966", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE163966" } ] }, "title" : "mRNA array in liver tissue samples of Sprague-Dawley rats", "dateAssigned" : "2020-12-29T00:00:00.000-06:00", "summary" : "Non-alcoholic fatty liver disease (NAFLD) has increased over the last decades and may evolve into hepatocellular carcinoma (HCC). As HCC is challenging to treat, knowledge on the modifia-ble risk factors for NAFLD/HCC, (e.g. hypercaloric diets rich in fructose) is essential. We used a model of diethyl nitrosamine-induced hepatocarcinogenesis to investigate the liver cancer-promoting effects of a diet supplemented with 10% liquid fructose, administered to male and female rats for 11 months. A subset of the fructose-supplemented rats received resveratrol in the last 4 months of treatment. We observed metabolic abnormalities mainly in the female fructose-supplemented rats (increases in weight, adiposity, and plasma glucose and triglycerides, as well as liver triglycerides and a reduced insulin sensitivity index), which were partially reversed by resveratrol. The livers of fructose-supplemented rats showed no de visu or histological evi-dence of liver tumorigenesis. Targeted analysis of 84 cancer-related genes in the female liver samples revealed expression changes associated with cancer-related pathways, but individual genes indicated that some changes increased the risk of hepatocarcinogenesis (Sfrp2, Ccl5, Socs3, and Gstp1), while others exerted a protective/preventive effect (Bcl2 and Cdh1). In conclusion, our data do not clearly demonstrate that chronic fructose supplementation promotes HCC development in rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164007" }, "primaryId" : "GEO:GSE164007", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164007" } ] }, "title" : "Transcriptomic Characterization of Inhalation Phosphine Toxicity in Adult Male Sprague-Dawley Rats", "dateAssigned" : "2020-12-29T00:00:00.000-06:00", "summary" : "To better characterize the mechanism(s) driving PH3-induced toxicity we have performed transcriptomic analysis on conscious adult male Sprague-Dawley rats following whole-body inhalation exposure to phosphine gas at three concentrations. PH3 exposure induced concentration- and time-dependent changes in gene expression across multiple tissues.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164018" }, "primaryId" : "GEO:GSE164018", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164018" } ] }, "title" : "Transcriptomic Characterization of Inhalation Phosphine Toxicity in Adult Male Sprague-Dawley Rats (16,500 ppm x min)", "dateAssigned" : "2020-12-29T00:00:00.000-06:00", "summary" : "To better characterize the mechanism(s) driving PH3-induced toxicity we have performed transcriptomic analysis on conscious adult male Sprague-Dawley rats following whole-body inhalation exposure to phosphine gas at three concentrations. PH3 exposure induced concentration- and time-dependent changes in gene expression across multiple tissues.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164019" }, "primaryId" : "GEO:GSE164019", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164019" } ] }, "title" : "Transcriptomic Characterization of Inhalation Phosphine Toxicity in Adult Male Sprague-Dawley Rats (21,252 ppm x min)", "dateAssigned" : "2020-12-29T00:00:00.000-06:00", "summary" : "To better characterize the mechanism(s) driving PH3-induced toxicity we have performed transcriptomic analysis on conscious adult male Sprague-Dawley rats following whole-body inhalation exposure to phosphine gas at three concentrations. PH3 exposure induced concentration- and time-dependent changes in gene expression across multiple tissues.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164050" }, "primaryId" : "GEO:GSE164050", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164050" } ] }, "title" : "Expression data from the carotid artery at 2 wks after Intimal injury", "dateAssigned" : "2020-12-30T00:00:00.000-06:00", "summary" : "We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33738288" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164152" }, "primaryId" : "GEO:GSE164152", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164152" } ] }, "title" : "Next Generation Sequencing (RNA-Seq) of stem cell-treated rats for quantitative analyses of retinal transcriptomes", "dateAssigned" : "2021-01-03T00:00:00.000-06:00", "summary" : "Conclusions: Our study represents the first detailed analysis of MSCEPO-treated retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for further investigations in MSC enhancement methods. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within the retina. We conclude that RNA-seq based retinal transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions, especially in regards to MSC-mediated tissue repair and phototransduction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33987180" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164176" }, "primaryId" : "GEO:GSE164176", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164176" } ] }, "title" : "Transcriptomic landscape and metabolic phenotypization of Polydactylous rat with metabolic syndrome after high fat diet challenge", "dateAssigned" : "2021-01-04T00:00:00.000-06:00", "summary" : "We used microarray aproach to unravel gene expression differences between SHR, PD and BN responsible for the different phenotypes in our rat strains.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33923085" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164361" }, "primaryId" : "GEO:GSE164361", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164361" } ] }, "title" : "Comparative Chromatin Dynamics and Expression Profiles of Neural Progenitor and Definitive Endoderm Lineage Differentiation in Two Mammalian Species", "dateAssigned" : "2021-01-06T00:00:00.000-06:00", "summary" : "One of the fundamental questions in developmental biology is how lineage specification is regulated and what regulatory transcription factors and signaling molecules are required. Lineage specification and differentiation are driven, at least in part, by chromatin remodeling causing changes in the accessibility of transcription factor binding sites. Changes in expression of required transcription factors are also important in the regulation of differentiation. To better understand which transcription factors drive differentiation and how these transcription factors differ between different species and differentiation lineages we differentiated ESCs into two different lineages, definitive endoderm and neural progenitors, and performed pooled RNA-seq and ATAC-seq in two different species, human and rat.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164440" }, "primaryId" : "GEO:GSE164440", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164440" } ] }, "title" : "Evolutionary Analysis of Transcriptional Regulation Mediated by Cdx2 in Rodents", "dateAssigned" : "2021-01-08T00:00:00.000-06:00", "summary" : "Evolutionary Analysis of Transcriptional Regulation Mediated by Cdx2 in Rodents", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:40729530" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164496" }, "primaryId" : "GEO:GSE164496", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164496" } ] }, "title" : "ATP-Competitive Partial Antagonists—'PAIR's—Segregate IRE1α’s RNase-Mediated Biological Outputs", "dateAssigned" : "2021-01-09T00:00:00.000-06:00", "summary" : "During mammalian cell growth and differentiation, the unfolded protein response (UPR) homeostatically adjusts endoplasmic reticulum (ER) protein-folding capacity to match changing cellular secretory demands. However, under high/chronic ER stress conditions the UPR triggers apoptosis. This dichotomy is promoted in part by differential activation levels of the ER transmembrane kinase/endoribonuclease (RNase) IRE1a. IRE1a kinase auto-phosphorylation operates as a rheostat to control downstream RNase-induced outputs that either sustain adaptive ER protein-folding or cause apoptosis. We have previously shown that IRE1a’s RNase activity can be activated or fully inactivated by ATP-competitive kinase inhibitors. Here we developed a new class of ATP-competitive kinase inhibitors that partially antagonize the RNase of IRE1a at full occupancy. An atomic level resolution co-crystal structure shows that these small molecule partial antagonists—which we named ‘PAIR’s for (Partial Antagonists of IRE1a RNase)—occupy the ATP-binding site of IRE1a and partially displace a helix (helix aC) in the kinase domain that forms part of a dimeric interface. In insulin-producing beta cells, PAIRs permit adaptive XBP1 mRNA splicing, while quelling destructive/terminal outputs from extra-XBP1 mRNA endonucleolytic decay, thus preventing apoptosis. Preservation of XBP1 splicing by PAIRs permits B lymphocytes to differentiate into immunoglobulin-producing plasma cells. In summary, we propose that an intermediate RNase-inhibitory “sweet spot,” achieved by PAIR-bound IRE1a, may capture a structural conformation naturally available to IRE1a that could represent a desirable therapeutic state for drugging this master UPR sensor/effector.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164537" }, "primaryId" : "GEO:GSE164537", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164537" } ] }, "title" : "Fine particulate matter (PM2.5) promotes IgE-mediated mast cell activation through ROS/Gadd45b/JNK axis", "dateAssigned" : "2021-01-11T00:00:00.000-06:00", "summary" : "Conclusions: PM2.5 regulates ROS production through Gadd45b/MEKK4/JNK pathway, facilitating IgE-mediated mast cell activation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164727" }, "primaryId" : "GEO:GSE164727", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164727" } ] }, "title" : "Transcriptome analysis and differentially expressed gene screening for hypoxic-ischemic brain damage in rats treated with acupuncture", "dateAssigned" : "2021-01-13T00:00:00.000-06:00", "summary" : "Conclusion: we found several significant lncRNAs whose corresponding target genes might be the targets of acupuncture therapy for HIBD. The results of our study may provide new perspectives on the mechanism of acupuncture and affect the diagnosis and therapy of HIBD", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164763" }, "primaryId" : "GEO:GSE164763", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164763" } ] }, "title" : "RNA sequencing of iAM-1 cells at different stages during one cycle of differentiation and subsequent dedifferentiation", "dateAssigned" : "2021-01-13T00:00:00.000-06:00", "summary" : "RNA sequencing of iAM-1 cells at different stages during one cycle of differentiation and subsequent dedifferentiation", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164800" }, "primaryId" : "GEO:GSE164800", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164800" } ] }, "title" : "Protocol matters – reproducibility and rigor of DNA methylation data sets [RNA-seq]", "dateAssigned" : "2021-01-13T00:00:00.000-06:00", "summary" : "While epigenetics continues to be a burgeoning research area in neuroscience, unaddressed issues related to data reproducibility across laboratories remain. Indeed, separating meaningful experimental changes from background variability is a challenge in epigenomic studies. Genome-wide DNA methylation analysis of hippocampal tissues from wild-type rats across three independent laboratories revealed that seemingly minor protocol differences resulted in significant epigenome profile changes, even in the absence of experimental intervention. Difficult-to-match factors such as animal vendors and a subset of husbandry and tissue extraction procedures produced quantifiable variations between wild-type animals across the three laboratories. To enhance scientific rigor, we conclude that strict adherence to protocols is necessary for the execution and interpretation of epigenetic studies and that protocol-sensitive epigenetic changes, amongst naive animals, may confound experimental results.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35013473" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164831" }, "primaryId" : "GEO:GSE164831", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164831" } ] }, "title" : "Protocol matters – reproducibility and rigor of DNA methylation data sets [BiSulfite-seq]", "dateAssigned" : "2021-01-14T00:00:00.000-06:00", "summary" : "While epigenetics continues to be a burgeoning research area in neuroscience, unaddressed issues related to data reproducibility across laboratories remain. Indeed, separating meaningful experimental changes from background variability is a challenge in epigenomic studies. Genome-wide DNA methylation analysis of hippocampal tissues from wild-type rats across three independent laboratories revealed that seemingly minor protocol differences resulted in significant epigenome profile changes, even in the absence of experimental intervention. Difficult-to-match factors such as animal vendors and a subset of husbandry and tissue extraction procedures produced quantifiable variations between wild-type animals across the three laboratories. To enhance scientific rigor, we conclude that strict adherence to protocols is necessary for the execution and interpretation of epigenetic studies and that protocol-sensitive epigenetic changes, amongst naive animals, may confound experimental results.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35013473" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164878" }, "primaryId" : "GEO:GSE164878", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164878" } ] }, "title" : "Rat transcriptomic profiling of liver sinusoidal endothelial cells during chronic liver disease reveals stage-specific secretory signature", "dateAssigned" : "2021-01-14T00:00:00.000-06:00", "summary" : "RNAseq was applied to define the transcriptome of primary LSECs from rats with acute liver injury, mild liver fibrosis and advanced chronic liver disease (CLD) (due to CCl4 or thioacetamide administration). Results showed different transcriptomic profile during progression of CLD, and a large number of significant de-regulated genes (1412) were shared in cirrhotic CCl4- and TAA-LSECs (fold-change>1.5 and p-vale<0.05)compared with their respective healthy-LSECs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34072510" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164919" }, "primaryId" : "GEO:GSE164919", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE164919" } ] }, "title" : "Gene expression profilings in human induced pluripotent stem cell-derived cardiomyocytes in vivo and in vitro", "dateAssigned" : "2021-01-15T00:00:00.000-06:00", "summary" : "RNA sequencing of human induced pluripotent stem cell-derived cardiomyocytes", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37679796" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165069" }, "primaryId" : "GEO:GSE165069", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165069" } ] }, "title" : "Neuroinflammatory astrocyte subtypes in the mouse brain [bulk RNA-seq, Interferon_in_vitro]", "dateAssigned" : "2021-01-19T00:00:00.000-06:00", "summary" : "RNA-seq of primary astrocytes exposed to different cytokines", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34413515" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165104" }, "primaryId" : "GEO:GSE165104", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165104" } ] }, "title" : "Transplanted human organoids empower PK/PD assessment of drug candidate for the clinic", "dateAssigned" : "2021-01-19T00:00:00.000-06:00", "summary" : "Pharmacokinetic/pharmacodynamic (PK/PD) studies are an essential component of pre-clinical drug discovery. Current best approaches for PK/PD studies, including the analysis of novel kidney disease targeting therapeutic agents, are limited to animal models with unclear translatability to the human condition. To address this challenge, we developed a novel approach for PK/PD studies using transplanted human kidney organoids. We performed PK studies with GFB-887, an investigational new drug now in Phase 2 trials. Orally dosed GFB-887 to athymic rats that had undergone organoid transplantation resulted in measurable drug exposure in human transplanted organoids. Importantly, we established the efficacy of orally dosed GFB-887 in PD studies, where quantitative analysis showed significant protection of kidney filter cells in human organoids and endogenous rat host kidneys. This widely applicable approach demonstrates, for the first time, feasibility of using transplanted human organoids in PK/PD studies, empowering organoids to revolutionize drug discovery.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165153" }, "primaryId" : "GEO:GSE165153", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165153" } ] }, "title" : "B cells and their progenitors reside in homeostatic meninges", "dateAssigned" : "2021-01-20T00:00:00.000-06:00", "summary" : "The central nervous system (CNS) is ensheathed by the meninges and cerebrospinal fluid. Recent findings suggest complex immunological functions of these CNS-associated border tissues. Unlike myeloid lineage cells, lymphocytes in border compartments have been largely disregarded in previous studies. Based on single cell transcriptomics, we here identified a highly location-specific composition and expression profile of tissue-resident leukocytes in every border compartment. Only the dura layer of the meninges contained a large population of B cells under homeostatic conditions in multiple species. Murine dura B cells exhibited slow turnover, long-term tissue residency and matured in experimental neuroinflammation. The dura also contained B lineage progenitors at the pro-B cell stage unexpected outside of bone marrow, without direct influx from the periphery or the skull bone marrow. This identifies the dura as an unexpected site of B cell residence and potentially development in homeostasis and neuroinflammation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34253922" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165206" }, "primaryId" : "GEO:GSE165206", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165206" } ] }, "title" : "Expression data from Rat neuronal Schwann cells (SCs) that under different extracellular matrix (ECM) conditions", "dateAssigned" : "2021-01-20T00:00:00.000-06:00", "summary" : "We used microarray to illustrate the interplays between SC regenerative gene expression and different ECM conditions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34062912" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165219" }, "primaryId" : "GEO:GSE165219", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165219" } ] }, "title" : "RIP1 perturbation induces chondrocyte necroptosis and promotes osteoarthritis pathogenesis", "dateAssigned" : "2021-01-21T00:00:00.000-06:00", "summary" : "Receptor-interacting protein kinase 1 (RIP1)-mediated necroptosis plays a vital role in various diseases, but the involvement of RIP1 and its functional mechanism in osteoarthritis pathogenesis remains largely unknown. To identify molecular targets of RIP1 in chondrocytes, RNA sequencing was performed in chondrocytes treated with adenovirus expressing RIP1 or vector control. We found that 9857 genes were differentially expressed in chondrocytes after RIP1 overexpression. GO analysis indicated that DNA replication, chromosome segregation and regulation of cell cycle process were upregulated, while terms including cartilage development, skeletal system development, extracellular matrix organization, skeletal system morphogenesis, chondrocyte differentiation, collagen fibril organization and limb development were downregulated. Pathway analysis revealed that IL-17 signaling pathway, cell cycle, DNA replication, proteasome, TNF signaling pathway, cellular senescence and p53 signaling pathway were significantly upregulated by RIP1, meanwhile, ECM-receptor interaction, other glycan degradation and glycosaminoglycan degradation were downregulated. These results underscore the importance of RIP1 in OA by perturbing a series of essential events during disease progression such like cell cycle regulation, chondrocyte differentiation, inflammation and ECM remodeling. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33937236" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165221" }, "primaryId" : "GEO:GSE165221", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165221" } ] }, "title" : "Neuroinflammatory gene expression changes in the brain in a rat model of Gulf War Illness – effects of rosiglitazone", "dateAssigned" : "2021-01-21T00:00:00.000-06:00", "summary" : "Gulf War Illness (GWI) is a diverse set of neurologic and systemic symptoms affecting many veterans deployed in the Persian Gulf War, but its etiology is unknown and treatment options are limited. Veterans with GWI were exposed to a variety of agents, including pyridostigmine bromide, used as prophylaxis against nerve agents, intranasal lipopolysaccharide (LPS) from desert sandstorms, and chronic unpredictable stress (CUS) from combat. Here, we investigated the gene expression effects of these three Gulf War-related exposures (GWE) in adult rat frontal cortex (FC) and lateral amygdala (LA) using Clariom S microarrays. We found 138 transcript clusters (TCs) in LA and 38 TCs in FC differentially expressed between the group with GWE (n=2) compared to naïve controls (n=3, FDR <10%). These TCs included genes involved in inflammation such as Fosb (pmin=1.02e-5) and Junb (pmin=1.13e-5). Gene ontology analysis found enrichment of differentially expressed genes in “T cell differentiation” (pmin=8.71e-5) and “response to organophosphorus” (pmin=1.74e-8), among other categories. Lastly, we found that prophylactic treatment with rosiglitazone, a PPAR- agonist, reduced gene expression changes associated with GWE (in LA: 115/138 [83.3%] TCs with reduced changes, χ2=61.33, p=4.82e-15). These results suggest our rat model of GWI is associated with gene expression changes related to neuroinflammation and that some of these molecular changes may be mitigated by rosiglitazone prophylaxis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165225" }, "primaryId" : "GEO:GSE165225", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165225" } ] }, "title" : "Exploration of SQC formula effect on Type 2 diabetes mellitus by whole transcriptome profile in rats", "dateAssigned" : "2021-01-21T00:00:00.000-06:00", "summary" : "Gene microarray experiments were performed to explore the molecular mechanism of SQC treatment. In addition, a western medicine, metformin was employed as a comparison.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165342" }, "primaryId" : "GEO:GSE165342", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165342" } ] }, "title" : "Astragaloside IV attenuates macrophage-derived exosomes induced peritoneal fibrosis after inflammatory injury through the miR-204-5p/Foxc1 pathway", "dateAssigned" : "2021-01-22T00:00:00.000-06:00", "summary" : "Peritoneal dialysis (PD) is a successful renal replacement therapy for end-stage renal disease that effectively improves the quality of life. Long-term PD causes epithelial mesenchymal transformation (MMT) of peritoneal mesothelial cells, leading to peritoneal fibrosis which reduces the efficiency of PD. Macrophages are considered players in the onset and perpetuation of peritoneal injury. Yet, the mechanisms employed by macrophage-mesothelial cells communication to regulate peritoneal fibrosis are not fully elucidated resulting in lack of disease-modified drugs. This study analyzes the role of macrophage-mesothelial cell communication by intraperitoneal injection of macrophage derived exosomes in PD model rats. These results show that macrophages secrete exosomal miR-204-5p that directly targets Foxc1, leading to the activation of MMT in mesothelial cells. The data also shows that intraperitoneal injection of dissolved AS-IV can improve MMT by altering macrophage derived exosomal miRNAs. This study indicates that intercellular crosstalk between peritoneal macrophages and mesothelial cells is mediated by macrophage derived miR-204-5p-containing exosomes that control the MMT progression, providing AS-IV for prevention and treatment of PD induced peritoneal fibrosis. Our results demonstrate, for the first time, a novel role of the AS-IV on miR-204-5p/Foxc1/β-catenin axis in improving peritoneal fibrosis in vivo and vitro.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165369" }, "primaryId" : "GEO:GSE165369", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165369" } ] }, "title" : "RNAseq of perivascular adipose tissue from mesenteric arteries from normotensive and hypertensive Dahl S rats", "dateAssigned" : "2021-01-22T00:00:00.000-06:00", "summary" : "We report the results from RNA-seq analysis of perivascular adipose tissues (PVAT) collected from mesenteric arteries from Dahl S rats. Animals were on a control or a high fat diet for 24 weeks. At the moment of collection, rats fed high fat diet were hypertensive. In contrast, rats on the control diet were normotensive.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33815135" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165520" }, "primaryId" : "GEO:GSE165520", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165520" } ] }, "title" : "The Alteration of M6A-tagged Transcript Profiles in The Retina of Rats After Traumatic Optic Neuropathy", "dateAssigned" : "2021-01-26T00:00:00.000-06:00", "summary" : "Messager RNA (mRNA) can be modified in a variety of ways, among which the modification of N6-methyladenosine (m6A) is one of the most common ones. Recent studies have found that the m6A modification in mRNA could functionally regulate the splicing, localization, translation and stability of mRNA, which might be closely related to multiple diseases. However, the roles of m6A modification in traumatic optic neuropathy (TON) are unknown. Herein, we detected the expression of m6A-related genes via quantitative real-time PCR (qRT-PCR) and performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) as well as RNA-sequencing to analyze the alteration profiles of m6A modification after TON. The results showed that the expression of m6A-related genes (METTL3, WTAP, FTO and ALKBH5) were all upregulated after TON. In all, 2810 m6A peaks were differentially upregulated and 689 m6A peaks were downregulated. In addition, the hypermethylated and hypomethylated profiles of mRNA transcripts were also identified. To sum up, our study revealed the differentially expressed m6A modification in the early stage of TON, which may provide novel insights into the mechanism and treatment of TON.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33664770" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165635" }, "primaryId" : "GEO:GSE165635", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165635" } ] }, "title" : "Rationally designed, self-assembly, multifunctional hydrogel depot repairs severe spinal cord injury", "dateAssigned" : "2021-01-27T00:00:00.000-06:00", "summary" : "Following severe spinal cord injury (SCI), dysregulated neuroinflammation causes neuronal and glial apoptosis, resulting in scar and cystic cavity formation during wound healing process and ultimately atrophic nerve regrowth inhibitory microenvironment. Because of this complex and dynamic nature of SCI pathophysiology, a systemic solution for scar and cavity free wound healing while remodeling microenvironment for nerve regrowth has been rarely explored. To address this challenge, we provided a one-step solution through a self-assembly, multifunctional hydrogel depot punctually releasing the anti-inflammatory drug methylprednisolone sodium succinate (MPSS) and growth factors locally according to its pathophysiology to repair severe SCI. We found release of growth factors alone could only provide some tissues/axons protection, but failed to eliminate all cystic cavity formation. Sustained release of MPSS is sufficient to modulate dysregulated neuroinflammation and eliminate almost all cystic cavity but unable to alleviate impenetrable scar boundaries, which are largely responsive for nerve regrowth failure. Strikingly, synergically releasing anti-inflammatory drugs MPSS and growth factors in the hydrogel depot along SCI pathophysiology protected spared tissues/axons from secondary injury, promoted scar boundary and cavity free wound healing and made permissive bridges for remarkable axonal regrowth. Behavior and electrophysiology studies indicated that the remnant of spared axons but not regenerating axons mediated functional recovery, strongly suggesting that additional interventions are still required to make the rebuilt neuronal circuits perform functions. Taken together, these findings pave the way to develop a systemic solution to treat acute SCI.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165655" }, "primaryId" : "GEO:GSE165655", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165655" } ] }, "title" : "Histone modification profile in animal models of neurodevelopmental disorders treated with TAK-418", "dateAssigned" : "2021-01-27T00:00:00.000-06:00", "summary" : "We report the histone modification profiles in the brain cortex of animal models of neurodevelopmental disorders (rat with prenatal exposure to valproate and mouse with prenatal exposure to poly I:C) treated with TAK-418.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33712455" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165660" }, "primaryId" : "GEO:GSE165660", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165660" } ] }, "title" : "RNA expression profile in animal models of neurodevelopmental disorders treated with TAK-418", "dateAssigned" : "2021-01-27T00:00:00.000-06:00", "summary" : "We report the RNA expression profiles in the brain cortex of animal models of neurodevelopmental disorders (rat with prenatal exposure to valproate and mouse with prenatal exposure to poly I:C) treated with TAK-418.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33712455" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165675" }, "primaryId" : "GEO:GSE165675", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165675" } ] }, "title" : "DNA methylation profile in animal models of neurodevelopmental disorders treated with TAK-418", "dateAssigned" : "2021-01-27T00:00:00.000-06:00", "summary" : "We report the DNA methylation profiles in the brain cortex of animal models of neurodevelopmental disorders (rat with prenatal exposure to valproate and mouse with prenatal exposure to poly I:C) treated with TAK-418.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33712455" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165743" }, "primaryId" : "GEO:GSE165743", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165743" } ] }, "title" : "Microglial activation protects from vascular degeneration in a rat model of inflammatory retinal vasoregression.", "dateAssigned" : "2021-01-28T00:00:00.000-06:00", "summary" : "Microglial activation represents a hallmark of inflammatory retinal diseases like diabetic retinopathy. Anti-inflammatory and especially microglia modulating approaches have been proposed as therapies for these diseases. In this study, clodronate-coated liposomes were intravitreally injected to investigate the effects of increased microglial activation on vasoregression in a model of retinal degeneration. Clodronate-coated liposomes, injected twice over a period of 5 weeks to study the effects of long term clodronate treatment on microglial activation, vasoregression (acellular capillary formation and pericyte loss) and to identify the pathways mediating the observed effects.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33981252" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165858" }, "primaryId" : "GEO:GSE165858", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE165858" } ] }, "title" : "Gene Transcriptional Variation of Hepatic Progenitor Cells after TGF-𝛽1-Induced EMT Transition and EGF-Induced MET Reversion", "dateAssigned" : "2021-01-31T00:00:00.000-06:00", "summary" : "TGF-b1 induces hepatic progenitor cells experience an epithelial-mesenchymal transition, and EGF could reverse this process via mesenchymal-epithelial transition. Yet, the mechanism underline these EMT and MET processes are not clear. The aim of this study is to reveal the genes with significant difference during these EMT and MET process in hepatic progenitor cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35379781" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166009" }, "primaryId" : "GEO:GSE166009", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166009" } ] }, "title" : "Differentially expressed messenger RNAs and long noncoding RNAs after spinal cord injury", "dateAssigned" : "2021-02-02T00:00:00.000-06:00", "summary" : "Spinal cord injury (SCI) is a severely disastrous event that occurs in the central nervous system (CNS) that is associated with high disability and mortality rates.To further explore the expression of mRNAs and lncRNAs and the potential roles of differentially expressed mRNAs and lncRNAs after SCI, we examined the expression of mRNAs and lncRNAs in a rat model at 2 hours, 2 days and 7 days after SCI and identified the differentially expressed lncRNAs (DE lncRNAs) and differentially expressed mRNAs (DE mRNAs) using microarray analysis. A total of 992 mRNAs were differentially expressed at 2 hours after SCI, among which 730 mRNAs were up-regulated and 262 mRNAs were down-regulated. A total of 4308 mRNAs were differentially expressed at 2 days after SCI, including 2229 mRNA with up-regulated expression and 2079 mRNAs with down-regulated expression. A total of 4113 mRNAs were differentially expressed at 7 days after SCI, including 2339 up-regulated and 1774 down-regulated mRNAs. After SCI, 772 lncRNAs were differentially expressed in the 2-hour group (528 were up-regulated, 244 were downregulated) , 3193 lncRNAs were differentially expressed in the 2-day group (1332 were up-regulated, 1861 were downregulated) ,3093 lncRNAs were differentially expressed in the 7-day group (1290 were up-regulated, 1803 were downregulated) .The current study on provides novel insights into how lncRNAs and mRNAs regulate the pathogenesis of the immediate phase after SCI.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166040" }, "primaryId" : "GEO:GSE166040", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166040" } ] }, "title" : "Characterization of a KDM5 Small Molecule Inhibitor with Antiviral Activity in Rodent Livers", "dateAssigned" : "2021-02-02T00:00:00.000-06:00", "summary" : "Chronic hepatitis B (CHB) is a global health care challenge and a major cause of liver disease. Existing therapies do not result in a functional cure in most individuals, necessitating new antiviral strategies against Hepatitis B virus (HBV). To identify additional therapeutic avenues, we performed a focused screen of epigenetic modifiers to identify inhibitors of HBV replication. From this work we identified small molecule inhibitors of the histone lysine demethylase 5 (KDM5) with antiviral activity against HBV. To enhance the cellular permeability and liver accumulation of the most potent KDM5 inhibitor identified (GS-080) a prodrug was developed (GS-5801) that resulted in improved bioavailability and liver exposure as well as increased accumulation of the H3K4me3:H3 ratio on chromatin. GS-5801 treatment of HBV-infected primary human hepatocytes inhibited HBV replication and antigen levels. Evaluation of GS 5801 antiviral activity in a humanized mouse model of HBV infection, however, did not result in antiviral efficacy, despite achieving pharmacodynamic levels of H3K4me3:H3 predicted to be efficacious. Together these data highlight discordance between the antiviral effects of GS 5801 observed in rodent livers.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166073" }, "primaryId" : "GEO:GSE166073", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166073" } ] }, "title" : "X-ray causes mRNA transcripts change to enhance Orai2-meadated Ca2+ influx in rat brain microvascular endothelial cells", "dateAssigned" : "2021-02-03T00:00:00.000-06:00", "summary" : "We utilized high-throughput sequencing and subsequent signaling pathway analyses to find all the 2 fold change expression of transcripts in comparison of brain microvascular endothelial cells derived from six Sprague Dawley rats without or with irradiation at the dose of 5 Gy or 20 Gy and then cultured for 12 h or 24 h", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34595206" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166094" }, "primaryId" : "GEO:GSE166094", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166094" } ] }, "title" : "Behavioral Sensitization Induced by Methamphetamine Causes Differential Alterations in Gene Expression and Histone Acetylation of the Prefrontal Cortex in Rats (mRNA dataset)", "dateAssigned" : "2021-02-03T00:00:00.000-06:00", "summary" : "Background: Methamphetamine (METH) is one of the most widely abused illicit substances worldwide; unfortunately, its addiction mechanism remains unclear. Based on accumulating evidence, changes in gene expression and chromatin modifications might be related to the persistent effects of METH on the brain. In the present study, we took advantage of METH-induced behavioral sensitization as an animal model that reflects some aspects of drug addiction and examined the changes in gene expression and histone acetylation in the prefrontal cortex (PFC) of adult rats. Methods: We conducted mRNA microarray and chromatin immunoprecipitation (ChIP) coupled to DNA microarray (ChIP-chip) analyses to screen and identify changes in transcript levels and histone acetylation patterns. Functional enrichment analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, were performed to analyze the differentially expressed genes. We then further identified alterations in ANP32A (acidic leucine-rich nuclear phosphoprotein-32A) and POU3F2 (POU domain, class 3, transcription factor 2) using qPCR and ChIP-PCR assays. Results: In the rat model of METH-induced behavioral sensitization, METH challenge caused 275 differentially expressed genes and a number of hyperacetylated genes (821 genes with H3 acetylation and 10 genes with H4 acetylation). Based on mRNA microarray and GO and KEGG enrichment analyses, 24 genes may be involved in METH-induced behavioral sensitization, and 7 were confirmed using qPCR. We further examined the alterations in the levels of the ANP32A and POU3F2 transcripts and histone acetylation at different periods of METH-induced behavioral sensitization. H4 hyperacetylation contributed to the increased levels of ANP32A mRNA and H3/H4 hyperacetylation contributed to the increased levels of POU3F2 mRNA induced by METH challenge-induced behavioral sensitization, but not by acute METH exposure. Conclusions: The present results revealed alterations in transcription and histone acetylation in the rat PFC by METH exposure and provided evidence that modifications of histone acetylation contributed to the alterations in gene expression caused by METH-induced behavioral sensitization.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166095" }, "primaryId" : "GEO:GSE166095", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166095" } ] }, "title" : "Behavioral Sensitization Induced by Methamphetamine Causes Differential Alterations in Gene Expression and Histone Acetylation of the Prefrontal Cortex in Rats (Histone acetylation dataset)", "dateAssigned" : "2021-02-03T00:00:00.000-06:00", "summary" : "Background: Methamphetamine (METH) is one of the most widely abused illicit substances worldwide; unfortunately, its addiction mechanism remains unclear. Based on accumulating evidence, changes in gene expression and chromatin modifications might be related to the persistent effects of METH on the brain. In the present study, we took advantage of METH-induced behavioral sensitization as an animal model that reflects some aspects of drug addiction and examined the changes in gene expression and histone acetylation in the prefrontal cortex (PFC) of adult rats. Methods: We conducted mRNA microarray and chromatin immunoprecipitation (ChIP) coupled to DNA microarray (ChIP-chip) analyses to screen and identify changes in transcript levels and histone acetylation patterns. Functional enrichment analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, were performed to analyze the differentially expressed genes. We then further identified alterations in ANP32A (acidic leucine-rich nuclear phosphoprotein-32A) and POU3F2 (POU domain, class 3, transcription factor 2) using qPCR and ChIP-PCR assays. Results: In the rat model of METH-induced behavioral sensitization, METH challenge caused 275 differentially expressed genes and a number of hyperacetylated genes (821 genes with H3 acetylation and 10 genes with H4 acetylation). Based on mRNA microarray and GO and KEGG enrichment analyses, 24 genes may be involved in METH-induced behavioral sensitization, and 7 were confirmed using qPCR. We further examined the alterations in the levels of the ANP32A and POU3F2 transcripts and histone acetylation at different periods of METH-induced behavioral sensitization. H4 hyperacetylation contributed to the increased levels of ANP32A mRNA and H3/H4 hyperacetylation contributed to the increased levels of POU3F2 mRNA induced by METH challenge-induced behavioral sensitization, but not by acute METH exposure. Conclusions: The present results revealed alterations in transcription and histone acetylation in the rat PFC by METH exposure and provided evidence that modifications of histone acetylation contributed to the alterations in gene expression caused by METH-induced behavioral sensitization.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166117" }, "primaryId" : "GEO:GSE166117", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166117" } ] }, "title" : "PolyA-selected RNA expression in whole brains of male BN-Lx/CubPrin and SHR/OlaIpcvPrin", "dateAssigned" : "2021-02-03T00:00:00.000-06:00", "summary" : "As part of the PhenoGen Project (http://phenogen.org), RNA-Seq data has been collected from whole brain samples of two inbred strains that represent the parental strains from the HXB/BXH recombinant inbred panel, which is part of the Hybrid Rat Diversity Panel. Processed data were generated as part of manuscript, Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high throughput RNA sequencing and DNA sequence.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166162" }, "primaryId" : "GEO:GSE166162", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166162" } ] }, "title" : "Expression data from the cortex after middle cerebral artery occlusion (MCAO) between young and aged rats", "dateAssigned" : "2021-02-04T00:00:00.000-06:00", "summary" : "We conducted analysis of the gene expression pattern on our samples (Transient MCAO for 60 minutes established acute ischemic stroke followed by 3 days reperfusion) by the Affymetrix rat 230 2.0 chip.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33716719" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166195" }, "primaryId" : "GEO:GSE166195", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166195" } ] }, "title" : "Gene expression changes in rat lung induced by six pyrrolizidine alkaloids", "dateAssigned" : "2021-02-04T00:00:00.000-06:00", "summary" : "Transcriptomic analysis with six structurally different PA heliotrine, echimidine, lasiocarpine, senecionine, senkirkine, and platyphylline after subacute treatment of rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34185104" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166229" }, "primaryId" : "GEO:GSE166229", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166229" } ] }, "title" : "Universal Toxicity Gene Signatures for Early Identification of Drug-induced Tissue Injuries in Rats", "dateAssigned" : "2021-02-04T00:00:00.000-06:00", "summary" : "A new safety testing paradigm that relies on gene expression biomarker panels was developed that can easily and quickly identify dose-dependent drug-induced injuries across a number of different tissues in rats prior to drug candidate selection. The resource-sparing approach has yielded positive impact on early compound de-risking, enabling drug advancement in a cost-effective manner while reducing later probability ofattrition. Here we describe the development,qualification, and implementation of gene expression signatures that diagnose tissue degeneration/necrosis for use in an early rat Safety Lead Optimization (SLO) tolerability study or other early exploratory rat study conducted to assess drug action. Microarray data were used to first identify approximately 400 differentially expressed genes that were discovered as being shared consistently across 4 prioritized tissues (liver, kidney, heart, and skeletal muscle), following injuries induced by known toxicants and so were termed ‘universal’. Quantitative PCR on ~100 of those genes followed, and the approach was extended across 4 other tissues (pancreas, 5 sections of the gastrointestinal tract (GI), bladder, and testes) where acute toxicities are historically less common. The most consistent and robustly responding transcripts were selected, resulting in a final 22-gene set (16 universal genes and 6 tissue-specific genes) from which unique sets of 12 genes were chosen as optimal for each of 8 tissues. Mathematical algorithms were generated to convert each tissue's gene expression fold change values for the 12 genes to a single metric, scaled between 0 and 1, and a positive threshold set. For liver, kidney, heart, and skeletal muscle, this was established using a training set of 22 compounds and the performance determined by testing a set of approximately 100 additional rat studies resulting in approximately 90% sensitivity and 100% specificity. Similar performance was observed across a more limited set of 15 studies for pancreas, GI, bladder, and testes. Bundled together, we have incorporated these gene expression signature panels into a 4 day rat SLO toxicity study design, which provides a rapid objective assessment of more commonly seen compound liabilities, benchmarks non-toxic and toxic doses and exposures, and guides selection of lead candidates to reduce attrition without the necessity to perform time-consuming tissue and slide preparation, and expert microscopic histopathologic analyses, which can be reserved for advancing more optimized compounds at later development stages.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33837425" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166285" }, "primaryId" : "GEO:GSE166285", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166285" } ] }, "title" : "Towards 3D-bioprinting of an endocrine pancreas: A building block concept for bioartificial insulin-secreting tissue", "dateAssigned" : "2021-02-05T00:00:00.000-06:00", "summary" : "Conclusion: A defined end-to-end process for multidisciplinary bioconvergence research on a bioartificial endocrine pancreas was developed. A modular, patient-specific device architecture is proposed for future research studies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35462988" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166363" }, "primaryId" : "GEO:GSE166363", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166363" } ] }, "title" : "Targeted inhibition of two specific microRNAs in the brainstem prevents the development of hypertension through the cumulative effect of gene network changes [Fig2]", "dateAssigned" : "2021-02-08T00:00:00.000-06:00", "summary" : "We here test the concept that disease states may result not from a single cause but from small changes in a network that are collectively significant. We recently showed that development of hypertension (HTN) in the spontaneously hypertensive rat (SHR) model of human essential hypertension is accompanied by changes in microRNA expression levels in the brainstem tracking the development of HTN 1,2. This led to the hypothesis that preventing the change in microRNA levels could prevent the development of HTN. We propose that hypertension emerges from a network that has been pushed out of a normotensive equilibrium into a compensatory, pathological state. We show that small perturbations in the gene regulatory networks in the brainstem by selectively blocking two microRNAs highlighted in our previous results, miR-135a and miR-376a, is sufficient to prevent development of hypertension in the SHR model with a 38% reduction in blood pressure after one week persisting to 29% reduction after two weeks with no change in blood pressure in WKY controls at either timepoint. This effect appears driven by only modest, yet sometimes significant, changes in the expression of rate-limiting genes including IL1a, IL1b, Agtr1a, and Dbh among others. Many of these genes are direct targets of these miRNAs, suggesting that the combination of genes that are targeted in the network is responsible for the effect. The demonstration that hypertension is an emergent property of an underlying regulatory network suggests that a new treatment paradigm altogether is needed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166365" }, "primaryId" : "GEO:GSE166365", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166365" } ] }, "title" : "Targeted inhibition of two specific microRNAs in the brainstem prevents the development of hypertension through the cumulative effect of gene network changes [Fig3]", "dateAssigned" : "2021-02-08T00:00:00.000-06:00", "summary" : "We here test the concept that disease states may result not from a single cause but from small changes in a network that are collectively significant. We recently showed that development of hypertension (HTN) in the spontaneously hypertensive rat (SHR) model of human essential hypertension is accompanied by changes in microRNA expression levels in the brainstem tracking the development of HTN 1,2. This led to the hypothesis that preventing the change in microRNA levels could prevent the development of HTN. We propose that hypertension emerges from a network that has been pushed out of a normotensive equilibrium into a compensatory, pathological state. We show that small perturbations in the gene regulatory networks in the brainstem by selectively blocking two microRNAs highlighted in our previous results, miR-135a and miR-376a, is sufficient to prevent development of hypertension in the SHR model with a 38% reduction in blood pressure after one week persisting to 29% reduction after two weeks with no change in blood pressure in WKY controls at either timepoint. This effect appears driven by only modest, yet sometimes significant, changes in the expression of rate-limiting genes including IL1a, IL1b, Agtr1a, and Dbh among others. Many of these genes are direct targets of these miRNAs, suggesting that the combination of genes that are targeted in the network is responsible for the effect. The demonstration that hypertension is an emergent property of an underlying regulatory network suggests that a new treatment paradigm altogether is needed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166599" }, "primaryId" : "GEO:GSE166599", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166599" } ] }, "title" : "The changes of the nuclear landscape upon stimulation of neuronal cells are dependent on the histone deacetylase HDAC1", "dateAssigned" : "2021-02-11T00:00:00.000-06:00", "summary" : "Spatial chromatin organization is crucial for transcriptional regulation and might therefore be particularly dynamic in neurons since these terminally differentiated cells dramatically change their transcriptome in response to external stimuli. Here, we show that stimulation of neurons causes condensation of large chromatin domains. We find that this phenomenon is not only induced in rat hippocampal neurons cultured in vitro, but is also present in vivo in amygdala neurons of rats subjected to fear conditioning, and hippocampal neurons of animals subjected to kainate evoked seizures or High-Frequency Stimulation (HFS). The activity-induced chromatin condensation is an active, very rapid, and reversible process, that is independent of transcription and precedes the expression of Immediate Early Genes (IEG). It is accompanied by the redistribution of posttranslational modifications of histones, and rearrangements in the spatial organization of chromosome territories. Moreover, it leads to the reorganization of nuclear speckles and active domains located in their proximity. Finally, we find that neurons depleted of the histone deacetylase HDAC1 fail to condense chromatin upon stimulation, a phenomenon that can be fully reversed by the introduction of human HDAC1. Taken together, our results suggest that the HDAC1-dependent chromatin reorganization might constitute an important level of fine-tuning of transcriptional regulation in stimulated neurons.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166604" }, "primaryId" : "GEO:GSE166604", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166604" } ] }, "title" : "ENVIRONMENTAL STRESSORS IMPACT PLACENTATION THROUGH ACTIONS ON TROPHOBLAST, IMMUNE , AND ENDOTHELIAL CELL DYNAMICS [RNA-Seq]", "dateAssigned" : "2021-02-11T00:00:00.000-06:00", "summary" : "Our environment is replete with chemicals that can affect embryonic and extraembryonic development. Dioxins, such as 2,3,7,8-tetrachlorodibenzodioxin (TCDD), are compounds affecting development through the aryl hydrocarbon receptor (AHR). TCDD exposures can lead to placental adaptations and at higher doses pregnancy termination. Deep intrauterine endovascular trophoblast cell invasion was a prominent placentation site adaptation to TCDD. TCDD-mediated placental adaptations were dependent upon maternal AHR signaling but not placental or fetal AHR nor the presence of a prominent AHR target, cytochrome P450 1A1 (CYP1A1). At the placentation site, TCDD stimulated CYP1A1 transcription within endothelial cells but not trophoblast cells. Immune and trophoblast cell behaviors at the uterine-placental interface were guided by the actions of TCDD on endothelial cells. In summary, we have identified an AHR regulatory pathway activated by environmental stressors affecting uterine and trophoblast cell dynamics and the formation of the hemochorial placenta.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34747641" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166627" }, "primaryId" : "GEO:GSE166627", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166627" } ] }, "title" : "A TNFR2-hnRNPK axis promotes primary liver cancer development via activation of YAP signaling in hepatic progenitor cells", "dateAssigned" : "2021-02-11T00:00:00.000-06:00", "summary" : "Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, Tnfrsf1α-/- and Tnfrsf1β-/- (with or without TNFα treat) HPCs Transcriptomes.The mRNA profiles of Wild Type, Tnfrsf1α-/- and Tnfrsf1β-/- (with or without TNFα treat) HPCs were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level . qRT–PCR validation was performed using TaqMan and SYBR Green assays.We performed RNA-seq analysis to assess the global impacts of TNFR2 on HPCs' response to TNFα. Upon TNFα treatment, 519 genes were significantly upregulated in wild type HPCs . 39% of these genes (203 out of 519) were further upregulated in Tnfrsf1a-/- HPCs treated with TNFα. However, these 203 genes were dramatically downregulated in TNFα-treated Tnfrsf1b-/- HPCs relative to their expression in either TNFα-treated Tnfrsf1a-/- HPCs or wild type HPCs, indicating an inhibitory role for deletion of TNFR2 in the regulation of these genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33619115" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166659" }, "primaryId" : "GEO:GSE166659", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166659" } ] }, "title" : "ENVIRONMENTAL STRESSORS IMPACT PLACENTATION THROUGH ACTIONS ON TROPHOBLAST, IMMUNE , AND ENDOTHELIAL CELL DYNAMICS [scRNA-Seq]", "dateAssigned" : "2021-02-12T00:00:00.000-06:00", "summary" : "Our environment is replete with chemicals that can affect embryonic and extraembryonic development. Dioxins, such as 2,3,7,8-tetrachlorodibenzodioxin (TCDD), are compounds affecting development through the aryl hydrocarbon receptor (AHR). TCDD exposures can lead to placental adaptations and at higher doses pregnancy termination. Deep intrauterine endovascular trophoblast cell invasion was a prominent placentation site adaptation to TCDD. TCDD-mediated placental adaptations were dependent upon maternal AHR signaling but not placental or fetal AHR nor the presence of a prominent AHR target, cytochrome P450 1A1 (CYP1A1). At the placentation site, TCDD stimulated CYP1A1 transcription within endothelial cells but not trophoblast cells. Immune and trophoblast cell behaviors at the uterine-placental interface were guided by the actions of TCDD on endothelial cells. In summary, we have identified an AHR regulatory pathway activated by environmental stressors affecting uterine and trophoblast cell dynamics and the formation of the hemochorial placenta.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34747641" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166919" }, "primaryId" : "GEO:GSE166919", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166919" } ] }, "title" : "Translation of Circular RNAs in Neural Retina", "dateAssigned" : "2021-02-17T00:00:00.000-06:00", "summary" : "We performed Ribosome-protected mRNA fragment sequencing (Ribo-Seq) to determine if retinal circular RNAs are undergoing translation", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166957" }, "primaryId" : "GEO:GSE166957", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166957" } ] }, "title" : "Identifying metabolic adaptations of rat cardiomyocytes in response to cardiotoxicity", "dateAssigned" : "2021-02-17T00:00:00.000-06:00", "summary" : "Improvements in the diagnosis and treatment of cancer has revealed the long-term side effects of chemotherapeutics, particularly cardiotoxicity. Current clinical measures to track cardiotoxicity are insufficient to diagnose damage before it has been done, necessitating new, early biomarkers of cardiotoxicity. Here, we collected paired transcriptomics and metabolomics data characterizing in vitro cardiotoxicity to three compounds: 5-fluorouracil, acetaminophen, and doxorubicin. Standard gene enrichment and metabolomics approaches identify some commonly affected pathways and metabolites but are not able to readily identify mechanisms of cardiotoxicity. Here, we integrate this paired data with a genome-scale metabolic network reconstruction (GENRE) of the heart to identify shifted metabolic functions, unique metabolic reactions, and changes in flux in metabolic reactions in response to these compounds. Using this approach, we are able to confirm known mechanisms of doxorubicin-induced cardiotoxicity and provide hypotheses for mechanisms of cardiotoxicity for 5-fluorouracil and acetaminophen.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166985" }, "primaryId" : "GEO:GSE166985", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE166985" } ] }, "title" : "Transcriptional profiles reveal deregulation of lipid metabolism and inflammatory pathways in neurons exposed to palmitic acid", "dateAssigned" : "2021-02-17T00:00:00.000-06:00", "summary" : "The effects of the consumption of high-fat diets (HFD) have been studied to unravel the molecular pathways they are altering in order to understand the link between increased caloric intake, metabolic diseases, and the risk of cognitive dysfunction.The saturated fatty acid, palmitic acid (PA), is the main component of HFD and it has been found increased in the circulation of obese and diabetic people. In the central nervous system, PA has been associated with inflammatory responses in astrocytes, but the effects on neurons exposed to PA have not been largely investigated. Given that PA affect a variety of metabolic pathways, we aimed to analyze the genomic profile activated by this fatty acid to shed light on the mechanisms of neuronal dysfunction. In the current study, we profiled the transcriptome response after PA exposition at non-toxic doses in primary hippocampal neurons. Gene ontology and Reactome analysis revealed a pattern of gene expression which is associated with inflammatory pathways and, importantly, with the activation of lipid metabolism that is considered not very active in neurons. Validation by qRT-PCR of Hmgcs2, Angptl4, Ugt8 and Rnf145 confirmed the results obtained by RNAseq. Overall, these findings suggest that neurons are able to respond to saturated fatty acids changing the expression pattern of genes associated with inflammatory response and lipid utilization that may be involved in the neuronal damage associated with metabolic diseases", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34155583" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167038" }, "primaryId" : "GEO:GSE167038", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167038" } ] }, "title" : "Examination of CA1 hippocampal DNA methylation as a mechanism for closing of estrogen’s critical window", "dateAssigned" : "2021-02-18T00:00:00.000-06:00", "summary" : "The study presents several novel findings that relate to the idea that alterations in DNA methylation occurs during aging and may be linked to senescent physiology, including a decline in circulating E2. In addition, the evidence has been provided that DNA methylation contributes to the closing of the critical window for E2 effects on synaptic function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34421577" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167102" }, "primaryId" : "GEO:GSE167102", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167102" } ] }, "title" : "Rat model of breast cancer to dissect mechanisms of immune escape and immunotherapy sensitivity", "dateAssigned" : "2021-02-19T00:00:00.000-06:00", "summary" : "NMU-induced sprague dawley rat model of breast cancer treated with immunotherapy to prevent tumor progression", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35446942" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167238" }, "primaryId" : "GEO:GSE167238", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167238" } ] }, "title" : "Sustained splenic contraction after daily cocaine administration in rats", "dateAssigned" : "2021-02-22T00:00:00.000-06:00", "summary" : "Total RNAs from the control and cocaine groups (day 7) were subjected to DNA microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34086815" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167253" }, "primaryId" : "GEO:GSE167253", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167253" } ] }, "title" : "Neuronal Enhancers are Hotspots for DNA Single-Strand Break Repair [ChIP-seq]", "dateAssigned" : "2021-02-22T00:00:00.000-06:00", "summary" : "Defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons. The cellular genome is subjected to a constant barrage of endogenous DNA damage, but surprisingly little is known about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here, we show that post-mitotic neurons accumulate unexpectedly high levels of DNA single-strand breakage at specific sites within the genome. Genome-wide mapping reveals that these single-strand breaks (SSBs) are located within enhancers at or near to CpG dinucleotides and sites of DNA demethylation, and are repaired by PARP1 and XRCC1-dependent mechanisms. Notably, deficiencies in XRCC1-dependent short-patch repair elevate the extent of DNA repair synthesis at neuronal enhancers, whereas deficiencies in long-patch repair reduce synthesis, suggesting that the high steady-state level of SSB repair in neuronal enhancers is sustained by both short-patch and long-patch processes. These data provide the first evidence of site- and cell type-specific SSB repair, revealing unexpected levels of localized and continuous DNA single-strand breakage in neurons. In addition, these data suggest an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33767446" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167257" }, "primaryId" : "GEO:GSE167257", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167257" } ] }, "title" : "Neuronal Enhancers are Hotspots for DNA Single-Strand Break Repair [SAR-seq]", "dateAssigned" : "2021-02-22T00:00:00.000-06:00", "summary" : "Defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons. The cellular genome is subjected to a constant barrage of endogenous DNA damage, but surprisingly little is known about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here, we show that post-mitotic neurons accumulate unexpectedly high levels of DNA single-strand breakage at specific sites within the genome. Genome-wide mapping reveals that these single-strand breaks (SSBs) are located within enhancers at or near to CpG dinucleotides and sites of DNA demethylation, and are repaired by PARP1 and XRCC1-dependent mechanisms. Notably, deficiencies in XRCC1-dependent short-patch repair elevate the extent of DNA repair synthesis at neuronal enhancers, whereas deficiencies in long-patch repair reduce synthesis, suggesting that the high steady-state level of SSB repair in neuronal enhancers is sustained by both short-patch and long-patch processes. These data provide the first evidence of site- and cell type-specific SSB repair, revealing unexpected levels of localized and continuous DNA single-strand breakage in neurons. In addition, these data suggest an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33767446" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167369" }, "primaryId" : "GEO:GSE167369", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167369" } ] }, "title" : "Dynamics of global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain", "dateAssigned" : "2021-02-23T00:00:00.000-06:00", "summary" : "Shared transcriptomic and epigenetic changes in two animal models improves our understanding of how chromatin structural changes alter dorsal root ganglion (DRG) gene expression under persistent pain conditions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34446036" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167430" }, "primaryId" : "GEO:GSE167430", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167430" } ] }, "title" : "Fibroblast growth factor 2 promotes bladder hypertrophy caused by partial bladder outlet obstruction", "dateAssigned" : "2021-02-24T00:00:00.000-06:00", "summary" : "The current study aims to investigate molecular alterations and biomarkers associated with partial BOO (PBOO) in rats. RNA-seq analyses were conducted to identify molecular alterations. Rats with PBOO experienced hypertrophy of smooth muscle cells and hyperplasia of interstitial cells during the first 4 weeks after the initiation of obstruction. Four weeks later, rats with PBOO showed activation of the adaptive immune response, cell death and apoptosis. The levels of BDNF and FGF2 in the serum gradually increased in the first four weeks and gradually decreased after week 4. FGF2 levels slightly correlated with prostate volume (R=0.156, P=0.0028) but not with age or BMI in BPH patients. FGF2 is involved in the development of hypertrophy in the PBOO bladder and shows a positive correlation with prostate volume in BPH patients.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33859983" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167433" }, "primaryId" : "GEO:GSE167433", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167433" } ] }, "title" : "Generation of functional rat spermatozoa in sterile mice utilizing blastocyst complementation with pluripotent stem cells [bulk RNA-seq]", "dateAssigned" : "2021-02-24T00:00:00.000-06:00", "summary" : "Pluripotent stem cells (PSCs) provide a powerful tool to produce transgenic animals for biomedical research. However, impaired PSC contribution to chimerism and most notably the germline oftentimes impedes production of genetically modified animals, rendering techniques that expediate PSC contribution to the germline highly desirable. Blastocyst complementation denotes a technique which purposes to generate organs, tissues or cells in animal chimeras via microinjection of PSCs into genetically compromised blastocyst-stage embryos. Here we report on successful blastocyst complementation of the male germline in adult chimeras following microinjection of mouse or rat PSCs into mouse blastocysts mutated for Tsc22d3, an essential gene for spermatozoa production. Microinjection of mouse embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) into Tsc22d3-KnockOut (KO) blastocyst-stage embryos gave rise to intraspecies chimeras embodying functional spermatozoa, which were solely derived from microinjected PSCs. Furthermore, microinjection of rat ESCs into Tsc22d3-KO mouse embryos gave rise to viable mouse-rat chimeras that exhibited extensive contribution of rat cells to various organs. Notably, multiple mouse-rat chimeras showed contribution of rat ESCs to the male germline, solely harboring rat spermatids and spermatozoa that were rat ESC-derived and could fertilize rat oocytes. Collectively, this study reports a method for exclusive production of functional germ cells of one species in another via blastocyst complementation with PSCs. Implications of this study extend to development of transgenic rats via sterile mice, and may further assist efforts to generate xenogeneic gametes from endangered animal species. ", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35931077" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167513" }, "primaryId" : "GEO:GSE167513", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167513" } ] }, "title" : "Transcriptome Investigation of Anti-inflammation and Immuno-Regulation Mechanism of Taurochenodeoxycholic acid", "dateAssigned" : "2021-02-25T00:00:00.000-06:00", "summary" : "Conclusions: The anti-inflammatory and immuno-regulatory activities of TCDCA are proven to be related to the up-regulation expression of GPX3, SRSF9 and CSTB.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33926569" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167579" }, "primaryId" : "GEO:GSE167579", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167579" } ] }, "title" : "Comparative 3D Genome Architecture in Vertebrates (Hi-C)", "dateAssigned" : "2021-02-25T00:00:00.000-06:00", "summary" : "Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. Further, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35524220" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167580" }, "primaryId" : "GEO:GSE167580", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167580" } ] }, "title" : "Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)", "dateAssigned" : "2021-02-25T00:00:00.000-06:00", "summary" : "Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. Further, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35524220" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167904" }, "primaryId" : "GEO:GSE167904", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167904" } ] }, "title" : "Transcriptomic Analysis Reveals that Atf3/c-Jun/Lgals3 axis is associated with Central Diabetes Insipidus after Hypothalamic Injury", "dateAssigned" : "2021-02-28T00:00:00.000-06:00", "summary" : "Conclusions: We revealed that RNA-seq based transcriptome characterization would expedite genetic network analyses of hypothalamic SON, PVN and permit the dissection of complex biologic functions during the process of central diabetes insipidus after PEL surgery.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167905" }, "primaryId" : "GEO:GSE167905", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167905" } ] }, "title" : "Identification of competing endogenous RNA (ceRNA) and micro-RNA profiles and regulatory networks in 4-nonylphenol-induced impairment of sertoli cells I", "dateAssigned" : "2021-02-28T00:00:00.000-06:00", "summary" : "Purpose: To uncover the mechanism of 4-nonylphenol-induced impairment of sertoli cells, we used RNA sequencing technology to compare the lncRNA expression differences between the control groups and the 4-nonylphenol treated groups. Sertoli cells lncRNA, circRNA, mRNA profiles of the control groups and the 4-nonylphenol treated groups were generated by deep sequencing, in duplicate. The library quality was determined using a Bioanalyzer 2100 (Agilent). The Illumina hiseq X ten platform was used for lnc RNA sequencing. The quality of RNA-seq reads was examined using FastQC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34084133" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167909" }, "primaryId" : "GEO:GSE167909", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167909" } ] }, "title" : "Identification of competing endogenous RNA (ceRNA) and micro-RNA profiles and regulatory networks in 4-nonylphenol-induced impairment of sertoli cells II", "dateAssigned" : "2021-02-28T00:00:00.000-06:00", "summary" : "Purpose: To uncover the mechanism of 4-nonylphenol-induced impairment of sertoli cells, we used RNA sequencing technology to compare the small RNA expression differences between the control groups and the 4-nonylphenol treated groups. Sertoli cells small RNA profiles of the control groups and the 4-nonylphenol treated groups were generated by deep sequencing, in triplicate. The library quality was determined using a Bioanalyzer 2100 (Agilent). The Illumina BGISEQ platform was used for small RNA sequencing. The quality of RNA-seq reads was examined using FastQC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34084133" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167948" }, "primaryId" : "GEO:GSE167948", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167948" } ] }, "title" : "Urine miRNAs as potential biomarkers for systemic reactions induced by exposure to embedded metal", "dateAssigned" : "2021-03-01T00:00:00.000-06:00", "summary" : "Many veterans live with military grade heavy metal fragments retained in soft tissue. Retained heavy metal fragments may negatively impact health in various organ systems and can manifest as gastrointestinal, neurocognitive, pulmonary and renal disturbances. As such, a better understanding of the long-term effects of retained metals and identification of biomarkers indicative of detrimental health outcomes would benefit clinical decision making. In this study, we analyzed urine microRNAs from rats with military-relevant pure metals implanted in the gastrocnemius muscle for 1, 3, 6, and 12 months. Our results provide potential tissue targets affected by metal exposure and a list of unique or common urine microRNA biomarkers indicative of exposure to one or more metals, highlighting a complex systemic response.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34541869" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167980" }, "primaryId" : "GEO:GSE167980", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167980" } ] }, "title" : "Gene expression signatures for rat liver grafts", "dateAssigned" : "2021-03-01T00:00:00.000-06:00", "summary" : "Acute rejection remains an important risk factor affecting the survival of recipients following transplantation. Bone marrow mesenchymal stem cells (BMMSCs) are used in the treatment of organ transplantation due to their immunomodulatory ability. BMMSCs were isolated from rat bone marrow and modified with the adenovirus for heme oxygenase 1 (HO-1) gene. Saline solution, BMMSCs or HO-1/BMMSCs were perfused into the donor liver in vitro using a normothermic machine perfusion (NMP) system, followed by liver transplantation. The liver grafts were collected at 7 days post-transplantation. Gene chip technology was used to detect differential gene expression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167981" }, "primaryId" : "GEO:GSE167981", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167981" } ] }, "title" : "Single nuclei RNAseq of rat area postrema and nucleus tractus solitarius", "dateAssigned" : "2021-03-01T00:00:00.000-06:00", "summary" : "We performed single-nuclei RNAseq of Sprague Dawley rat area postrema and nucleus tractus solitarius brain samples to identify cellular subtypes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37245848" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167991" }, "primaryId" : "GEO:GSE167991", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE167991" } ] }, "title" : "Single nuclei RNAseq of rat area postrema and nucleus tractus solitarius after GDF15 treatment", "dateAssigned" : "2021-03-01T00:00:00.000-06:00", "summary" : "We performed single-nuclei RNAseq of Sprague Dawley rat area postrema and nucleus tractus solitarius brain samples from animals treated with GDF-15 to identify cellular subtype specific changes in the neural transcriptome.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37245848" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168151" }, "primaryId" : "GEO:GSE168151", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168151" } ] }, "title" : "Multi- and transgenerational disruption of maternal behavior and female puberty by Endocrine Disrupting Chemical (EDC) mixture exposure", "dateAssigned" : "2021-03-03T00:00:00.000-06:00", "summary" : "We report gene expression profiles in the median basal hypothalamus of 21-day old female wistar rats from the F1 and F3 generation after exposure to a mixture of Endocrine Disrupting Chemicals or vehicle", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34383603" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168156" }, "primaryId" : "GEO:GSE168156", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168156" } ] }, "title" : "Adult rat ventral tegmental area single-nucleus RNA-seq dataset for \"An atlas of transcriptionally defined cell populations in the rat ventral tegmental area\"", "dateAssigned" : "2021-03-03T00:00:00.000-06:00", "summary" : "This dataset contains single-nucleus RNA sequencing results from adult rat brain (ventral tegmenal area, or VTA). The goal of this experiment was to define the transcriptional landscapes of distinct cell types in the VTA. Single-cell sequencing was carried out with nuclei suspensions (sorted using flow cytometry) using the 10X Genomics Chromium single cell sequencing platform.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168232" }, "primaryId" : "GEO:GSE168232", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168232" } ] }, "title" : "Transcriptional responses to maternal trichloroethylene and/or N-acetyl cysteine exposure in Wistar rat placental tissue", "dateAssigned" : "2021-03-04T00:00:00.000-06:00", "summary" : "Trichloroethylene (TCE) is a persistent and pervasive environmental contaminant. N-acetyl cysteine (NAC) is an antioxidant that may reduce TCE effects. Pregnant Wistar rats were exposed to 480 mg TCE mg/kg/day, 200 mg/kg/day NAC or co-exposure with both chemicals via ingestion (mini vanilla wafer) on gestation days 6-16 (tissue collection day). TCE- and/or NAC-induced changes to gene expression were evaluated in male and female rat placentae.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168267" }, "primaryId" : "GEO:GSE168267", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168267" } ] }, "title" : "The expression profile of miRNA in the testis of STZ-induced diabetic rats", "dateAssigned" : "2021-03-04T00:00:00.000-06:00", "summary" : "The number of patients with diabetes is increasing worldwide. Diabetic testicular damage can cause spermiogenesis disorders and sexual dysfunction. We thus explored the role of miRNAs in diabetic testicular damage, and revealed that they could serve as effective prevention and treatment therapeutic targets.Streptozotocin (STZ) was used to generate a rat model of type 2 diabetes. Rat testicular tissues were used for miRNA sequencing. we identified 19 differentially expressed miRNAs in the testes of diabetic rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34496750" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168287" }, "primaryId" : "GEO:GSE168287", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168287" } ] }, "title" : "mRNA expression profiling of BLM-Induced pulmonary fibrosis in rat", "dateAssigned" : "2021-03-04T00:00:00.000-06:00", "summary" : "Pulmonary fibrosis includes a variety of underlying causes of fibrosing interstitial lung diseases (ILDs). Pulmonary fibrosis is usually considered to be related to chronic inflammation of lung tissue and excessive proliferation of fibroblasts, however, the mechanism is complex and unclear.To study the underlying molecular mechanisms, we further applied high-throughput sequencing to analyze the differentially expressed genes in rat lung tissues induced by Bleomycin.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168328" }, "primaryId" : "GEO:GSE168328", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168328" } ] }, "title" : "Tissue-specific chromatin accessibility cis-regulatory regions in rat white adipose and muscle", "dateAssigned" : "2021-03-05T00:00:00.000-06:00", "summary" : "Chromatin accessibility is a key factor influencing gene expression. We developed a modified protocol, ruptor-ATAC, which with RNA-seq was used to investigate regulatory elements underlying gene expression in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. Integration of both datasets showed that promoter accessibility correlated with RNA expression and identified 44,798 tissue-specific differentially accessible regions (DARs), predominantly localized in intergenic and intron regions. Tissue-specific DARs mapped to differentially expressed genes that were enriched in distinct biological processes. Motif enrichment analysis on DARs predicted binding sites for transcription factors (TFs). Significant up-regulation of 11 TFs recognizing enriched cis-motifs in each tissue indicated their functional relevance. Positive correlation between motif accessibility and target gene expression further supported the role of selected TFs as transcriptional regulators. Our study identifies non-promoter cis-regulatory regions that likely play a major role in the control of tissue-specific gene expression in adipose and muscle.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34547403" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168390" }, "primaryId" : "GEO:GSE168390", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168390" } ] }, "title" : "Effect of ecdysterone on the hepatic transcriptome and lipid metabolism in lean and obese Zucker rats", "dateAssigned" : "2021-03-06T00:00:00.000-06:00", "summary" : "Ecdysteroids are a class of steroid hormones occurring in insects, where they are referred as zooecdysteroids, and in plants, where they are termed phytoecdysteroids. While zooecdysteroids in insects regulate important developmental processes, such as embryogenesis, molting (ecdysis), metamorphosis, reproduction, and diapause, phytoecdysteroids provide protection against invertebrate predators by acting as feeding deterrents and by disrupting critical developmental processes of such invertebrates. The ecdysteroids in insects and plants comprise a great number of different analogues, with 20‐hydroxyecdysone, also called ecdysterone, being the quantitatively dominating biologically active analogue in both, insects and plants. Although phytoecdysteroids are effective toxins or antifeedants towards non-adapted herbivorous invertebrate predators, ecdysteroids are apparently non-toxic to mammals and even have been shown to exert a variety of interesting metabolic actions, such as antiobesity, hypoglycemic and protein-anabolic effects. In the present study aimed to test the hypothesis that ecdysterone causes lipid-lowering effects in obese Zucker rats. To test this hypothesis, two groups of obese Zucker rats were fed a nutrient-adequate diet supplemented without or with 0.05% ecdysterone. This ecdysterone concentration was appropriate to achieve a similar dose of ecdysterone per kg body weight BW as applied in other rodent studies, in which ecdysterone caused either hepatic and plasma lipid-lowering effects or antiobesity effects in different rodent models. In order to decipher the potential lipid-lowering actions of ecdysteroids in Zucker rats, measurements of liver and plasma lipid concentrations and hepatic transcriptome analysis was carried out. To further study if ecdysterone is capable of alleviating the strong lipid-synthetic activity in the liver of obese Zucker rats, the study included also two groups of lean Zucker rats which also received either the ecdysterone-supplemented or the non-supplemented diet.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34063487" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168465" }, "primaryId" : "GEO:GSE168465", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168465" } ] }, "title" : "Primary brain cell infection by Toxoplasma gondii reveals the dynamics of spontaneous bradyzoite differentiation and the extend of modification of neuron biology after infection", "dateAssigned" : "2021-03-08T00:00:00.000-06:00", "summary" : "Toxoplasma gondii is a eukaryotic parasite that form latent cyst in the brain of immunocompetent individuals. The latent parasites infection of the immune privileged central nervous system is linked to most complications. With no drug currently available to eliminate the latent cysts in the brain of infected hosts, the consequences of neurons long-term infection are unknown.. It has long been known that T. gondii specifically differentiate into a latent form (bradyzoite) in neurons, but how the infected neuron is responding to the infection remain to be elucidated. We have established a new in vitro model resulting in the production of fully mature bradyzoites cysts in brain cells. Using dual, host and parasite, RNA-seq we characterized the dynamics of differentiation of the parasite, revealing the involvement of key pathways in this process. Moreover, we identified how the infected brain cells responded to the parasite infection revealing the drastic changes that take place. We showed that neuronal specific pathways are strongly affected, with synapse signaling being particularly affected, especially glutamatergic synapse. The establishment of this new in vitro model allows to investigate both the dynamics of the parasite differentiation and the specific response of neurons to the long term infection by this parasite.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34610266" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168545" }, "primaryId" : "GEO:GSE168545", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168545" } ] }, "title" : "Single-Cell Transcriptomic Atlas of Penile Corpus Cavernosum Aging", "dateAssigned" : "2021-03-09T00:00:00.000-06:00", "summary" : "Conclusions: We plotted a cellular atlas of penile corpus cavernosum, and revealed the molecular alterations of aging cells, especially fibroblasts. Our work will deepen the understanding of the heterogeneity among certain cell types during penile corpus cavernosum aging and provide novel entry points for the age-associated ED treatment.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168599" }, "primaryId" : "GEO:GSE168599", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168599" } ] }, "title" : "Sex and cell-specific gene expression in corticolimbic brain regions associated with psychiatric disorders revealed by bulk and single-nuclei RNA sequencing", "dateAssigned" : "2021-03-09T00:00:00.000-06:00", "summary" : "that strongly implicates the NAcS.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168711" }, "primaryId" : "GEO:GSE168711", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168711" } ] }, "title" : "Next generation sequencing for lncRNA profile of bone marrow mesenchymal stem cells through establishing exercise rat model by treadmill running experiment", "dateAssigned" : "2021-03-11T00:00:00.000-06:00", "summary" : "In this study, we proved the exercise-induced promotion of osteogenic differentiation and inhibition of adipogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) through establishing exercise animal model by treadmill running experiment. lncRNA sequencing analysis identified 44 upregulated lncRNAs and 39 downregulated lncRNAs in exercise group.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34109424" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168712" }, "primaryId" : "GEO:GSE168712", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168712" } ] }, "title" : "Next generation sequencing for miRNA profile of bone marrow mesenchymal stem cells through establishing exercise rat model by treadmill running experiment", "dateAssigned" : "2021-03-11T00:00:00.000-06:00", "summary" : "In this study, we proved the exercise-induced promotion of osteogenic differentiation and inhibition of adipogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) through establishing exercise animal model by treadmill running experiment. miRNA sequencing analysis identified 16 upregulated and 2 downregulated miRNAs in exercise group.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34109424" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168757" }, "primaryId" : "GEO:GSE168757", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE168757" } ] }, "title" : "Serum miRNAs as potential biomarkers for exposure to embedded military-relevant metals", "dateAssigned" : "2021-03-11T00:00:00.000-06:00", "summary" : "Many veterans live with military grade heavy metal fragments retained in soft tissue. Retained heavy metal fragments may negatively impact health in various organ systems and can manifest as gastrointestinal, neurocognitive, pulmonary and renal disturbances. As such, a better understanding of the long-term effects of retained metals and identification of biomarkers indicative of detrimental health outcomes would benefit clinical decision making. In this study, we analyzed serum microRNAs from rats with military-relevant pure metals implanted in the gastrocnemius muscle for 1, 3, 6, and 12 months in order to identify potential microRNA biomarkers that are indicative of exposure to one or more metals.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37058270" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169063" }, "primaryId" : "GEO:GSE169063", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169063" } ] }, "title" : "Comparison of gene expression profiles of neonate rat cardiomyocytes (NRCMs) transfected with LacZ, 23k prolactin (PRL), or 16k PRL.", "dateAssigned" : "2021-03-17T00:00:00.000-05:00", "summary" : "Recently, it is reported that multiple signaling pathways are involved with the pathogenesis of PPCM. Here, we show that 23k PRL activates PERK signaling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34548576" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169085" }, "primaryId" : "GEO:GSE169085", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169085" } ] }, "title" : "RNA-Sequencing Characterisation of the Renal Cortical Response to Diet-Induced Weight Loss and Medical Therapy in the Zucker Diabetic Sprague Dawley Rat Model of Diabetic Kidney Disease", "dateAssigned" : "2021-03-17T00:00:00.000-05:00", "summary" : "We report results from renal cortical transcriptomic analysis of responses to diet-induced weight loss plus medical therapy in the Zucker Diabetic Sprague Dawley (ZDSD) rat model of diabetic kidney disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36259366" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169130" }, "primaryId" : "GEO:GSE169130", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169130" } ] }, "title" : "The expression profile of circRNA, lncRNA and mRNA in the testis of STZ-induced diabetic rats", "dateAssigned" : "2021-03-17T00:00:00.000-05:00", "summary" : "The number of patients with diabetes is increasing worldwide. Diabetic testicular damage can cause spermiogenesis disorders and sexual dysfunction. We thus explored the role of circRNA, lncRNA and mRNA in diabetic testicular damage, and revealed that they could serve as effective prevention and treatment therapeutic targets. Streptozotocin (STZ) was used to generate a rat model of type 2 diabetes. Rat testicular tissues were used for circRNA, lncRNA and mRNA sequencing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34496750" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169157" }, "primaryId" : "GEO:GSE169157", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169157" } ] }, "title" : "Small RNA-seq comparing transcriptome (small RNAs) of spermatozoa from rat fed either a standard-Diet (SD) or a High-Protein-Diet (HPD)", "dateAssigned" : "2021-03-18T00:00:00.000-05:00", "summary" : "Gene expression analysis of sperm small RNA obtained from rat fed either a standard (SD) or High Protein Diets (HPD). The aim of the study is to identify differentially expressed small RNA in sperm of SD-fed and HPD-fed males which might be involved in the epigenetic inheritance of glucose sensitivity induced by a High Protein Diet.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34069853" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169181" }, "primaryId" : "GEO:GSE169181", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169181" } ] }, "title" : "The effect of Repeated Social defeat stress (RSD) on transcriptomic profiles of rat heart", "dateAssigned" : "2021-03-18T00:00:00.000-05:00", "summary" : "This study investigated risk factors that may contribute to stress-related cardiac disease susceptibility and progression in a rodent model. The experiment was designed to evaluate the transcriptomic changes in in the heart of male adult rats after repeated episodes of social defeat stress.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169185" }, "primaryId" : "GEO:GSE169185", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169185" } ] }, "title" : "RNA-seq analysis of CREB3L2 dimers in Hippocampal Neurons", "dateAssigned" : "2021-03-18T00:00:00.000-05:00", "summary" : "To investigate differential gene expression profiles mediated by CREB3L2 transcription factor dimers in order to assess their differential contribution to Alzheimer's disease pathogenesis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169296" }, "primaryId" : "GEO:GSE169296", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169296" } ] }, "title" : "Sex differences in transcriptome profiles in hypothalamic and extrahypothalamic nuclei of rats impacted by adolescent stress", "dateAssigned" : "2021-03-22T00:00:00.000-05:00", "summary" : "In order to generate data worthy of translatability to known sex differences in human stress-induced maladies, adolescent male and female rats underwent chronic restraint stress (stress) or not (nonstress, control) from postnatal day (PD)32-PD44. Specific brain nuclei (PVN, VMH, ARC, BLA, CEA, CA1, CA3, DG, and OFC) were analyzed for genome-wide transcriptome using RNA sequencing (RNA-Seq). Global transcriptome profiles were generated, and genes differentially expressed (DE) due to stress were identified for each nuclear subregion listed. Canonical pathway analyses identified DE genes that are likely crucial for causing well-known stress-induced sex differences.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169301" }, "primaryId" : "GEO:GSE169301", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169301" } ] }, "title" : "scRNAseq analysis of rat and human dorsal root ganglions", "dateAssigned" : "2021-03-22T00:00:00.000-05:00", "summary" : "Peripheral sensory neurons located in dorsal root ganglia relay sensory information from the peripheral tissue to the brain. Satellite glial cells (SGC) are unique glial cells that form an envelope completely surrounding each sensory neuron soma. This organization allows for close bi-directional communication between the neuron and it surrounding glial coat. Morphological and molecular changes in SGC have been observed in pathological conditions such as inflammation, chemotherapy-induced neuropathy, viral infection and nerve injuries. SGC play critical roles in neuronal excitability and nociception, as well as contribute to promote axon regeneration. Whether findings made in rodent model systems are relevant to human physiology has not been investigated. Here we present a detailed characterization of SGC across species. We characterized the transcriptional profile of SGC in mouse, rat and human at the single cell level. Our findings suggest that key features of SGC in rodent models are conserved in human. These results support the notion that SGC in the sensory system are largely conserved between species. Our study provides the potential to leverage on rodent and human SGC properties and unravel novel mechanisms and potential targets for treating nerve injuries.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35503034" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169386" }, "primaryId" : "GEO:GSE169386", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169386" } ] }, "title" : "Transcriptional profiling of brain tissues from a Q130 Long Evans Knock-in rat model of Huntington’s disease at 10-, 19- and 24-months of age", "dateAssigned" : "2021-03-22T00:00:00.000-05:00", "summary" : "Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that is characterized by motor, cognitive, and psychiatric alterations. The mutation responsible for this disease is an abnormally expanded and unstable CAG repeat within the coding region of the gene encoding huntingtin (Htt). A collaboration between the CHDI Foundation and Dr. H.P. Nguyen (huu.nguyen-r7w@ruhr-uni-bochum.de) at Universitat Bochum focused on generating a knock-in rat model of HD that contains expanded CAG repeats inserted within the rat huntingtin gene (Hdh) in order to provide a genetic reconstruction of the human causative mutation within the rat model. The goal of this study is RNA expression profiling by RNA sequencing (RNA-seq) in brain tissues of 10-, 19- and 24-month-old heterozygous knock-in rats with uninterrupted CAG length approaching 130 along with littermate control wild-type animals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169400" }, "primaryId" : "GEO:GSE169400", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169400" } ] }, "title" : "The role of intestinal iron absorption machinery in regulating gut hormone secretion and systemic metabolism [Ileum]", "dateAssigned" : "2021-03-23T00:00:00.000-05:00", "summary" : "Bariatric surgeries remain the most effective treatments for sustained weight loss and remission of type 2 diabetes. In addition to decreased body weight and improved glucose regulation, these procedures also dramatically increase secretion of several gut hormones including GLP-1. Despite these benefits, there are deleterious side effects to these procedures that include an increased incidence of iron-deficiency related anemias. The transcription factor HIF2a is heavily expressed in the duodenum and regulates the molecular machinery of iron absorption from the lumen. Lower iron levels after both gastric bypass and sleeve gastrectomy procedures occur despite dramatic upregulation of HIF2a signaling in the duodenum and are likely the result of increased hepcidin levels. Low iron diets also stimulate increased HIF2a signaling in the duodenum and produce effects similar to bariatric surgery that include reduced body weight/fat, improved glucose regulation and increased secretion of the GLP-1. Gut-specific deletion of VHL results in a constitutive upregulation of HIF2a signaling in the small intestine and produces a dramatic phenotype that includes reduced body weight/fat, improved glucose tolerance and increased GLP-1 secretion from the intestine. These data demonstrate an important role of HIF2a signaling in the duodenum to regulate multiple aspects of systemic metabolism and gut hormone secretion pointing towards critical cross-talk between the systems that regulate iron and other aspects of systemic physiology important to prevalent metabolic diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35045308" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169402" }, "primaryId" : "GEO:GSE169402", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169402" } ] }, "title" : "The role of intestinal iron absorption machinery in regulating gut hormone secretion and systemic metabolism [Duodenum]", "dateAssigned" : "2021-03-23T00:00:00.000-05:00", "summary" : "Bariatric surgeries remain the most effective treatments for sustained weight loss and remission of type 2 diabetes. In addition to decreased body weight and improved glucose regulation, these procedures also dramatically increase secretion of several gut hormones including GLP-1. Despite these benefits, there are deleterious side effects to these procedures that include an increased incidence of iron-deficiency related anemias. The transcription factor HIF2a is heavily expressed in the duodenum and regulates the molecular machinery of iron absorption from the lumen. Lower iron levels after both gastric bypass and sleeve gastrectomy procedures occur despite dramatic upregulation of HIF2a signaling in the duodenum and are likely the result of increased hepcidin levels. Low iron diets also stimulate increased HIF2a signaling in the duodenum and produce effects similar to bariatric surgery that include reduced body weight/fat, improved glucose regulation and increased secretion of the GLP-1. Gut-specific deletion of VHL results in a constitutive upregulation of HIF2a signaling in the small intestine and produces a dramatic phenotype that includes reduced body weight/fat, improved glucose tolerance and increased GLP-1 secretion from the intestine. These data demonstrate an important role of HIF2a signaling in the duodenum to regulate multiple aspects of systemic metabolism and gut hormone secretion pointing towards critical cross-talk between the systems that regulate iron and other aspects of systemic physiology important to prevalent metabolic diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35045308" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169501" }, "primaryId" : "GEO:GSE169501", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169501" } ] }, "title" : "RNA-seq analysis on the liver of darkness rats treated with Limosilactobacillus reuteri", "dateAssigned" : "2021-03-24T00:00:00.000-05:00", "summary" : "We have previously demonstrated that the arrhythmic expressions of circadian clock genes due to constant darkness induce glycometabolic and reproductive hallmarks of polycystic ovary syndrome (PCOS) in rats. Limosilactobacillus reuteri (L.reuteri) is a promising dietary intervention for host dysmetabolism, while its potential effect on circadian dysrhythmia-induced PCOS remains elusive. Here, we evaluated the amelioration of L.reuteri regimen on constant darkness-induced PCOS-like rats through detecting hepatic gene expression profiles by RNA-seq.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169580" }, "primaryId" : "GEO:GSE169580", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169580" } ] }, "title" : "Neonatal rat ventricular cardiomyocytes Cells: Control vs. hypertrophic cardiomyocytes induced by isoproterenol", "dateAssigned" : "2021-03-24T00:00:00.000-05:00", "summary" : "the expression characteristics of lncRNAs among hypertrophic cardiomyocytes induced by isoproterenol in rat ventricular myocytes from newborn Sprague-Dawley rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169592" }, "primaryId" : "GEO:GSE169592", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169592" } ] }, "title" : "Sutural fibroblasts exhibit the function of vascular endothelial cell upon mechanical strain", "dateAssigned" : "2021-03-25T00:00:00.000-05:00", "summary" : "Midfacial hypoplasia is a kind of facial dysplasia. The technique of trans-sutural distraction osteogenesis(TSDO) can promote midface growth so as to ameliorate this symptom. Here, we used single-cell RNA sequencing to define the rat's cell classification of zygomatic maxillary suture and the changes of cell clusters in the suture before and after seven-day distraction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34599905" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169613" }, "primaryId" : "GEO:GSE169613", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169613" } ] }, "title" : "Polybrominated diphenyl ethers (PBDEs) exposure during pregnancy alters microRNA expression profile in rat placenta", "dateAssigned" : "2021-03-25T00:00:00.000-05:00", "summary" : "Polybrominated diphenyl ethers (PBDEs) are well-known endocrine disrupting chemicals (EDCs), and have been found to affect reproduction and development. The placenta, as the interface between maternal and fetal circulation, is constantly exposed to maternal EDCs. The present study investigated PBDEs-induced changes in miRNAs in rat placenta, and the potential mechanism of developmental toxicity. Female rats were exposed to 500 mg/kg/day decabromodiphenyl ether (BDE-209) from gestational day 0 (GD 0) to GD 20. miRNAs were isolated from the placenta on GD 20. Expression of miRNAs were analyzed using next-generation sequencing, and validated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). A total of 55 miRNAs were found changed significantly in the exposure group, among which 46 were down-regulated and 9 were up-regulated. Rno-miR-17-5p, rno-miR-503-5p, rno-miR-374-5p, rno-miR-369-3p, rno-miR-29a-3p were confirmed to be down-regulated, rno-miR-148a-3p was validated up-regulated in the exposure group. The bioinformatic analysis showed that the predicted miRNAs target genes were involved in vascular endothelial growth factor (VEGF) signaling pathway, suggesting the role of PBDEs-induced developmental toxicity via the interference with the angiogenesis process in placenta. Our findings demonstrated evidence of altered microRNA expression with PBDEs exposure, thus providing novel insights into mechanisms of PBDEs developmental toxicity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169628" }, "primaryId" : "GEO:GSE169628", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169628" } ] }, "title" : "Histone H3 dopaminylation in ventral tegmental area underlies heroin-induced maladaptive plasticity", "dateAssigned" : "2021-03-25T00:00:00.000-05:00", "summary" : "Persistent transcriptional events in ventral tegmental area (VTA) and other reward relevant brain regions contribute to enduring behavioral adaptations that characterize substance use disorder (SUD). Recent data from our laboratory indicate that aberrant accumulation of the newly discovered histone post-translational modification (PTM), H3 dopaminylation at glutamine 5 (H3Q5dop), contributes significantly to cocaine-seeking behavior following prolonged periods of abstinence. It remained unclear, however, whether this modification is important for relapse vulnerability in the context of other drugs of abuse, such as opioids. Here, we showed that H3Q5dop plays a critical role in heroin-mediated transcriptional plasticity in midbrain. In rats undergoing abstinence from heroin self-administration (SA), we found acute and persistent accumulation of H3Q5dop in VTA. By attenuating H3Q5dop during abstinence, we both altered gene expression programs associated with heroin withdrawal and reduced heroin-primed reinstatement behavior. These findings thus establish an essential role for H3Q5dop, and its downstream transcriptional consequences, in opioid-induced plasticity in VTA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35094023" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169652" }, "primaryId" : "GEO:GSE169652", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169652" } ] }, "title" : "Carbonic anhydrase inhibition improves right ventricular metabolic dysregulation and function in experimental pulmonary arterial hypertension", "dateAssigned" : "2021-03-25T00:00:00.000-05:00", "summary" : "In the Sugen 5416/hypoxia (SuHx) rat model of severe PAH, RV transcriptomic analysis was performed by RNA-seq", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34222363" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169665" }, "primaryId" : "GEO:GSE169665", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169665" } ] }, "title" : "Comparison of gene expression in the nucleus accumbens of rats expressing or not the conditioned place preference to cocaine [CPPE, nCPPE, Saline]", "dateAssigned" : "2021-03-25T00:00:00.000-05:00", "summary" : "Substance use disorder emerges in a small proportion of drug users and has the characteristics of a chronic relapsing pathology. The objective of our study was to demonstrate and characterize the variability in the expression of the reinforcing effects of cocaine in the conditioned place preference (CPP) paradigm. An unbiased cocaine-CPP paradigm in Sprague-Dawley rats with an extinction period of 12 days and reinstatement was conducted. We developed a statistical model to distinguish rats that express or do not express cocaine-induced place preference. Two groups of rats were identified: rats that did express reinforcing effects (CPP expression (CPPE), score > 102 s) and rats that did not (no CPP expression (nCPPE), score between −85 and 59 s). These two groups did not show significant differences in a battery of behavioral tests. To identify differentially expressed genes in the CPPE and nCPPE groups, we performed a whole-transcriptome RNA-sequencing analysis in the nucleus accumbens (Nac) 24 h after the CPP test. Four immediate early genes (Fos, Egr2, Nr4a1 and Zbtb37) were differentially expressed in the Nac of CPPE rats after CPP memory retrieval. Variability in cocaine-induced place preference persisted in the CPPE and nCPPE groups after the extinction and reinstatement phases. Transcriptomic differences observed after reinstatement were distinct from those observed immediately after CPP memory retrieval. These new findings provide insights into the identification of mechanisms underlying interindividual variability in the response to cocaine's reinforcing effects.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169666" }, "primaryId" : "GEO:GSE169666", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE169666" } ] }, "title" : "Comparison of gene expression in the nucleus accumbens of rats expressing or not the conditioned place preference to cocaine [CPPE, nCPPE, Saline after cocaine reinstatement]", "dateAssigned" : "2021-03-25T00:00:00.000-05:00", "summary" : "Substance use disorder emerges in a small proportion of drug users and has the characteristics of a chronic relapsing pathology. The objective of our study was to demonstrate and characterize the variability in the expression of the reinforcing effects of cocaine in the conditioned place preference (CPP) paradigm. An unbiased cocaine-CPP paradigm in Sprague-Dawley rats with an extinction period of 12 days and reinstatement was conducted. We developed a statistical model to distinguish rats that express or do not express cocaine-induced place preference. Two groups of rats were identified: rats that did express reinforcing effects (CPP expression (CPPE), score > 102 s) and rats that did not (no CPP expression (nCPPE), score between −85 and 59 s). These two groups did not show significant differences in a battery of behavioral tests. To identify differentially expressed genes in the CPPE and nCPPE groups, we performed a whole-transcriptome RNA-sequencing analysis in the nucleus accumbens (Nac) 24 h after the CPP test. Four immediate early genes (Fos, Egr2, Nr4a1 and Zbtb37) were differentially expressed in the Nac of CPPE rats after CPP memory retrieval. Variability in cocaine-induced place preference persisted in the CPPE and nCPPE groups after the extinction and reinstatement phases. Transcriptomic differences observed after reinstatement were distinct from those observed immediately after CPP memory retrieval. These new findings provide insights into the identification of mechanisms underlying interindividual variability in the response to cocaine's reinforcing effects.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE170810" }, "primaryId" : "GEO:GSE170810", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE170810" } ] }, "title" : "Single-cell RNA sequencing analysis reveals Greater Epithelial Ridge cells degeneration during postnatal development of cochlea in Rats", "dateAssigned" : "2021-03-27T00:00:00.000-05:00", "summary" : "Greater epithelial ridge cells, atransientneonatalcell group in the cochlear duct, which plays a crucial role in the functional maturation of hair cell, structural development of tectorial membrane, and refinement of audio localization before hearing. Greater epithelial ridge cells are methodologically homogeneous, while whether different cell subtypes are existence in this intriguing region and the degeneration mechanism during postnatal cochlear development are poorly understood. In the present study, single-cell RNA sequencing was performed on the cochlear duct of postnatal rats at day 1 (P1) and day 7 (P7) to identify subsets of greater epithelial ridge cell and progression. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were used to examine genes enriched biological processes in these clusters. We identified a total of 26 clusters at P1 and P7 rats and found that the cell number of five cell clusters decreased significantly, while four clusters had similar gene expression patterns and biological properties. The genes of these four cell populations were mainly enriched in Ribosome and P13K-Akt signal pathway. Among them, Rps16, Rpsa, Col4a2, Col6a2, Ctsk, and Jun are particularly interesting as their expression might contribute to the greater epithelial ridge cells degeneration. In conclusion, our study provides an important reference resource of greater epithelial ridge cells landscape and mechanism insights for further understanding greater epithelial ridge cells degeneration during postnatal rat cochlear development", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34540839" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171007" }, "primaryId" : "GEO:GSE171007", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171007" } ] }, "title" : "RNA-sequencing identifies novel transcriptomic signatures in parenteral nutrition-associated liver disease", "dateAssigned" : "2021-03-28T00:00:00.000-05:00", "summary" : "RNA-sequencing in liver from control and parenteral nutrition-associated liver disease (PNALD) rats", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171051" }, "primaryId" : "GEO:GSE171051", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171051" } ] }, "title" : "RNA-sequencing in rat hippocampus following chronic ethanol and withdrawal", "dateAssigned" : "2021-03-29T00:00:00.000-05:00", "summary" : "The objective of The Center for Alcohol Research in Epigenetics (CARE) is to identify gene regulatory pathways in hippocampus that are altered in response to chronic ethanol administration and withdrawal.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34016951" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171144" }, "primaryId" : "GEO:GSE171144", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171144" } ] }, "title" : "Study of the pathology and the underlying molecular mechanism of tissue injury around hematoma following intracerebral hemorrhage", "dateAssigned" : "2021-03-30T00:00:00.000-05:00", "summary" : "We compare the perihematoma tissues before and after intracerebral hemorrhage in rats. Gene Ontology functional annotation, Protein interaction network analysis, reverse transcription quantitative PCR technology, Western blot technology, immunofluorescence technology and Causal network analysis are used to detect the changes of RET before and after intracerebral hemorrhage and the pathways in which RET might be involved.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34368865" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171165" }, "primaryId" : "GEO:GSE171165", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171165" } ] }, "title" : "Single nuclei RNAseq of rat area nucleus accumbens after morphine exposure", "dateAssigned" : "2021-03-30T00:00:00.000-05:00", "summary" : "We performed single-nuclei RNAseq of Brown Norway rat nucleus accumbens after a single injection of morphine or after morhpine self-administration", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36075888" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171243" }, "primaryId" : "GEO:GSE171243", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171243" } ] }, "title" : "Collection of RNA-Seq data from early muscle tissue after skeletal muscle injury", "dateAssigned" : "2021-03-31T00:00:00.000-05:00", "summary" : "Following skeletal muscle injury (SMI), from post-injury reaction to repair consists of a complex series of dynamic changes.In this study, skeletal muscle tissue in rats was taken at 4h to 48h after injury for next-generation sequencing. We examined the transcriptional kinetics characteristics during above time periods after injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34220936" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171293" }, "primaryId" : "GEO:GSE171293", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171293" } ] }, "title" : "The expression profile of miRNA in the bladder tissue of partial bladder outlet obstruction rats before and after treatment of human urine-derived stem cells", "dateAssigned" : "2021-04-01T00:00:00.000-05:00", "summary" : "Obstruction in any part between the outlet of the bladder and the external urethra is called partial Bladder outlet obstruction (pBOO), which is a common disease in urology, which may cause bladder dysfunction. We have comfirmed that human urine-derived stem cells (hUSCs) could improve the bladder function of pBOO rats in our previous study. We thus explored the role of miRNAs in pBOO rats before and after treatment of hUSCs, and revealed that they could serve as effective prevention and treatment therapeutic targets. Rat bladder tissues were used for miRNA sequencing. We identified 8 differentially expressed miRNAs in the pBOO rats before and after treatment of hUSCs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171366" }, "primaryId" : "GEO:GSE171366", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171366" } ] }, "title" : "The expression profile of circRNA, lncRNA and mRNA in the bladder tissue of partial bladder outlet obstruction rats before and after treatment of human urine-derived stem cells", "dateAssigned" : "2021-04-02T00:00:00.000-05:00", "summary" : "Obstruction in any part between the outlet of the bladder and the external urethra is called partial Bladder outlet obstruction (pBOO), which is a common disease in urology, which may cause bladder dysfunction. We have comfirmed that human urine-derived stem cells (hUSCs) could improve the bladder function of pBOO rats in our previous study. We thus explored the role of miRNAs in pBOO rats before and after treatment of hUSCs, and revealed that they could serve as effective prevention and treatment therapeutic targets. Rat bladder tissues were used for circRNA, lncRNA and mRNA sequencing.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171399" }, "primaryId" : "GEO:GSE171399", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171399" } ] }, "title" : "Acute alcohol produces epigenomic changes in the amygdala", "dateAssigned" : "2021-04-02T00:00:00.000-05:00", "summary" : "ATAC-sequencing of adult rat amygdala tissue following acute ethanol treatment, compared to saline-treated controls.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36089615" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171400" }, "primaryId" : "GEO:GSE171400", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171400" } ] }, "title" : "Acute alcohol produces transcriptomic changes in the amygdala", "dateAssigned" : "2021-04-02T00:00:00.000-05:00", "summary" : "RNA-sequencing of adult rat amygdala tissue following acute ethanol treatment, compared to saline-treated controls.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36089615" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171438" }, "primaryId" : "GEO:GSE171438", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171438" } ] }, "title" : "Dysregulation of miRNA regulatory networks by chronic ethanol consumption impairs liver regeneration", "dateAssigned" : "2021-04-03T00:00:00.000-05:00", "summary" : "In this study, we elucidated the role of miRNA dysregulation in liver regeneration after partial hepatectomy (PHx) in chronic ethanol-treated rats. Male Sprague-Dawley rats were fed a liquid diet containing 36% of total calories derived from ethanol for 5 weeks; corresponding pair-fed calorie-matched controls were fed diets in which ethanol calories were replaced by carbohydrate. After 5 weeks, locked nucleic acid (LNA)-modified oligo antisense to miR-21 (AM21, Exiqon) was used to inhibit miRNA in vivo, and rats were subjected to 70% PHx. Liver samples were collected at 6 h, 24 h and 72 h after the surgery. The excised liver samples at t=0 served as within-animal controls.NanoString rat miRNA panel was used to obtain miRNA expression profile from 48 liver samples.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34796728" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171647" }, "primaryId" : "GEO:GSE171647", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171647" } ] }, "title" : "Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regualtion", "dateAssigned" : "2021-04-07T00:00:00.000-05:00", "summary" : "Ultradian glucocorticoid rhythms are highly conserved across mammalian species, however, their functional significance is not yet fully understood. Here we demonstrate that pulsatile corticosterone replacement in adrenalectomised rats induces a dynamic pattern of glucocorticoid receptor (GR) binding at ~3,000 genomic sites in liver at the pulse peak, subsequently not found during the pulse nadir. In contrast, constant corticosterone replacement induced prolonged binding at the majority of these sites. Additionally, each pattern further induced markedly different transcriptional responses. During pulsatile treatment, intragenic occupancy by active RNA polymerase II exhibited pulsatile dynamics with transient changes in enrichment, either decreased or increased depending on the gene, which mostly returned to baseline during the inter-pulse interval. In contrast, constant corticosterone exposure induced prolonged effects on RNA polymerase II occupancy at the majority of gene targets, thus acting as a sustained regulatory signal for both transactivation and repression of glucocorticoid target genes. The nett effect of these differences were consequently seen in the liver transcriptome as RNA-seq analysis indicated that despite the same overall amount of corticosterone infused, twice the number of transcripts were regulated by constant corticosterone infusion, when compared to pulsatile. Target genes that were found to be differentially regulated in a pattern-dependent manner were enriched in functional pathways including carbohydrate, cholesterol, glucose and fat metabolism as well as inflammation, suggesting a functional role for dysregulated glucocorticoid rhythms in the development of metabolic dysfunction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34375333" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171753" }, "primaryId" : "GEO:GSE171753", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171753" } ] }, "title" : "Intersection of Regulatory Pathways Controlling Hemostasis and Hemochorial Placentation [rat I]", "dateAssigned" : "2021-04-08T00:00:00.000-05:00", "summary" : "Tissue factor pathway inhibitor (TFPI) is a prominent regulator of blood coagulation and an intriguing constituent of trophoblast cells situated at the maternal-fetal interface. The actions of TFPI extend beyond controlling hemostasis and directly affect trophoblast cell development. TFPI facilitates the differentiation of rat and human trophoblast stem cells into the invasive trophoblast/extravillous cell lineage and promotes intrauterine trophoblast invasion and trophoblast-guided uterine spiral artery remodeling at the maternal-fetal interface. Thus, TFPI is a conserved regulator of a fundamental event determining the efficacy of the hemochorial placenta.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171754" }, "primaryId" : "GEO:GSE171754", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171754" } ] }, "title" : "Intersection of Regulatory Pathways Controlling Hemostasis and Hemochorial Placentation [rat II]", "dateAssigned" : "2021-04-08T00:00:00.000-05:00", "summary" : "Tissue factor pathway inhibitor (TFPI) is a prominent regulator of blood coagulation and an intriguing constituent of trophoblast cells situated at the maternal-fetal interface. The actions of TFPI extend beyond controlling hemostasis and directly affect trophoblast cell development. TFPI facilitates the differentiation of rat and human trophoblast stem cells into the invasive trophoblast/extravillous cell lineage and promotes intrauterine trophoblast invasion and trophoblast-guided uterine spiral artery remodeling at the maternal-fetal interface. Thus, TFPI is a conserved regulator of a fundamental event determining the efficacy of the hemochorial placenta.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171814" }, "primaryId" : "GEO:GSE171814", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171814" } ] }, "title" : "Analysis of gastrocnemius muscle transcriptome from chow-fed WT-control and UCP1 knockout female rats at room temerature and after exposure to 4 degrees Celsius", "dateAssigned" : "2021-04-09T00:00:00.000-05:00", "summary" : "To determine the effects of cold exposure on skeletal muscle gene expression in rats with and without UCP1, we assessed gastrocnemius muscle in chow-fed control and whole body UCP1 knockout rats using RNA-seq.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171866" }, "primaryId" : "GEO:GSE171866", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171866" } ] }, "title" : "Integrated analysis of the transcriptome wide m6A methylome in Peripheral nerve injury", "dateAssigned" : "2021-04-11T00:00:00.000-05:00", "summary" : "N6-methyladenosine(m6A) is the most plentiful internal RNA modification, especially in eukaryotic messenger RNA (mRNA), which plays pivotal roles in mRNA life cycle and nerve development processes. In this study, samples were collected from Sciatic Nerve Injury (SNI) after 7 days and control rats. Altered peaks of m6A-modified transcripts were mainly related to immune system process, cell activation and nervous system development. KEGG pathway analyses highlighted the Axon guidance pathway, Calcium signaling pathway and B cell receptor signaling pathway. These data further enrich the contents of epigenetics in Peripheral Nerve Injury and provide a new opinion to promote the function recovery", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34306026" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171923" }, "primaryId" : "GEO:GSE171923", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE171923" } ] }, "title" : "Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle", "dateAssigned" : "2021-04-12T00:00:00.000-05:00", "summary" : "Chromatin accessibility is a key factor influencing gene expression. We developed a modified protocol, ruptor-ATAC, which together with RNA-seq was used to investigate regulatory elements underlying tissue-specific gene expression in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. While promoter accessibility correlated with RNA expression, integration of the two datasets identified tissue-specific differentially accessible regions (DARs) that predominantly localized in intergenic and intron regions. DARs mapped to differentially expressed genes that were enriched in distinct biological processes in each tissue. Motif enrichment analysis on tissue-specific DARs predicted binding sites for transcription factors (TFs), several of which were up-regulated in the corresponding tissue. Positive relationship between DARs and target gene expression further supported a functional role for these TF binding motifs. Our study identifies cis-regulatory regions that likely play a major role in the regulation of tissue-specific gene expression in adipose and muscle.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34547403" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172109" }, "primaryId" : "GEO:GSE172109", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172109" } ] }, "title" : "Experience modulates the effects of histone deacetylase inhibitors on gene and protein expression in the hippocampus: Impaired plasticity in aging", "dateAssigned" : "2021-04-14T00:00:00.000-05:00", "summary" : "The therapeutic potential of histone deacetylase inhibitor (HDACi) treatment has attracted considerable attention in the emerging area of cognitive neuroepigenetics. The possibility that ongoing cognitive experience importantly regulates the cell biological effects of HDACi administration, however, has not been systematically examined. In an initial experiment addressing this issue, we tested whether water maze training influences the gene expression response to acute systemic HDACi administration in the young adult rat hippocampus. Training powerfully modulated the response to HDACi treatment, increasing the total number of genes regulated to nearly 3000, including many not typically linked to neural plasticity, compared with <300 following HDACi administration alone. Although water maze training itself also regulated nearly 1800 genes, the specific mRNAs, gene networks, and biological pathways involved were largely distinct when the same experience was provided together with HDACi administration. Next, we tested whether the synaptic protein response to HDACi treatment is similarly dependent on recent cognitive experience, and whether this plasticity is altered in aged rats with memory impairment. Whereas synaptic protein labeling in the young hippocampus was selectively increased when HDACi administration was provided in conjunction with water maze training, combined treatment had no effect on synaptic proteins in the aged hippocampus. Our findings indicate that ongoing experience potently regulates the molecular consequences of HDACi treatment and that the interaction of recent cognitive experience with histone acetylation dynamics is disrupted in the aged hippocampus.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:26290249" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172133" }, "primaryId" : "GEO:GSE172133", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172133" } ] }, "title" : "A Transcriptomic Analysis of Neuropathic Pain in the Anterior Cingulate Cortex after Nerve Injury", "dateAssigned" : "2021-04-15T00:00:00.000-05:00", "summary" : "Neuropathic pain is a troublesome pathological condition without suitable treatments. In this study, we performed RNA sequencing (RNA-seq) analysis to reveal transcriptomic profiles of Anterior Cingulate Cortex (ACC) from chronic constriction injury (CCI) rats. We found 1628 differentially expressed genes (DEGs) were mainly involved in the inflammatory and immune process. Besides, cytokine signaling and other cell-defense related pathways mainly contribute to the occurrence and development of neuropathic pain. Then we classified the DEGs based on the time trend. Our results suggested that chemokines played a vital role in pain, and moreover, CCL5, CXCL9 and CXCL13, compared with CCL2, CCL3, CCL4, CCL6 and CCL7 had different time-dependent manners. In a word, targeting chemokines is of great significance to explore specific mechanisms and develop suitable drugs for neuropathic pain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35030976" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172259" }, "primaryId" : "GEO:GSE172259", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172259" } ] }, "title" : "Identification of miRNAs that regulate tinnitus development", "dateAssigned" : "2021-04-16T00:00:00.000-05:00", "summary" : "To investigate which miRNAs regulate the development of tinnitus, we have performed microarray for miRNAs as a discovery platform. The changes in dorsal cochlear nucleus after noise exposure have been suggested to play an important role in the development of tinnitus. This study was performed using 12 week-old-male Sprague-Dawley rats. Based on our previous experiment about the development of tinnitus, we set a time point for harvesting dorsal cochlear nuclei: 3 weeks after the exposure of 6-8 kHz narrow-band noise (110 dB SPL for 2 h) at right side. Eight animals were divided into two experimental groups: tinnitus group showing evidence of tinnitus (n = 5); and non-tinnitus group showing no evidence of tinnitus (n = 3) in the gap pre-pulse inhibition of acoustic startle reflex (GPIAS) recordings. Three animals of each group were anesthetized deeply and euthanized at 3 weeks post noise exposure. Dorsal cochlear nucleus at right side was harvested. Microarray for miRNAs was performed using the Affymetrix miRNA 4.0 microarray. Considering the fold change of normalized signal intensities between tinnitus and non-tinnitus groups, miR-375-3p was selected as the candidate miRNA. This result was validated by quantitative reverse transcription-PCR.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34036397" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172269" }, "primaryId" : "GEO:GSE172269", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172269" } ] }, "title" : "Landscape of rat microRNA BodyMap across 11 organs, four ages, and two sexes", "dateAssigned" : "2021-04-17T00:00:00.000-05:00", "summary" : "The rat has been used extensively as a model system for biological studies. However, its microRNA (miRNA) transcriptome has not been well established. Here, we constructed a comprehensive rat miRNA BodyMap based on miRNA-seq of 320 samples from 11 organs of both sexes of juvenile, adolescent, adult, and aged Fischer 344 rats. We quantified the expression profiles of 993 rat miRNAs, including 268 novel miRNA candidates. A large number of miRNAs showed organ-specific, age-dependent, or sex-specific expression patterns. Particularly, brain exhibited the strongest organ-enriched expression patterns, and testis showed the most strikingly age-dependent expression patterns. Interestingly, the expression levels of two clusters of miRNAs were highly correlated with those of mRNAs and were highly age dependent. The miRNA dataset along with previously reported mRNA data from the same set of samples represents a unique resource to improve understanding of rat transcriptome and subsequently better utilize rats for biomarker discovery.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35551205" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172290" }, "primaryId" : "GEO:GSE172290", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172290" } ] }, "title" : "miRNA Alterations in Lung Macrophages after Nitrogen Mustard Exposure", "dateAssigned" : "2021-04-18T00:00:00.000-05:00", "summary" : "Activated macrophages have been implicated in lung injury and fibrosis induced by the cytotoxic alkylating agent, nitrogen mustard (NM). Herein, we determined if macrophage activation is associated with altered miRNA expression. Treatment of rats with NM (0.125 mg/kg, i.t.) resulted in significant increases in miRNA expression 1, 3, 7, and 28 d post exposure as determined by PCR array analysis of miRNAs (miR)s involved in inflammation and fibrosis. Expression of many miRNAs were significantly increased at multiple time-points while one miRNA was uniquely expressed 1 d post-NM, one at 3 d, two at 7 d, and five at 28 d. An IPA Core Analysis of predicted mRNA targets of differentially expressed miRNAs identified significant enrichment of Diseases and Functions related to cell cycle arrest, apoptosis, cell movement, cell adhesion, and inflammation 1 d and 28 d post NM. Significant enrichment of pathways related to lipid metabolism is consistent with previous studies reporting the development of macrophage foam cells after NM exposure. miRNA-mRNA interaction network analysis identified highly connected miRNAs representing key upstream regulators of mRNAs involved in significantly enriched Diseases and Functions including miR-34c-5p and miR-27a-3p at 1 d post NM and miR-125b-5p, miR-16-5p, miR-30c-5p, miR-19b-3p, and miR-148b-3p at 28 d post NM. Collectively, these data show that NM promotes histone remodeling and alterations in miRNA expression linked to lung macrophage responses during inflammatory injury and fibrosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:33971176" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172385" }, "primaryId" : "GEO:GSE172385", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172385" } ] }, "title" : "Project_Summary_Rat_primary_cortical_neurons_asyn_3K_RNA_Seq", "dateAssigned" : "2021-04-20T00:00:00.000-05:00", "summary" : "Identify early and late stage expression/pathway changes induced during aSyn 3K mediated cellular toxicity (AAV9 with human a-syn 3K model)", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34301719" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172462" }, "primaryId" : "GEO:GSE172462", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172462" } ] }, "title" : "Single nucleus RNA-seq atlas of rat mediobasal hypothalamus", "dateAssigned" : "2021-04-20T00:00:00.000-05:00", "summary" : "To uncover the cellular identifies of the rat mediobasal hypothalamic cells, we used single nucleus RNA-seq (snRNA-seq).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172497" }, "primaryId" : "GEO:GSE172497", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE172497" } ] }, "title" : "Quantitative analysis of transscriptomes from rat OPCs treated with DMSO or ZJU-37", "dateAssigned" : "2021-04-21T00:00:00.000-05:00", "summary" : "Our previous data showed ZJU-37 promotes OPCs proliferation both in vitro and in vivo, the results of RNA-Seq indicated that up-regulation of cell cycle related genes may be related to it.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35365618" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173085" }, "primaryId" : "GEO:GSE173085", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173085" } ] }, "title" : "Identification of significantly differential expression of long noncoding RNAs and pathways in hepatic fibrosis rat liver issues", "dateAssigned" : "2021-04-22T00:00:00.000-05:00", "summary" : "Objective: To identify the long noncoding (lncRNA) and its potential roles in hepatic fibrosis rat liver issues induced by CCl4. Methods: LncRNAs and genes were analyzed in fibrosis rat liver issues by RNA sequencing and verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Differential expressed lncRNAs and genes were subjected to bioinformatics analysis and involved to construct co-expression network.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34597331" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173136" }, "primaryId" : "GEO:GSE173136", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173136" } ] }, "title" : "Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Nucleus accumbens core]", "dateAssigned" : "2021-04-22T00:00:00.000-05:00", "summary" : "Research into the genetic influences of impulsivity and reward motivated behavior relies heavily on outbred animal populations, including Heterogeneous Stock (HS) rats, for the genetic diversity necessary to identify genotype-trait associations. Many such associations have been detected, but it is not always clear which gene or other feature near the identified genomic location is functionally responsible for the association. Since these traits are in part mediated by gene expression, mapping the associations between genotype and gene expression in these animals will enable the discovery and deeper understanding of these trait associations. We therefore obtained genotypes and RNA-Seq gene expression for five brain regions from 88 HS rats and mapped expression quantitative trait loci (eQTLs) for each region. We identified cis-eQTLs in over 3,000 genes per brain region and validated their effect sizes using allele specific expression. This resource will enable new discoveries of the genetic influences of complex behavioral traits.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36263809" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173137" }, "primaryId" : "GEO:GSE173137", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173137" } ] }, "title" : "Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Infralimbic cortex]", "dateAssigned" : "2021-04-22T00:00:00.000-05:00", "summary" : "Research into the genetic influences of impulsivity and reward motivated behavior relies heavily on outbred animal populations, including Heterogeneous Stock (HS) rats, for the genetic diversity necessary to identify genotype-trait associations. Many such associations have been detected, but it is not always clear which gene or other feature near the identified genomic location is functionally responsible for the association. Since these traits are in part mediated by gene expression, mapping the associations between genotype and gene expression in these animals will enable the discovery and deeper understanding of these trait associations. We therefore obtained genotypes and RNA-Seq gene expression for five brain regions from 88 HS rats and mapped expression quantitative trait loci (eQTLs) for each region. We identified cis-eQTLs in over 3,000 genes per brain region and validated their effect sizes using allele specific expression. This resource will enable new discoveries of the genetic influences of complex behavioral traits.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36263809" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173138" }, "primaryId" : "GEO:GSE173138", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173138" } ] }, "title" : "Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Lateral habenula]", "dateAssigned" : "2021-04-22T00:00:00.000-05:00", "summary" : "Research into the genetic influences of impulsivity and reward motivated behavior relies heavily on outbred animal populations, including Heterogeneous Stock (HS) rats, for the genetic diversity necessary to identify genotype-trait associations. Many such associations have been detected, but it is not always clear which gene or other feature near the identified genomic location is functionally responsible for the association. Since these traits are in part mediated by gene expression, mapping the associations between genotype and gene expression in these animals will enable the discovery and deeper understanding of these trait associations. We therefore obtained genotypes and RNA-Seq gene expression for five brain regions from 88 HS rats and mapped expression quantitative trait loci (eQTLs) for each region. We identified cis-eQTLs in over 3,000 genes per brain region and validated their effect sizes using allele specific expression. This resource will enable new discoveries of the genetic influences of complex behavioral traits.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36263809" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173139" }, "primaryId" : "GEO:GSE173139", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173139" } ] }, "title" : "Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Prelimbic cortex]", "dateAssigned" : "2021-04-22T00:00:00.000-05:00", "summary" : "Research into the genetic influences of impulsivity and reward motivated behavior relies heavily on outbred animal populations, including Heterogeneous Stock (HS) rats, for the genetic diversity necessary to identify genotype-trait associations. Many such associations have been detected, but it is not always clear which gene or other feature near the identified genomic location is functionally responsible for the association. Since these traits are in part mediated by gene expression, mapping the associations between genotype and gene expression in these animals will enable the discovery and deeper understanding of these trait associations. We therefore obtained genotypes and RNA-Seq gene expression for five brain regions from 88 HS rats and mapped expression quantitative trait loci (eQTLs) for each region. We identified cis-eQTLs in over 3,000 genes per brain region and validated their effect sizes using allele specific expression. This resource will enable new discoveries of the genetic influences of complex behavioral traits.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36263809" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173140" }, "primaryId" : "GEO:GSE173140", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173140" } ] }, "title" : "Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Orbitofrontal cortex]", "dateAssigned" : "2021-04-22T00:00:00.000-05:00", "summary" : "Research into the genetic influences of impulsivity and reward motivated behavior relies heavily on outbred animal populations, including Heterogeneous Stock (HS) rats, for the genetic diversity necessary to identify genotype-trait associations. Many such associations have been detected, but it is not always clear which gene or other feature near the identified genomic location is functionally responsible for the association. Since these traits are in part mediated by gene expression, mapping the associations between genotype and gene expression in these animals will enable the discovery and deeper understanding of these trait associations. We therefore obtained genotypes and RNA-Seq gene expression for five brain regions from 88 HS rats and mapped expression quantitative trait loci (eQTLs) for each region. We identified cis-eQTLs in over 3,000 genes per brain region and validated their effect sizes using allele specific expression. This resource will enable new discoveries of the genetic influences of complex behavioral traits.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36263809" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173142" }, "primaryId" : "GEO:GSE173142", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173142" } ] }, "title" : "eNampt, CRH and Il-6 influence on gene expression of rat primary corticotropes.", "dateAssigned" : "2021-04-22T00:00:00.000-05:00", "summary" : "We used microarrays to detail the global programme of gene expression in isolated rat pituitary corticotropes, 24h after administration of eNampt, CRH and Il-6.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173228" }, "primaryId" : "GEO:GSE173228", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173228" } ] }, "title" : "Microvessels support engraftment and functionality of human islets and hESC-derived pancreatic progenitors in diabetes models", "dateAssigned" : "2021-04-23T00:00:00.000-05:00", "summary" : "Single nuclei sequencing of grafts developed 14 weeks post transplantation of human embryonic stem cell derived pancreatic progenitors alone (PP) or with rat adipose derived microvessels (PPMV) into the subcutaneous pocket of diabetic (STZ-induced) Scid-beige mice.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34480863" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173360" }, "primaryId" : "GEO:GSE173360", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173360" } ] }, "title" : "Aging-Induced Alterations in Gene Transcripts and Functional Activity of Mitochondrial Oxidative Phosphorylation Complexes in the Heart", "dateAssigned" : "2021-04-26T00:00:00.000-05:00", "summary" : "High-throughput transcription profiles of genes coding for mitochondrial proteins in ventricles from adult and aged rats were compared using microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:18400259" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173380" }, "primaryId" : "GEO:GSE173380", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173380" } ] }, "title" : "Illumina NGS RNA-seq and RRBS Sequencing on Rat Kidney", "dateAssigned" : "2021-04-26T00:00:00.000-05:00", "summary" : "We reported the kidney transcriptome and methylome profiles of rat Brown Norway (BN) and Sprague Dawley (CD) strains at late pregnancy (day 18/21) compared to non-pregnancy. The renal transcriptome was characterized from 326 million single-end 100bp RNA-seq data. The methylome dataset included 234 million 75-bp RRBS DNA methylation reads. We identified 297 differentially expressed genes (DEGs) induced by pregnancy in CD rats and 174 DEGs induced in BN rats, based on the RNA-seq dataset. 237 of the 297 DEGs in CD pregnant rats and 114 of the 174 DEGs in BN pregnant rats are strain specific, indicating differential adaptation to pregnancy. Methylome data reveals that strain differences is the major factor in determining methylation differences. We also found that pregant BN showed higher methylation than non-pregnant BN at transcription starter site (TSS) and promoter regions. Functional analysis based on DEGs and DMGs revealed that pregnant BN rats showed renal transcriptomic changes that induce vitamin D deficiency and renal pro-inflammatory gene expression that can partly explain pregnancy-specific proteinuria. Integrated analysis based on transcriptome and methylome suggested that modifications on DNA methylation were correlated with transcriptome changes for several significant biological processes and/or pathways.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35709218" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173464" }, "primaryId" : "GEO:GSE173464", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173464" } ] }, "title" : "Ribosome profiling and RNA-seq of Rat whole brain", "dateAssigned" : "2021-04-28T00:00:00.000-05:00", "summary" : "Local translation in neurons is mediated in part by the reactivation of stalled polysomes. However, the mechanism for stalling of the polysomes is not understood. Stalled polysomes may be enriched in neuronal RNA granules defined by dense collections of compacted ribosomes found in the pellet of sucrose gradients used to separate polysomes from monosomes. We find that this fraction, isolated from P5 rat brains of both sexes, is enriched in proteins implicated in stalled polysome function, such as the fragile X mental retardation protein (FMRP) and Up-frameshift mutation 1 homolog (UPF1). Ribosome profiling of this fraction showed an abundance of footprint reads derived from mRNAs of cytoskeletal proteins implicated in neuronal development, as well as an enrichment of footprint reads on RNA binding proteins. The footprint reads were extended than those usually found in ribosome profiling studies on the 3’end and were found in reproducible peaks in the mRNAs with a bias towards the first half of the message. These footprint reads were enriched in motifs previously associated with mRNAs cross-linked to FMRP in vivo, independently linking the ribosomes in the sedimented pellet to the ribosomes associated with FMRP in the cell. The data supports a model in which specific sequences in mRNAs act to stall translation elongation in neurons, attracting FMRP and beginning a process where stalled ribosomes are packaged and transported in RNA granules.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36849416" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173481" }, "primaryId" : "GEO:GSE173481", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173481" } ] }, "title" : "Integrated transcriptomic and proteomic analysis reveals up regulation of apoptosis and small heat shock proteins in lens of rats under low temperature", "dateAssigned" : "2021-04-28T00:00:00.000-05:00", "summary" : "Cold cataract is the reversible opacification of the lens when the temperature decreases. However, we observed that when temperature of the rats lens was maintained at a lower temperature for a prolonged time, the opacification of lens was only partly reversible. To review the potential molecular mechanism of the irreversible part of opacification under cold stimulation, we applied comparative transcriptomic and proteomic analysis to systematically investigate the molecular changes that occurred in the lens capsules of rats under low temperature treatments. The RNA sequencing based transcriptomic analysis showed a significant up-regulation of genes related to the lens structure and development in the Hypothermia Group. Hub genes were small heat shock proteins (sHSPs). Besides the same findings as the transcriptomic results, the liquid chromatography-tandem mass spectrometry based proteomic analysis also revealed the up-regulation of the apoptotic process. To further analyze the regulatory mechanism in this process, we subsequently performed integrated analysis and identified the down-regulation of Notch3/Hes1 and PI3K/Akt/Xiap signaling axis. Our research revealed the activation of the apoptotic process in rats lens under cold stimulation, and the sHSP related heat shock response as a potential protective factor through our transcriptomic and proteomic data.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34220548" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173596" }, "primaryId" : "GEO:GSE173596", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173596" } ] }, "title" : "Pumilio2 and Staufen2 selectively balance the synaptic proteome", "dateAssigned" : "2021-04-29T00:00:00.000-05:00", "summary" : "Cells, in particular neurons, have the capacity to adapt to environmental stimuli, a phenomenon termed cellular plasticity. The underlying processes are controlled by a network of RNA-binding proteins (RBPs). Their impact on cellular plasticity, however, is largely unknown. To address this important question, we chose Pumilio2 (Pum2) and Staufen2 (Stau2) that both regulate synaptic transmission. Surprisingly, even though both RBPs dynamically interact with each other in neurons, their respective impact on the transcriptome and proteome is highly selective. While Pum2 deficiency leads to reduced translation and protein expression, Stau2 depletion preferentially impacts RNA levels and increases protein abundance. Furthermore, we show that Pum2 activates expression of key GABAergic synaptic components, e.g. the GABAA receptor scaffold protein Gephyrin. Consequently, Pum2 depletion selectively reduced the amplitude of miniature inhibitory postsynaptic currents. Together, our data clearly demonstrate that RBPs are needed to maintain proteostasis in order to control distinct signaling pathways which critically balance synaptic transmission.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34161769" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173622" }, "primaryId" : "GEO:GSE173622", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173622" } ] }, "title" : "Transcriptome analysis of periodontal tissue response after immediate replantation and delayed replantation", "dateAssigned" : "2021-04-30T00:00:00.000-05:00", "summary" : "Conclusions: Transcriptome profiles were significantly different between immediate replantation and delayed replantation. The responses of periodontal tissues were associated with TNF–α signaling via NF–κB pathway. However, the enrichment score of this pathway were changed with time–dependent manner between immediate replantation and delayed replantation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173637" }, "primaryId" : "GEO:GSE173637", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173637" } ] }, "title" : "Periostin induces early articular cartilage degeneration in developmental dysplasia of the hip", "dateAssigned" : "2021-04-30T00:00:00.000-05:00", "summary" : "Developmental dysplasia of the hip (DDH) is one of the significant risk factors for hip osteoarthritis. In order to investigate the factors that induce early articular cartilage degeneration of the hip joints that are exposed to reduced dynamic loads arising from hip dislocation , we created rodent models of hip dislocation by swaddling. Notably, expression of periostin (Postn) was increased in the acetabular articular cartilage of the DDH models; Postn was a candidate gene associated with early articular cartilage degeneration. We showed that early articular cartilage degeneration was suppressed in Postn-/- DDH mice. Furthermore, a microgravity environment induced the expression of Postn in chondrocytes through STAT3 signaling. Postn induced catabolic factors, interleukin-6 and matrix metalloproteinase 3, in articular chondrocytes through integrin-nuclear factor κB signaling. Additionally, interleukin-6 stimulated Postn expression through STAT3 signaling. Thus, Postn plays a critical role in early articular cartilage degeneration associated with hip dislocation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35842459" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173659" }, "primaryId" : "GEO:GSE173659", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173659" } ] }, "title" : "Highly conserved sperm function-related transcripts across three species: human, rat and mouse.", "dateAssigned" : "2021-04-30T00:00:00.000-05:00", "summary" : "mRNA sequences were analyzed in mouse, rat and human sperm samples to identify sperm transcriptomic similarities across species that could be used as biomarkers to predict male reproductive toxicity in animal models.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173723" }, "primaryId" : "GEO:GSE173723", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173723" } ] }, "title" : "Impaired GR expression in liver disrupts feeding induced gene expression, glucose uptake and glycogen storage", "dateAssigned" : "2021-05-03T00:00:00.000-05:00", "summary" : "The transition from a fasted to a fed state is associated with extensive transcriptional remodeling in hepatocytes facilitated by hormonal- and nutritional-regulated transcription factors. Here, we use a liver-specific glucocorticoid receptor (GR) knock-out (L-GRKO) model and primary hepatocytes to investigate the temporal expression of GR target genes in response to feeding. Interestingly, in addition to the well described fasting-regulated genes, we identify a subset of hepatic feeding-induced genes that requires GR for full expression, adding new insights to hepatic GR function. The GR-controlled feeding-induced genes include Gck encoding the glucokinase, which is important for hepatic glucose uptake, utilization and storage. We show that insulin and glucocorticoids cooperatively regulate Gck expression in primary hepatocytes in a GR-dependent manner. ChIP-seq experiments suggest direct GR regulation of Gck by GR occupancy of the promoter and two putative regulatory regions near the Gck gene (Gck -1kb and Gck -4.6kb). Enhancer-reporter assays and CRISPRi suggest that the 4.6kb upstream GR binding site is a functional Gck enhancer. L-GRKO blunts preprandial and early postprandial Gck expression and GR disruption ultimately affects early postprandial hepatic glucose uptake, phosphorylation and glycogen storage. Collectively, our study demonstrates how GR is positively involved in the hepatic feeding response exemplified in the direct regulation of the feeding-induced transcription of glucokinase, important for hepatic glucose metabolism.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34731602" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173737" }, "primaryId" : "GEO:GSE173737", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173737" } ] }, "title" : "Targeting Cytoplasmic SAM by Expressing Slc25a26 Inhibits Protein Synthesis in Cardiac Hypertrophy via SAMTOR/mTOR signaling", "dateAssigned" : "2021-05-03T00:00:00.000-05:00", "summary" : "Excess protein synthesis is the major pathological manifestation of cardiac hypertrophy; however, the underlying mechanism remains elusive. Here we found that a SAM transporter Slc25a26 translocated to mitochondria during cardiac hypertrophy. Silencing Slc25a26 aggravated phenylephrine-induced cardiomyocyte hypertrophy in neonatal rat ventricular myocytes. Transcriptome analysis revealed a specific regulation of ribosome genes by Slc25a26. Puromycin incorporation assay showed a negative regulation of protein synthesis rate by Slc25a26. The translational regulation was independent of ribosome assembly, but abolished by mTOR inhibitor rapamycin. Administration of SAM, or silencing Samtor, reversed the inhibitory impact of Slc25a26 on protein synthesis. AAV9-mediated Slc25a26 overexpression in mouse heart increased the SAM level in mitochondria, but reduced that in nucleus and cytoplasm. Transaortic-constriction-induced hypertrophic pathologies, including pathological gene induction, cardiomyocyte enlargement, myocardial remodeling and heart dysfunction were significantly alleviated by Slc25a26 overexpression. Our data demonstrate a crucial role of subcellular SAM homeostasis in translational control during cardiac hypertrophy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34977198" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173806" }, "primaryId" : "GEO:GSE173806", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173806" } ] }, "title" : "Cellular and extracellular tRNA-derived fragments demonstrate distinct signatures in cellular stress", "dateAssigned" : "2021-05-04T00:00:00.000-05:00", "summary" : "The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints of distinct stress responses may yield novel biomarkers for different diseases, and potentially identify key signaling pathways important for disease progression . tRNA and tRNA-derived small RNAs (tDRs) comprise one of the most abundant RNA species in cells and have been associated with cellular stress responses. However, systematic characterization of tDRs have been challenged by the technical difficulties in accurately profiling tDRs with normal small RNA sequencing techniques due to the presence of RNA modifications. Here we use AlkB-facilitated methylation sequencing (ARM-seq) to uncover a comprehensive landscape of cellular and extracellular tDRs expression in a variety of human and rat cells during common stress responses, including nutrition deprivation, hypoxia, and oxidative stress. We found that extracellular tDRs have a distinct fragmentation signature with a predominant length of 31-33 nts and a highly specific termination position when compared with intracellular tDRs, and comprise signatures that improve discrimination of different cellular stress responses compared to extracellular miRNAs. Distinct extracellular tDR signatures for each profiled stressor are elucidated in 4 different types of cells. This distinct extracellular tDR fragmentation pattern is also noted in plasma extracellular RNA from patients on cardiopulmonary bypass with significant overlap with the signatures of nutrition depravation and oxidative stress in our cellular models, providing preliminary in vivo correlation of our findings. Future application of our findings to human disease models may have promise in yielding novel biomarkers.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35373532" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173885" }, "primaryId" : "GEO:GSE173885", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173885" } ] }, "title" : "Transcriptome of the audiogenic rat strain and identification of possible audiogenic epilepsy-associated genes", "dateAssigned" : "2021-05-04T00:00:00.000-05:00", "summary" : "Audiogenic epilepsy (AE), developing in rodent strains in response to loud sound, is widely used as the model of generalized convulsive epilepsy. The molecular and genetic mechanisms that determine the expression of AE are currently non well understood. In the present work we compared transcriptomes from the inferior and superior colliculi (corpora quadrigemina), the crucial epileptogenic midbrain zone for AE in order to identify genes associated to the AE phenotype. Transcriptomes of rats from three strains were compared: Krushinsky-Molodkina (KM) strain (100% AE-prone); Wistar outbred rats (with no AE proneness) and \"0\" strain, selected from F2 KMxWistar hybrids for the lack of AE. It is shown that KM strain gene expression profile have a number of characteristic differences from those of Wistar and \"0\" strains. In particular, KM has increased expression of a number of genes involved in positive regulation of the MAPK signaling cascade, as well as genes, responsible for positive regulation of apoptotic processes. The next characteristic difference between the KM strain from Wistar and \"0\" is a multiple increase in the expression level of the Ttr gene, which is known to be associated with family amyloid polyneuropathy in humans. Further, the KM strain showed a significant decrease in the expression of the Msh3 gene involved in the DNA mismatch repair system, Acsm5, coding a mitochondrial acyl-CoA synthetase specific for medium chain family member 5, and in a number of genes of the oxidative phosphorylation system, and a number of some other genes. Our data confirm the complex multigenic nature of AE inheritance in rodents. A comparison with the data obtained from other AE rodent strains suggests that the convulsive phenotype could develop differently in audiogenic rat strains selected independently. Although, the finding of parallel differences in certain genes expression in AE-prone hamsters (another rodent species) indicate the common (and crucial) neurogenetic defects, leading to AE phenotype in rodents in general.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34803604" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173898" }, "primaryId" : "GEO:GSE173898", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173898" } ] }, "title" : "Perinatal exposure to nicotine alters spermatozoal DNA methylation near genes controlling nicotine action", "dateAssigned" : "2021-05-05T00:00:00.000-05:00", "summary" : "Perinatal smoke/nicotine exposure alters lung development and causes asthma in exposed offspring, transmitted transgenerationally. The mechanism underlying the transgenerational inheritance of perinatal smoke/nicotine-induced asthma remains unknown, but germline epigenetic modulations may play a role. Using a well-established rat model of perinatal nicotine-induced asthma, we determined the DNA methylation pattern of spermatozoa of F1 rats exposed perinatally to nicotine in F0 gestation. To identify differentially methylated regions (DMRs), reduced representation bisulfite sequencing was performed on spermatozoa of F1 litters. The top regulated gene body and promoter DMRs were tested for lung gene expression levels, and key proteins involved in lung development and repair were determined. The overall CpG methylation in F1 sperms across gene bodies, promoters, 5’UTRs, exons, introns, and 3’UTRs was not affected by nicotine exposure. However, the methylation levels were different between the different genomic regions. 81 CpG sites, 16 gene bodies, and 3 promoter regions were differentially methylated. Gene enrichment analysis of DMRs revealed pathways involved in oxidative stress, nicotine response, alveolar and brain development, and cellular signaling. Among the DMRs, Dio1 and Nmu were the most hypermethylated and hypomethylated genes, respectively. Gene expression analysis showed that the mRNA expression and DNA methylation were incongruous. Key proteins involved in lung development and repair were significantly different (FDR < 0.05) between the nicotine and placebo-treated groups. Our data show that DNA methylation is remodeled in offspring spermatozoa upon perinatal nicotine exposure. These epigenetic alterations may play a role in transgenerational inheritance of perinatal smoke/nicotine induced asthma.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34153130" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173959" }, "primaryId" : "GEO:GSE173959", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173959" } ] }, "title" : "Opioid withdrawal produces sex-specific effects on fentanyl-vs.-food choice and mesolimbic transcription", "dateAssigned" : "2021-05-05T00:00:00.000-05:00", "summary" : "Background: Opioid withdrawal is a key driver of opioid addiction and an obstacle to recovery. However, withdrawal effects on opioid reinforcement and mesolimbic neuroadaptation are understudied and the role of sex is largely unknown. Methods: Male (n=13) and female (n=12) rats responded under a fentanyl-vs.-food “choice” procedure during daily 2h sessions. In addition to the daily choice sessions, rats were provided extended access to fentanyl during 12h self-administration sessions. After two weeks of this selfadministration regimen, the nucleus accumbens (NAc) and ventral tegmental area (VTA) of a subset of rats were subjected to RNA sequencing. In the remaining rats, a third week of this self-administration regimen was conducted, during which methadone effects on fentanyl-vs.-food choice were determined. Results: Prior to opioid dependence, male and female rats similarly allocated responding between fentanyl and food. Abstinence from extended fentanyl access elicited similar increases in somatic withdrawal signs in both sexes. Despite similar withdrawal signs and extended access fentanyl intake, opioid withdrawal was accompanied by a maladaptive increase in fentanyl choice in males, but not females. Behavioral sex differences corresponded with a greater number of differentially expressed genes in the NAc and VTA of opioidwithdrawn females relative to males. Methadone blocked withdrawal-associated increases in fentanyl choice in males, but failed to further decrease fentanyl choice in females. Conclusions: These results provide foundational evidence of sex-specific neuroadaptations to opioid withdrawal, which may be relevant to the female-specific resilience to withdrawal-associated increases in opioid choice and aid in the identification of novel therapeutic targets.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173975" }, "primaryId" : "GEO:GSE173975", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE173975" } ] }, "title" : "Transcriptional Pathology Evolves Over Time in Rat Hippocampus Following Lateral Fluid Percussion Traumatic Brain Injury", "dateAssigned" : "2021-05-06T00:00:00.000-05:00", "summary" : "Traumatic brain injury (TBI) causes acute and lasting impacts on the brain, driving pathology along anatomical, cellular, and behavioral dimensions. Rodent models offer the opportunity to study TBI in a controlled setting, and enable analysis of the temporal progression that occurs from injury to recovery. We applied transcriptomic and epigenomic analysis, characterize gene expression and in ipsilateral hippocampus at 1 and 14 days following moderate lateral fluid percussion (LFP) injury. This approach enabled us to identify differential gene expression (DEG) modules with distinct expression trajectories across the two time points. The major DEG modules represented genes that were up- or downregulated acutely, but largely recovered by 14 days. As expected, DEG modules with acute upregulation were associated with cell death and astrocytosis. Interestingly, acutely downregulated DEGs related to neurotransmission mostly recovered by two weeks. Upregulated DEG modules related to inflammation were not necessarily elevated acutely, but were strongly upregulated after two weeks. We identified a smaller DEG module with delayed downregulation at 14 days including genes related to cholesterol metabolism and amyloid beta clearance. Finally, differential expression was paralleled by changes in H3K4me3 at the promoters of differentially expressed genes at one day following TBI. Following TBI, changes in cell viability, function and ultimately behavior are dynamic processes. Our results show how transcriptomics in the preclinical setting has the potential to identify biomarkers for injury severity and/or recovery, to identify potential therapeutic targets, and, in the future, to evaluate efficacy of an intervention beyond measures of cell death or spatial learning.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34909768" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174098" }, "primaryId" : "GEO:GSE174098", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174098" } ] }, "title" : "Single-cell RNA sequencing of the rat carotid arteries uncovers mechanisms of in-stent restenosis", "dateAssigned" : "2021-05-08T00:00:00.000-05:00", "summary" : "Maps of heterogeneous cellular landscape in carotid artery were defined by single-cell RNA sequencing and revealed several cell types with their internal relations in the ISR model. This study highlights the crucial role of VSMC phenotype switching in the progression of ISR, and provides the clues of the underlying mechanism of ISR.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34957241" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174099" }, "primaryId" : "GEO:GSE174099", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174099" } ] }, "title" : "Differential expression profile of liver tissue in rats with hepatic fibrosis", "dateAssigned" : "2021-05-08T00:00:00.000-05:00", "summary" : "Liver fibrosis is a common pathological complication of end-stage liver disease, which is usually associated with chronic liver inflammation and injury. Liver fibrosis was induced by bile duct ligation (BDL) in rats. The differentially expressed genes in liver tissue of BDL rats were identified by microarray technique.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174235" }, "primaryId" : "GEO:GSE174235", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174235" } ] }, "title" : "Staphylococcus aureus modulate cellular metabolism to survive in epithelial cells", "dateAssigned" : "2021-05-11T00:00:00.000-05:00", "summary" : "This work aimed to investigate the metabolic changes of epithelial cell metabolism during S. aureus infection. We revealed that persistent S. aureus survived in epithelial cells by modulating the cellular pathways of one carbon pool by folate. These results highlight the persistence mechanisms of S. aureus survived in epithelial cells by regulation of cellular metabolism, shedding light on the development of intervention strategies to combat S. aureus associated infections.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174249" }, "primaryId" : "GEO:GSE174249", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174249" } ] }, "title" : "A systems-level analysis of bile acids effects on rat colon epithelial cells", "dateAssigned" : "2021-05-11T00:00:00.000-05:00", "summary" : "In addition, the study provides annotated rat colonic epithelial cell transcriptome and proteome with response to bile acid-feeding.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174289" }, "primaryId" : "GEO:GSE174289", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174289" } ] }, "title" : "Early molecular events mediating loss of aquaporin-2 in kidney collecting duct during ureteral obstruction", "dateAssigned" : "2021-05-11T00:00:00.000-05:00", "summary" : "Early stages of ureteral obstruction are marked by polyuria with impaired urinary concentrating ability, associated with loss of aquaporin-2 (AQP2) expression. Most mechanistic work in unilateral ureteral obstruction (UUO) models has been done at relatively late time points, making it difficult to discriminate the early effect on collecting ducts (CDs) in gene expression. Here, we use single-tubule RNA-Seq to identity signaling pathways at earlier time points after UUO in rat models.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35918145" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174299" }, "primaryId" : "GEO:GSE174299", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174299" } ] }, "title" : "Expression profiling of contralateral dorsal root ganglia of a rat model of complex regional pain syndrome type-I uncovers potential mechanisms involved in mirror-image pain", "dateAssigned" : "2021-05-12T00:00:00.000-05:00", "summary" : "Conclusions: We provided by far the first study to profile gene expression changes and pathway analysis of contralateral DRG for investigating MIP mechanisms. This work may provide novel insights into understanding the mysterious mechanisms underlying MIP.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34512013" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174455" }, "primaryId" : "GEO:GSE174455", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174455" } ] }, "title" : "Gene expression changes accompanying vascular tortuosity", "dateAssigned" : "2021-05-14T00:00:00.000-05:00", "summary" : "To gain insight into vascular tortuosity, we analyzed gene expression in normal and tortuous vessels. We induced vascular tortuosity in basilar artery using bilateral common carotid artery ligation in One-year old SD rats. Four weeks after the ligation, total RNA was extracted. Equal amounts of RNA from four rats were pooled and 50 ng RNA was subjected to microarray analysis. Pooled RNA from four Sham operated rats were used as a control.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34200411" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174549" }, "primaryId" : "GEO:GSE174549", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174549" } ] }, "title" : "Decoction mediates spinal cord repair in vitro and in vivo through the PI3K-AKT signaling pathway", "dateAssigned" : "2021-05-17T00:00:00.000-05:00", "summary" : "Conclusions: Our study represents the first detailed analysis of the spinal cord transcriptome generated by RNA-seq technology with biological replicates. Our results suggest that Modified Erxian decoction may mediate spinal cord repair through the PI3K-AKT pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36387579" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174567" }, "primaryId" : "GEO:GSE174567", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174567" } ] }, "title" : "Calibration data mammalian array: Human, Mouse, Rat", "dateAssigned" : "2021-05-17T00:00:00.000-05:00", "summary" : "The DNA samples from each species were enzymatically manipulated so that they would exhibit 0%, 25%, 50%, 75% and 100% percent methylation at each CpG location, respectively. The variable “ProportionMethylated” (with ordinal values 0, 0.25, 0.5, 0.75, 1) can be interpreted as a benchmark for each CpG that maps to the respective genome. Thus, the DNA methylation levels of each CpG are expected to have a high positive correlation with ProportionMethylated across the arrays measurement from a given species. The mammalian array was applied to synthetic DNA data from 3 species: human (n=10 mammalian arrays, 2 per methylation level), mouse (n=20, 4 per methylation level), and rat (n=15, 3 per methylation level).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35145108" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174568" }, "primaryId" : "GEO:GSE174568", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174568" } ] }, "title" : "Calibration data EPIC array: Mouse and Rat", "dateAssigned" : "2021-05-17T00:00:00.000-05:00", "summary" : "The DNA samples from each species were enzymatically manipulated so that they would exhibit 0%, 25%, 50%, 75% and 100% percent methylation at each CpG location, respectively. The variable “ProportionMethylated” (with ordinal values 0, 0.25, 0.5, 0.75, 1) can be interpreted as a benchmark for each CpG that maps to the respective genome. Thus, the DNA methylation levels of each CpG are expected to have a high positive correlation with ProportionMethylated across the arrays measurement for the human species. The human EPIC array was applied to calibration data from mouse (n=15 EPIC arrays, 3 per methylation level) and rat (n=10, 2 per methylation level). The EPIC array data were normalized using the noob method (R function preprocessNoob in minfi).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35145108" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174631" }, "primaryId" : "GEO:GSE174631", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174631" } ] }, "title" : "Integrated Analysis of Omics Data Reveal AP-1 as a Potential Regulation Hub in the Inflammation-Induced Hyperalgesia Rat Model", "dateAssigned" : "2021-05-18T00:00:00.000-05:00", "summary" : "Inflammation-associated chronic pain is a global clinical problem, affecting millions of people worldwide. However, the underlying mechanisms that mediate inflammation-associated chronic pain remain unclear. A rat model of cutaneous inflammation induced by Complete Freund’s Adjuvant (CFA) has been widely used as an inflammation-induced pain hypersensitivity model. We present the transcriptomics profile of CFA-induced inflammation in the rat dorsal root ganglion (DRG) via an approach that targets gene expression, DNA methylation, and post-transcriptional regulation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174722" }, "primaryId" : "GEO:GSE174722", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174722" } ] }, "title" : "Integrated Omic Analyses Identify Pathways and Regulators Associated with Chemical Alterations of in vitro Neural Network Formation", "dateAssigned" : "2021-05-19T00:00:00.000-05:00", "summary" : "Development of in vitro new approach methodologies (NAMs) has been driven by the need for developmental neurotoxicity (DNT) hazard data on thousands of chemicals. The network formation assay (NFA) characterizes DNT hazard based on changes in network formation but provides no mechanistic information. This study investigated nervous system signaling pathways and upstream physiological regulators underlying chemically-induced neural network dysfunction. Rat primary cortical neural networks grown on microelectrode arrays were exposed (0.1 -10 µM) for 12 days in vitro (DIV) to cytosine arabinoside (CA), 5 fluorouracil (5FU), domoic acid (DA), cypermethrin (CM), deltamethrin (DM), and haloperidol; these exposures targeted specific concentrations that altered network activity in previous studies. RNA-seq from cells and GC/MS of media extracts collected on DIV 12 provided gene expression and metabolomic identification, respectively. The integration of differentially expressed genes and metabolites for each neurotoxicant were analyzed using Ingenuity Pathway Analysis (IPA). All six compounds altered gene expression that linked to developmental disorders and neurological diseases. Other enriched canonical pathways overlapped among compounds of the same class; for example, genes altered by both CA and 5FU exposures are enriched in axonal guidance pathways. Analysis of upstream regulators was heterogeneous across compounds, but identified regulators included CREB1, BDNF, TGFβ1, NTRK2, and PRODH. These results demonstrate that transcriptomic and metabolomic changes following chemical exposure can be determined in the NFA and that different classes of compounds produce differing responses. This approach can enhance information obtained from NAMs and contribute to the identification and development of AOPs associated with DNT.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34927697" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174737" }, "primaryId" : "GEO:GSE174737", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174737" } ] }, "title" : "Transcriptomics in the nucleus accumbens shell reveal sex- and reinforcer-specific signatures associated with morphine and sucrose craving", "dateAssigned" : "2021-05-20T00:00:00.000-05:00", "summary" : "RNA-sequencing was performed using nucleus accumbens tissue from male and female rats following 1 or 30 days of morphine self-admininstration or sucrose self-adminnistration.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174753" }, "primaryId" : "GEO:GSE174753", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174753" } ] }, "title" : "Effects of early life adversity on male reproductive behavior and the medial preoptic area", "dateAssigned" : "2021-05-20T00:00:00.000-05:00", "summary" : "Early life adversity has been linked to altered reproductive development in humans, including changes in the timing of pubertal onset and sexual activity. One common form of early life adversity is having limited access to resources. This form of early life adversity can be modeled in rodents using the limited bedding and nesting model (LBN), in which rat dams and pups are placed in a low resource environment from postnatal day (PND) 2 through 9. Our laboratory has previously shown that male rats raised in LBN conditions have elevated levels of plasma estradiol compared to control males. Female rats, on the other hand, show no effect of LBN on plasma hormone levels, pubertal timing, or estrous cycle duration in adulthood. Here, we find that LBN males also show changes in adult reproductive behaviors. LBN males acquired the suite of reproductive behaviors more quickly than their control counterparts over the course of 3 weeks of testing, showing shorter latencies to mount, intromit, and ejaculate compared to controls prior to the final week of testing. We also characterized LBN-induced gene transcription changes across sex in the medial preoptic area (mPOA) which underlies reproductive behaviors. Interestingly, there was no effect of LBN on puberty onset (as measured by preputial separation) or masculinization of the sexually dimorphic nucleus of the preoptic area (SDN/POA; as measured by calbindin immunoreactivity) in males, suggesting LBN may not exert effects on hormone-dependent measures until after puberty.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174846" }, "primaryId" : "GEO:GSE174846", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174846" } ] }, "title" : "Chronic paternal morphine exposure increases sensitivity to morphine-derived antinociception", "dateAssigned" : "2021-05-21T00:00:00.000-05:00", "summary" : "Preclinical studies suggest that parental exposure to drugs of abuse such as opioids can have profound and long-lasting effects on reward processing and drug sensitivity across generations. However, little is known about the impact of long-term paternal morphine exposure on sensitivity to morphine-derived antinociception in offspring. We developed a novel sub-second pain scale with statistical modeling and machine learning to measure mechanical nociception in Long Evans and Sprague Dawley male and female rats. Next, we used this rat pain scale with a multigenerational paternal morphine exposure paradigm to determine whether chronic paternal morphine exposure impacts pain sensitivity in offspring. Finally, we used RNA sequencing to identify potential molecular correlates of sire exposure to morphine on offspring. Surprisingly, we found that von Frey hair filaments (VFHs), the most commonly-used noxious mechanical stimuli to test pain sensitivity, are not painful to rats as measured by this novel rat pain scale. Male progeny produced from morphine-treated sires did not exhibit any baseline changes in sensitivity to noxious mechanical stimuli but had greater sensitivity to the antinociceptive properties of morphine. Changes in gene expression within the periaqueductal gray, including primary members of the RGS family of proteins, were identified that may play a role in modified sensitivity to morphine within offspring. These findings reveal nuanced responses to VFHs that should be considered in future pain studies and demonstrate that long-term paternal exposure to morphine increases sensitivity to morphine-derived analgesia in the subsequent male generation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174896" }, "primaryId" : "GEO:GSE174896", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE174896" } ] }, "title" : "Expression data of GFP-GnRH neurons during rat embryonic development", "dateAssigned" : "2021-05-21T00:00:00.000-05:00", "summary" : "During development, gonadotropin releasing hormone (GnRH) neurons are born in the nasal placode and migrate to the hypothalamus, where they position to regulate sexual reproduction. Defective GnRH neuron development may lead to GnRH deficiency (GD) which is characterized by absent or delayed puberty. Several GD causative genes have been identified so far, but half of the cases are still idiopathic. The identification of candidate genes is also hampered by the difficulty in isolating and studying GnRH neurons, which are small in number, develop in a short developmental window and lack specific markers. Gene expression profiles of GnRH neurons are lacking, as obtaining primary GnRH neurons is challenging and no reports on gene expression profiles during the whole developmental process of GnRH neurons are available. In this work, we obtained the transcriptomic profile of sorted GFP-positive and unsorted GFP-negative cells from Gnrh1-GFP rat embryos at three developmental stages, representing the initiation (embryonic day (E)14), the peak (E17) and the completion of GnRH neuronal migration (E20).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36810932" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175390" }, "primaryId" : "GEO:GSE175390", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175390" } ] }, "title" : "miRNA expression data from sedentary and exercised rats", "dateAssigned" : "2021-05-23T00:00:00.000-05:00", "summary" : "We used miRNA microarrays to determine the changes in miRNA expression through time and the differences between sedentary and lifelong exercised rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36399890" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175461" }, "primaryId" : "GEO:GSE175461", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175461" } ] }, "title" : "Transcriptome of hypothalamic supraoptic nucleus in response to 72h water deprivation in Wistar Han rats", "dateAssigned" : "2021-05-24T00:00:00.000-05:00", "summary" : "The hypothalamic supraoptic nucleus (SON) is a core osmoregulatory control centre that deciphers information about the metabolic state of the organism and orchestrates appropriate homeostatic (endocrine) and allostatic (behavioural) responses. We have used RNA sequencing to describe the polyadenylated transcriptome of the SON of the male Wistar Han rat. These data have been mined to generate comprehensive catalogues of functional classes of genes (enzymes, transcription factors, endogenous peptides, G protein coupled receptors, transporters, catalytic receptors, channels and other pharmacological targets) expressed in this nucleus in the euhydrated state, and that together form the basal substrate for its physiological interactions. We have gone on to show that fluid deprivation for 3 days (dehydration) results in changes in the expression levels of 2247 RNA transcripts, which have similarly been functionally catalogued, and further mined to describe enriched gene categories and putative regulatory networks (Regulons) that may have physiological importance in SON function related plasticity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34297454" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175478" }, "primaryId" : "GEO:GSE175478", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175478" } ] }, "title" : "Gene expression profiling for cigarette smoke (CS) exposed lung treated with human umbilical cord mesenchymal stem cells derived extracellular vesicle (hUCMSC-EV) and human umbilical cord derived mesenchymal stem cells (hUC-MSC)", "dateAssigned" : "2021-05-24T00:00:00.000-05:00", "summary" : "To study the genes and pathway involved in cigarette smoke induced lung inflammation, and treatment with hUC-MSC-EV and hUC-MSC we have employed microarray expression profiling to identify the differentially expressed genes", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175710" }, "primaryId" : "GEO:GSE175710", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175710" } ] }, "title" : "Excessive mechanical strain accelerates intervertebral disc degeneration by disrupting the intrinsic circadian rhythm", "dateAssigned" : "2021-05-27T00:00:00.000-05:00", "summary" : "Nucleus pulposus cells were stretched using a FX-5000T Flexcell tension plus system (Flexcell International Corp., USA) with 18% elongation (0.2 Hz) for 24 h", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175760" }, "primaryId" : "GEO:GSE175760", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175760" } ] }, "title" : "A Transcriptomic Analysis of Neuropathic Pain in the Spinal Cord after Nerve Injury", "dateAssigned" : "2021-05-28T00:00:00.000-05:00", "summary" : "Neuropathic pain is a troublesome pathological condition without suitable treatments. In this study, we performed RNA sequencing (RNA-seq) analysis to reveal transcriptomic profiles of spinal cord from chronic constriction injury (CCI) rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35030976" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175884" }, "primaryId" : "GEO:GSE175884", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175884" } ] }, "title" : "Slc39a2-mediated Zinc Homeostasis Modulates Innate Immune Signaling in Phenylephrine-induced Cardiomyocyte Hypertrophy", "dateAssigned" : "2021-06-01T00:00:00.000-05:00", "summary" : "Zinc dyshomeostasis has been involved in the pathogenesis of cardiac hypertrophy; however, the dynamic regulation of intracellular zinc and its downstream signaling in cardiac hypertrophy remain largely unknown. Here we screened ZIP (SLC39) family members that were responsible for zinc uptake in a phenylephrine (PE)-induced cardiomyocyte hypertrophy model. We found that Slc39a2 was the only member that was altered at mRNA level by PE treatment in neonatal rat ventricular myocytes (NRVMs), but its protein level was not affected. Zincpyr1 staining showed a significant decrease in zinc uptake after PE treatment or after Slc39a2 knockdown in NRVMs, indicating an inhibition of its transport activity during hypertrophy. Slc39a2 deficiency caused spontaneous hypertrophy in NRVMs, and further exacerbated the hypertrophic responses after PE treatment. RNA sequencing analysis confirmed a largely aggravated pro-hypertrophic transcriptome reprogramming after Slc39a2 knockdown. Interestingly, the innate immune pathways, including NOD signaling, TOLL-like receptor, NFB, and IRFs, were substantially enriched after Slc39a2 knockdown. Whereas IRF7, the most sensitive among all IRFs, did not mediate the effect of Slc39a2 in hypertrophy, pro-hypertrophy phosphorylations of NFB and STAT3 were significantly enhanced after Slc39a2 knockdown, in parallel with degradation of IkBα protein. Our data demonstrate that SLC39A2-mediated zinc homeostasis contributes to the remodeling of innate immune signaling in cardiomyocyte hypertrophy, and provide novel insights into the pathogenesis of heart failure and its treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34790705" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175917" }, "primaryId" : "GEO:GSE175917", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE175917" } ] }, "title" : "Transthyretin alters cardiac fibroblast structure, function and inflammatory gene expression.", "dateAssigned" : "2021-06-01T00:00:00.000-05:00", "summary" : "Age-related wild type transthyretin amyloidosis (wtATTR) is characterized by systemic deposition of amyloidogenic fibrils of misfolded transthyretin (TTR) in the connective tissue of many organs. In the heart this leads to cardiac dysfunction, which is a significant cause of age-related heart failure. The hypothesis tested is that TTR affects cardiac fibroblasts in ways that may contribute to fibrosis. When primary cardiac fibroblasts were cultured on TTR-deposited substrates, the F-actin cytoskeleton disorganized, focal adhesion formation decreased, and nuclear shape was flattened. Fibroblasts had faster collective and single cell migration velocities on TTR-deposited substrates. Additionally, fibroblasts cultured on microposts with TTR deposition had reduced attachment and increased proliferation above untreated. Transcriptomic and proteomic analyses of fibroblasts grown on glass covered with TTR showed significant upregulation of inflammatory genes after 48 hours, indicative of progression in TTR-based diseases. Together, results suggest that TTR deposited in tissue extracellular matrix may affect both the structure, function and gene expression of cardiac fibroblasts. As therapies for wtATTR are cost-prohibitive and only slow disease progression, better understanding of cellular maladaptation may elucidate novel therapeutic targets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34018852" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176004" }, "primaryId" : "GEO:GSE176004", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176004" } ] }, "title" : "Riluzole administration to rats with levodopa-induced dyskinesia analyzed by RRBS", "dateAssigned" : "2021-06-02T00:00:00.000-05:00", "summary" : "Dyskinesias are characterized by abnormal repetitive involuntary movements due to dysfunctional neuronal activity. Although levodopa-induced dyskinesia, characterized by tic-like abnormal involuntary movements, has no clinical treatment for Parkinson’s disease patients, animal studies indicate that Riluzole, which interferes with glutamatergic neurotransmission, can improve the phenotype. The rat model of levodopa-induced dyskinesia is a unilateral lesion with 6-hydroxydopamine in the medial forebrain bundle, followed by the repeated administration of levodopa. The molecular pathomechanism of levodopa-induced dyskinesia is still not deciphered, however implication of epigenetic mechanisms was suggested. In this study, we investigated the striatum for DNA methylation alterations under chronic levodopa treatment with or without co-treatment with Riluzole. Our data show that the lesioned and contralateral striata have nearly identical DNA methylation profiles. Chronic levodopa and levodopa+Riluzole treatments led to DNA methylation loss, particularly outside of promoters, in gene bodies and CpG poor regions. We observed that several genes involved in the levodopa-induced dyskinesia underwent methylation changes. Furthermore, the Riluzole co-treatment, which improved the phenotype, pinpointed specific methylation targets, with more than 20% methylation difference relative to levodopa treatment alone. These findings indicate potential new druggable targets for levodopa-induced dyskinesia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34207710" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176009" }, "primaryId" : "GEO:GSE176009", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176009" } ] }, "title" : "Reelin and Thrombospondin1 regulate cardiomyocyte proliferation through Vldlr", "dateAssigned" : "2021-06-02T00:00:00.000-05:00", "summary" : "We performed RNA-Seq analysis of neoatal rat ventricular cardiomyocytes (NRVCs)which were treated with Reelin,or knocking down Vldlr,Thbs1,or overexpressing Vldlr to investigate the moleclular mechanism of Thbs1/Reelin-Vldlr to regulate cardiomyocyte proliferation.In addition,the day 1mouse cardiomyocytes in Myh6-Cre;Vldlr f/f mice ,Myh6-Cre;Vldlr f/+ mice ,versus Vldlr f/f mice were also performed to explore the fucntion of Vldlr which regulating cardiomyocyte proliferation in vivo.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176017" }, "primaryId" : "GEO:GSE176017", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176017" } ] }, "title" : "Dorsal root ganglion single-cell RNA-seq dataset of painful diabetic peripheral neuropathy rat, diabeitc rats, and health rats", "dateAssigned" : "2021-06-02T00:00:00.000-05:00", "summary" : "Painful diabetic peripheral neuropathy (PDPN) is a common complication of diabetes mellitus (DM). As one of the most disturbing symptoms, mechanical allodynia (MA) in PDPN remains largely unexplored. This dataset contains single-cell RNA sequencing results from rat dorsal root ganglion (DRG). The goal of this experiment was to investigate the transcriptional changes of distinct cell types in the DRG along MA development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35668789" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176082" }, "primaryId" : "GEO:GSE176082", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176082" } ] }, "title" : "Innate immunity-driven cell recruitment in rat autoimmune diabetes", "dateAssigned" : "2021-06-03T00:00:00.000-05:00", "summary" : "Comparative analysis of the response of wild-type (WT) and Ifnar1 knockout LEW.1WR1 rats to infection with Kilham rat virus (KRV) using the Seq-Well single-cell RNA-Seq method. KRV induces the equivalent of human type I diabetes (T1D) in WT rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34702762" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176099" }, "primaryId" : "GEO:GSE176099", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176099" } ] }, "title" : "Whole transcriptome resequencing of the cavernous tissue of the penis of rats", "dateAssigned" : "2021-06-03T00:00:00.000-05:00", "summary" : "Results: RNA transcriptome sequencing showed that 4,587 circRNAs, 762 miRNAs, and 21,661 mRNAs were dysregulated in the BCNC group. The top 20 differentially expressed circRNAs were further verified via RT-qPCR. The ceRNA network contained 23 circRNA-miRNA pairs and 227 miRNA-mRNA pairs, including ten circRNAs, six miRNAs, and 227 mRNAs. GO analysis suggested that these ten circRNAs could regulate various processes, such as oxidation-reduction processes, lipid metabolic processes, apoptotic processes, and proteolysis. Furthermore, KEGG analysis of mRNAs in the ceRNA network showed that they were involved in energy metabolism and communication between cells. A protein‐protein interaction network was constructed with the 227 mRNAs, and five hub genes (Ccna2, Cxcl10, Pld1, Mapk11, and Mboat2) were identified. In addition, Using circRNADb, we found 12 circRNAs with protein-coding potential, three of which were highly conserved in humans and rats. Our study revealed a potential link between circRNAs, miRNAs, and mRNAs in CNI-ED, suggesting that circRNAs may contribute to the occurrence of ED by regulating the cellular energy metabolism in CNI-ED.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34461805" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176295" }, "primaryId" : "GEO:GSE176295", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176295" } ] }, "title" : "Mild food restriction and gene expression profile (adipose)", "dateAssigned" : "2021-06-07T00:00:00.000-05:00", "summary" : "The aim of this study is to obtain the gene expression profiles of the adipose tissue of young growing rats after mild restriction of food intake for one week or one month.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34209243" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176297" }, "primaryId" : "GEO:GSE176297", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176297" } ] }, "title" : "Mild food restriction and gene expression profile (brain)", "dateAssigned" : "2021-06-07T00:00:00.000-05:00", "summary" : "The aim of this study is to obtain the gene expression profiles of the brain of young growing rats after mild restriction of food intake for one week or one month.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34209243" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176298" }, "primaryId" : "GEO:GSE176298", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176298" } ] }, "title" : "Mild food restriction and gene expression profile (intestine)", "dateAssigned" : "2021-06-07T00:00:00.000-05:00", "summary" : "The aim of this study is to obtain the gene expression profiles of the intestine of young growing rats after mild restriction of food intake for one month.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34209243" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176299" }, "primaryId" : "GEO:GSE176299", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176299" } ] }, "title" : "Mild food restriction and gene expression profile (muscle)", "dateAssigned" : "2021-06-07T00:00:00.000-05:00", "summary" : "The aim of this study is to obtain the gene expression profiles of the muscle of young growing rats after mild restriction of food intake for one week or one month.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34209243" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176352" }, "primaryId" : "GEO:GSE176352", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176352" } ] }, "title" : "RNA methylation in diabetes [RNA-Seq]", "dateAssigned" : "2021-06-08T00:00:00.000-05:00", "summary" : "The MeRIP-seq was carried out in Novogene (Beijing, China). Briefly, 2 μg total RNA was extracted from the retinas of both wide type mice and their littermates with diabetes. The integrity and concentration of extracted RNA was detected using an Agilent 2100 bioanalyzer (Agilent) and simpliNano spectrophotometer (GE Healthcare), respectively. Fragmented RNA (~100 nt) was incubated for 2 hours at 4 ℃ with anti-m6A polyclonal antibody (Synaptic Systems) in the immunoprecipitation experiment. Then, immunoprecipitated RNA or input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols. The sequencing was carried out with three independent biological replicates.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176353" }, "primaryId" : "GEO:GSE176353", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176353" } ] }, "title" : "RNA methylation in diabetes [MeRIP-seq]", "dateAssigned" : "2021-06-08T00:00:00.000-05:00", "summary" : "The MeRIP-seq was carried out in Novogene (Beijing, China). Briefly, 2 μg total RNA was extracted from the retinas of both wide type mice and their littermates with diabetes. The integrity and concentration of extracted RNA was detected using an Agilent 2100 bioanalyzer (Agilent) and simpliNano spectrophotometer (GE Healthcare), respectively. Fragmented RNA (~100 nt) was incubated for 2 hours at 4 ℃ with anti-m6A polyclonal antibody (Synaptic Systems) in the immunoprecipitation experiment. Then, immunoprecipitated RNA or input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols. The sequencing was carried out with three independent biological replicates.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176395" }, "primaryId" : "GEO:GSE176395", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176395" } ] }, "title" : "Neonatal nephron loss during active nephrogenesis results in altered expression of renal developmental genes and markers of kidney injury", "dateAssigned" : "2021-06-08T00:00:00.000-05:00", "summary" : "Preterm neonates are at high risk for nephron loss under adverse clinical conditions (e.g., cardiocirculatory decompensation, nephrotoxic drugs). Importantly, the onset of renal damage potentially collides with the proceeding nephrogenesis of prematurity prior 36 weeks of gestation. Recent animal studies suggest that early nephron loss within this vulnerable phase is associated with more severe glomerular and tubulointerstitial alterations later in life, irrespective of the occurrence of arterial hypertension. It is known that nephrogenic pathways are reactivated after acute kidney injury supporting renal repair and regeneration. In this study we hypothesized that nephron loss during nephrogenesis leads to an alteration of the kidney developmental program which in turn impairs homeostasis and repair and thus aggravates kidney injury later in life. Preterm infants prior to 36 weeks of gestation show an active nephrogenesis after birth. In rats, nephrogenesis is still active until day 10 of life. Mimicking the human situation of acute nephron loss in preterm neonates with ongoing nephrogenesis, rats were uninephrectomized at day 1 of life (UNXd1). A second group of animals was uninephrectomized at day 14 of life (UNXd14), which resembles a nephron loss after terminated nephrogenesis. Age-matched control groups were sham operated. Three days after uninephrectomy the animals were sacrificed. Transcriptional renal changes were analyzed by RNAseqencing, followed by in silico functional pathway analysis. In UNXd1 animals 1182 genes were differentially regulated compared to the respective control group. The functional groups “renal development” and “kidney injury” were among the most differentially regulated groups and revealed distinctive alterations in UNXd1 animals. Reduced expression levels of candidate genes concerning renal development (Bmp7, Gdnf, Pdgf-B, Wt1) and kidney injury (nephrin, podocin, Tgf-β1) were detected in the kidney of UNXd1 animals. The downregulation of Bmp7 and Gdnf expression in the remaining kidney of UNXd1 animals persisted until day 28 of life. In UNXd14 rats Six2 was upregulated and Pax22 downregulated compared to controls. We conclude that neonatal nephron loss during active nephrogenesis affects renal development and induces persistently reduced expression levels of genes which in turn might hinder tissue repair after kidney injury later in life.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176488" }, "primaryId" : "GEO:GSE176488", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176488" } ] }, "title" : "RNA-sequencing of orbitofrontal cortex following limited bedding and nesting stress model", "dateAssigned" : "2021-06-09T00:00:00.000-05:00", "summary" : "RNA-sequencing of the orbitofrontal cortex was performed in male and female rats following exposure to the limited bedding and nesting model of early life adversity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176507" }, "primaryId" : "GEO:GSE176507", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176507" } ] }, "title" : "Analysis of gastrocnemius muscle from chow-fed control and UCP1 knockout rats at room temperature and after exposure to 4 degrees Celsius", "dateAssigned" : "2021-06-09T00:00:00.000-05:00", "summary" : "To determine the transcriptomic effects of cold exposure on skeletal muscle gene expression in rats with and without UCP1, we assessed gastrocnemius muscle in chow-fed control and whole body UCP1 knockout rats using RNA-seq.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176515" }, "primaryId" : "GEO:GSE176515", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE176515" } ] }, "title" : "MicroRNA array expression during normal urinary bladder wound healing", "dateAssigned" : "2021-06-09T00:00:00.000-05:00", "summary" : "Urinary bladder wound healing is today pooorly chracterized. MicroRNAs are small non-coding RNA molecules with regulatory functions. In this study we aimed at identifying microRNAs expressed during bladder wound healing. We performed Affymetrix microRNA profiling of the rodent urinary bladder during healing of a surgically created wound.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34750474" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE177037" }, "primaryId" : "GEO:GSE177037", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE177037" } ] }, "title" : "An RNA-sequencing transcriptome of the rodent Schwann cell response to peripheral nerve injury", "dateAssigned" : "2021-06-11T00:00:00.000-05:00", "summary" : "Our dataset provides a helpful resource for further deciphering the SC injury response and provides a depth of transcriptional data that can complement the findings of recent single cell sequencing approaches. In addition, as more data becomes available on the response of CNS glia to injury, we anticipate that this dataset will provide a valuable platform for understanding key differences in the PNS and CNS glial responses to injury and for designing approaches to ameliorate CNS regeneration.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35501870" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE177078" }, "primaryId" : "GEO:GSE177078", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE177078" } ] }, "title" : "Integrated stress response couples mitochondria protein translation with oxidative stress control", "dateAssigned" : "2021-06-11T00:00:00.000-05:00", "summary" : "Under stress conditions, cells elicit integrated stress response (ISR) to cope with intracellular and extracellular disturbances. However, its role in ischemic heart disease remains to be elucidated. Here, we show that oxygen deprivation in cardiomyocytes triggers significant changes in protein translation. Importantly, ischemia and ischemia/reoxygenation leads to suppression of protein synthesis, which is caused by activation of the PERK/eIF2α axis of ISR. At the functional level, cardiac specific elimination of PERK exacerbates cardiac response to ischemia/reperfusion whereas selective activation of PERK in the heart confers cardioprotection against reperfusion injury. Mechanistically, PERK-mediated improvement in cardiomyocyte survival depends on suppression of protein synthesis and consequently relieves energetic demand on mitochondria. We went further to show that mitochondrial complex components are targeted by protein translation suppression, which significantly diminishes mitochondria-associated production of reactive oxygen species. Indeed, pharmacological activation of ISR protects the heart from ischemia/reperfusion damage, even after the release of occluded coronary artery, highlighting clinical significance for myocardial infarction. Taken together, these findings suggest that ISR improves cell survival through selectively suppressing mitochondrial protein synthesis and reducing oxidative stress in ischemic heart disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34583519" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178083" }, "primaryId" : "GEO:GSE178083", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178083" } ] }, "title" : "Gene expression profiles in rat alveolar macrophages exposure to submicron carbon fibers", "dateAssigned" : "2021-06-14T00:00:00.000-05:00", "summary" : "To evaluate the biological effects at the transcriptional level of manufactured nanomaterials, whole genome microarrays of rat alveolar macrophages (NR8383) exposed to three types of submicron-diameter carbon fibers (SCFs) with different physicochemical properties were performed. In comparison with the fibers of SCF1, the fibers of SCF2 were shorter, and the fibers of SCF3 were thinner.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34890706" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178224" }, "primaryId" : "GEO:GSE178224", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178224" } ] }, "title" : "Analysis of transriptomic dysregulation upon neonatal and adult downregulation of Taf1 isoforms in rodents", "dateAssigned" : "2021-06-15T00:00:00.000-05:00", "summary" : "We report the gene expression alterations observed in the striatum of 4 months old mice that received neonatal intracerebroventricular injection with specifically designed AAV1miRNA targeting nTaf1 and cnTaf or the scramble control", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34403156" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178265" }, "primaryId" : "GEO:GSE178265", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178265" } ] }, "title" : "A molecular census of midbrain dopaminergic neurons in Parkinsons disease", "dateAssigned" : "2021-06-15T00:00:00.000-05:00", "summary" : "Midbrain dopamine (DA) neurons in the substantia nigra pars compacta (SNpc) project widely throughout the central nervous system, playing critical roles in voluntary movements, reward processing, and working memory. Many of these neurons are highly sensitive to neurodegeneration in Parkinson’s Disease (PD), and their loss correlates strongly with the pathognomonic symptoms. To characterize these populations molecularly, we developed a protocol to enrich and transcriptionally profile DA neuron nuclei from postmortem human SNpc of both PD patients and matched controls. We identified a total of ten distinct populations, including one that was primate-specific. A single subtype, marked by the gene AGTR1, was highly susceptible to degeneration, and was enriched for expression of genes associated with PD in genetic studies, suggesting many risk loci act within this subtype to influence its neurodegeneration. The AGTR1 subtype also showed the strongest upregulation of TP53 and its downstream targets, nominating a potential pathway of degeneration in vivo. The transcriptional characterization of differentially disease-vulnerable DA neurons in the SNpc will inform the development of laboratory models, enable the nomination of novel disease biomarkers, and guide further studies of pathogenic disease mechanisms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35513515" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178294" }, "primaryId" : "GEO:GSE178294", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178294" } ] }, "title" : "Gene expression pattern analysis of rat articular cartilage and xiphoid cartilage", "dateAssigned" : "2021-06-16T00:00:00.000-05:00", "summary" : "We performed RNA-Seq analysis to investigate the gene expression patterns of rat articular cartilage and xiphoid cartilage.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178405" }, "primaryId" : "GEO:GSE178405", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178405" } ] }, "title" : "Endothelial cells synergize with fibroblasts to form a niche for engineering alveolar epithelium", "dateAssigned" : "2021-06-17T00:00:00.000-05:00", "summary" : "We perform single-cell RNA sequencing of whole engineered lungs generated either by alveolar epithelial type 2 cell (AEC2)/fibroblast (FB) co-culture or by AEC2/FB/endothelial cell (EC) tri-culture, to investigate AEC2 and FB phenotype in the presence and absence of endothelial cells. Primary postnatal day 7 (P7) AEC2s, P7 lung FBs, and primary rat lung microvascular ECs (from 4-6 week-old rats) used for engineered cultures, as well as native P7 whole rat lung, were sequenced for comparison. We find that native-like AEC2 phenotype, alveolar structure, and cellular signaling patterns are better recapitulated via epithelial-mesenchymal-endothelial tri-culture rather than by a more simplified system. FBs cultured in the presence of endothelial cells demonstrate reduced expression of contractile markers and upregulate features of an AEC2 niche-supportive signature.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37117221" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178407" }, "primaryId" : "GEO:GSE178407", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178407" } ] }, "title" : "Environmental Stressors Impact Placentation Through Actions On Trophoblast, Immune, and Endothelial Cell Dynamics", "dateAssigned" : "2021-06-17T00:00:00.000-05:00", "summary" : "Our environment is replete with chemicals that can affect embryonic and extraembryonic development. Dioxins, such as 2,3,7,8-tetrachlorodibenzodioxin (TCDD), are compounds affecting development through the aryl hydrocarbon receptor (AHR). TCDD exposures can lead to placental adaptations and at higher doses pregnancy termination. Deep intrauterine endovascular trophoblast cell invasion was a prominent placentation site adaptation to TCDD. TCDD-mediated placental adaptations were dependent upon maternal AHR signaling but not placental or fetal AHR nor the presence of a prominent AHR target, cytochrome P450 1A1 (CYP1A1). At the placentation site, TCDD stimulated CYP1A1 transcription within endothelial cells but not trophoblast cells. Immune and trophoblast cell behaviors at the uterine-placental interface were guided by the actions of TCDD on endothelial cells. In summary, we have identified an AHR regulatory pathway activated by environmental stressors affecting uterine and trophoblast cell dynamics and the formation of the hemochorial placenta.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34747641" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178409" }, "primaryId" : "GEO:GSE178409", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178409" } ] }, "title" : "Transcriptomic analysis of dorsal and ventral subiculum after induction of acute seizures by electric stimulation of the perforant pathway in rats", "dateAssigned" : "2021-06-17T00:00:00.000-05:00", "summary" : "Conclusion: These findings suggest preconditioning by PP electrical stimulations might induce synaptic reorganization, complement system activation, decreased glutamatergic transmission, and increased GABA transmission in subiculum areas. In the ventral subiculum, the down-regulation of proapoptotic genes and axon guidance indicates that preconditioning induces a neuroprotective environment in this region.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178439" }, "primaryId" : "GEO:GSE178439", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178439" } ] }, "title" : "Effects of Buyang Huanwu Decoction on circRNA-miRNA-mRNA transcriptional network of rats with cerebral ischemia", "dateAssigned" : "2021-06-17T00:00:00.000-05:00", "summary" : "To reveal the effects of Buyang Huanwu Decoction on circRNA-miRNA-mRNA transcriptional network of rats with cerebral ischemia, explore its molecular mechanism for the treatment of cerebral ischemia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34844103" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178504" }, "primaryId" : "GEO:GSE178504", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178504" } ] }, "title" : "Glucagon-like peptide-1 suppresses sympathetic activation via peripheral chemosensory inhibition", "dateAssigned" : "2021-06-20T00:00:00.000-05:00", "summary" : "In order to investigate the molecular basis of carotid body chemoreceptor sensitisation in the Spontaneously Hypertensive Rat (SHR) we have sequenced the transcriptomes of bilateral carotid body samples from aged-matched, male SHR and control Wistar-Kyoto rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35100822" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178505" }, "primaryId" : "GEO:GSE178505", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178505" } ] }, "title" : "Differential expression of myocardial microRNAs is implicated in dexmedetomidine induced cardioprotection in rats", "dateAssigned" : "2021-06-20T00:00:00.000-05:00", "summary" : "Using the highly sensitive miRNA array, we screened 83 microRNAs abundant in the myocardium and we explored the functions of these miRNAs by Gene Ontology and Kyoto Encyclopedia of Genes annotation. The enrichment results indicated that these miRNAs mainly participated in the phosphatidylinositol signaling system, PI3K-Akt, and MAPK. Furthermore, the TTC staining results showed that dexmedetomidine preconditioning attenuates myocardial ischemia-reperfusion injury by desregulation of several miRNAs and their potential target genes, which will give new insights into disclosing the mechanism of dexmedetomidine-induced cardioprotection.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178513" }, "primaryId" : "GEO:GSE178513", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178513" } ] }, "title" : "Wistar rat model of COPD: Cigarette smoking exposure and fine particulate matter (PM2.5) exposure vs. control.", "dateAssigned" : "2021-06-20T00:00:00.000-05:00", "summary" : "Genome-wide analysis of lncRNA expression profiles in COPD rat model exposed by cigarette smoking (CS) and fine particulate matter (PM2.5). Goal was to explore the differences and similarities lncRNAs expression in rats model of COPD exposed by CS and PM2.5.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178564" }, "primaryId" : "GEO:GSE178564", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178564" } ] }, "title" : "hUC-MSC-mediated recovery of subacute spinal cord injury through enhancing the pivotal subunits β3 and γ2 of the GABAA receptor", "dateAssigned" : "2021-06-21T00:00:00.000-05:00", "summary" : "We conducted a time-course RNA-seq of spinal cord segments at the lesion site without or with hUC-MSC treatment at subacute phase of SCI to identify genes involved in hUC-MSC-mediated recovery", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35547766" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178673" }, "primaryId" : "GEO:GSE178673", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178673" } ] }, "title" : "Chromatin landscape in perinatal cardiomyocytes", "dateAssigned" : "2021-06-22T00:00:00.000-05:00", "summary" : "In order to understand the transcriptional regulatory program of cardiomyocytes perinatal transition, we mapped chromatin accessibility, transcription-centered long-range chromatin interactions as well as gene expression in cardiomyocyte undergoing perinatal transition.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36653336" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178695" }, "primaryId" : "GEO:GSE178695", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178695" } ] }, "title" : "Nanostring derived microRNA of rats treated with lithium alone and in combination with amiloride for 6 months", "dateAssigned" : "2021-06-22T00:00:00.000-05:00", "summary" : "Differential analysis of microRNA in response to treatment with lithium and amiloride", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36028651" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178701" }, "primaryId" : "GEO:GSE178701", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178701" } ] }, "title" : "Functional primordial germ cell-like cells from pluripotent stem cells in rats", "dateAssigned" : "2021-06-22T00:00:00.000-05:00", "summary" : "In vitro generation of germ cells from pluripotent stem cells (PSCs) can crucially impact future reproductive medicine and animal breeding. A decade ago, in vitro gametogenesis was established in the mouse. However, induction of primordial germ cell-like cells (PGCLCs) to produce fertile gametes has not been achieved in any other species. Here, we demonstrate the induction of functional PGCLCs from rat PSCs. We show that epiblast-like cells in floating aggregates form rat PGCLCs. The gonadal somatic cells support maturation and epigenetic reprogramming of the PGCLCs. Notably, rat PGCLCs transplanted into the seminiferous tubules of germline-less rats produce spermatids, leading to the birth of viable offspring. Insights from our rat model will elucidate conserved and divergent mechanisms essential for the broad applicability of in vitro gametogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35389778" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178733" }, "primaryId" : "GEO:GSE178733", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178733" } ] }, "title" : "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits [snATAC-seq]", "dateAssigned" : "2021-06-23T00:00:00.000-05:00", "summary" : "Skeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases and mobility. It is composed of several different cell and muscle fiber types. Here, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell-specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We additionally perform multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33,862 nuclei and identify seven cell types ranging in abundance from 59.6% to 1.0% of all nuclei. We introduce a regression-based approach to infer cell types by comparing transcription start site-distal ATAC-seq peaks to reference enhancer maps and show consistency with RNA-based marker gene cell type assignments. We find heterogeneity in enrichment of genetic variants linked to complex phenotypes from the UK Biobank and diabetes genome wide association studies in cell-specific ATAC-seq peaks, with the most striking enrichment patterns in muscle mesenchymal stem cells (~3.5% of nuclei). Finally, we overlay these chromatin accessibility maps on GWAS data to nominate causal cell types, SNPs, transcription factor motifs, and target genes for type 2 diabetes signals. These chromatin accessibility profiles for human and rat skeletal muscle cell types are a useful resource for nominating causal GWAS SNPs and cell types.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34815310" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178734" }, "primaryId" : "GEO:GSE178734", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178734" } ] }, "title" : "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits [snRNA-seq]", "dateAssigned" : "2021-06-23T00:00:00.000-05:00", "summary" : "Skeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases and mobility. It is composed of several different cell and muscle fiber types. Here, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell-specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We additionally perform multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33,862 nuclei and identify seven cell types ranging in abundance from 59.6% to 1.0% of all nuclei. We introduce a regression-based approach to infer cell types by comparing transcription start site-distal ATAC-seq peaks to reference enhancer maps and show consistency with RNA-based marker gene cell type assignments. We find heterogeneity in enrichment of genetic variants linked to complex phenotypes from the UK Biobank and diabetes genome wide association studies in cell-specific ATAC-seq peaks, with the most striking enrichment patterns in muscle mesenchymal stem cells (~3.5% of nuclei). Finally, we overlay these chromatin accessibility maps on GWAS data to nominate causal cell types, SNPs, transcription factor motifs, and target genes for type 2 diabetes signals. These chromatin accessibility profiles for human and rat skeletal muscle cell types are a useful resource for nominating causal GWAS SNPs and cell types.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34815310" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178867" }, "primaryId" : "GEO:GSE178867", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178867" } ] }, "title" : "RNA-seq profiles of rat cardiomyocytes overexpressing hsa-miR-106b-5p, hsa-miR-93-5p, hsa-miR-25-3p or cel-miR-67", "dateAssigned" : "2021-06-24T00:00:00.000-05:00", "summary" : "Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. We report that the miR-106b~25cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. To identify the relevant targets of individual miRNAs in the miR-106b~15 cluster and elucidate the molecular mechanisms underlying the proliferative effects of this microRNA cluster, we assessed the global transcriptomic changes by deep-sequencing total neonatal mouse cardiomyocyte RNA after exogeneous transfection with hsa-miR-106b-5p, hsa-miR-93-5p, hsa-miR-25-3p and compared the transcriptomic profiles to cardiomyocytes transfected with cel-miR-67, a control miRNA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34376683" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178871" }, "primaryId" : "GEO:GSE178871", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178871" } ] }, "title" : "Differences in renal cortex transcriptional profiling of wild-type and novel type B cystinuria model rats", "dateAssigned" : "2021-06-24T00:00:00.000-05:00", "summary" : "Cystinuria is a genetic disorder of cystine transport that accounts for 1–2% of all cases of renal lithiasis. It is characterized by hyperexcretion of cystine in urine and recurrent cystine lithiasis. Defective transport of cystine into epithelial cells of renal tubules occurs because of mutations of the transport heterodimer, including protein b0,+AT (encoded by SLC7A9) and rBAT (encoded by SLC3A1) linked through a covalent disulfide bond. Study generated a novel type B cystinuria rat model by artificially deleting 7bp of Slc7a9 gene exon 3 using the CRISPR-Cas9 system, and those Slc7a9-deficient rats were proved to be similar with cystinuria in terms of genome, transcriptome, translation, and biologic phenotypes and typical secondary changes as medullary fibrosis. Study then established the first transcription database of type B cystinuria based on this novel cystinuria rat model. In accordance with the functional annotation of DEGs, the potential role of glutathione metabolism processes in kidney of cystinuria rat model was proposed, and KEGG analysis results showed that knock-out of Slc7a9 gene triggered more biological changes which has not been study. This rat model and its transcriptional database that mimics the pathogenesis and clinical consequences of human type B cystinuria was generated for a better understanding of pathophysiological mechanism underlying in cystinuria that can be used to provide references when looking for new target and strategies for reducing kidney damage of cystinuria patients.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35416493" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178950" }, "primaryId" : "GEO:GSE178950", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE178950" } ] }, "title" : "Effects of amiloride in lithium induced kidney interstitial fibrosis", "dateAssigned" : "2021-06-25T00:00:00.000-05:00", "summary" : "Result & Conclusion: Co-administration with amiloride at all time points contributed in the reduction of inflammation and fibrosis caused by lithium.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36028651" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179101" }, "primaryId" : "GEO:GSE179101", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179101" } ] }, "title" : "The transcriptome of rat hippocampal subfields", "dateAssigned" : "2021-06-29T00:00:00.000-05:00", "summary" : "Conclusion: The present findings contribute to a deeper understanding of the differences in the molecular machinery expressed by the rat hippocampal neuronal populations, further exploring underlying mechanisms responsible for each subflied specific functions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36247526" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179117" }, "primaryId" : "GEO:GSE179117", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179117" } ] }, "title" : "Next Generation Sequencing Quantitative Analysis of PCB-exposed and Sham-exposed Rats Liver, Brain, Thymus and Spleen Transcriptomes", "dateAssigned" : "2021-06-29T00:00:00.000-05:00", "summary" : "Our goal was to investigate the transcriptomes changes on rats liver, brain, thymus, and spleen after exposure to an indoor school air mixture (SAM+) of polychlorinated biphenyls (PCBs). Female Sprague-Dawley rats were exposed to SAM+ at a concentration of 45.5±5.9 µg/m^3 Σ209PCB or filtered air (sham group) 4 h/day, 6 days/week for 13 weeks using nose-only exposure systems. Twenty-four hours after the final exposure, rats were euthanized by carbon dioxide inhalation followed by cervical dislocation. Cardiac blood was collected and organs were excised and stored at -80 °C until analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179215" }, "primaryId" : "GEO:GSE179215", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179215" } ] }, "title" : "H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis [RNAseq]", "dateAssigned" : "2021-06-30T00:00:00.000-05:00", "summary" : "Epigenetic control of lineage-specific gene expression is essential for cell differentiation, acquisition of specialized functions, and tissue homeostasis. Here, we uncovered a unique epigenetic pathway critical for governing lineage identity in cells presenting milieu-dependent phenotypic modulation in adult organisms, by using vascular smooth muscle cells (SMC) as a model of highly specialized and differentiated cell type retaining phenotypic plasticity. We found that the histone modification H3K4me2 is essential for the maintenance of vascular SMC lineage identity and functions by performing H3K4me2 demethylation selectively on a SMC lineage-specific subset of genes. Removal of H3K4me2 on the myocardin-regulated genes led to a marked loss of contractility and alteration in SMC adaptive response capacities during vascular remodeling. Rather than presenting intrinsic gene activation properties, H3K4me2 serves as a stable preferential hub for the dynamic recruitment of the DNA methylcytosine dioxygenase Ten-Eleven Translocation 2 (TET2). Besides the SMC contractile apparatus, the H3K4me2/TET2 complex controls the expression of miR-145, a central microRNA promoting SMC differentiation and participation in vascular remodeling. Finally, H3K4me2 editing induced a profound loss of SMC lineage identity and gain of plasticity, characterized by the redistribution of H3K4me2 on genes associated with stemness and developmental programs and the greater ability of H3K4me2 edited SMC to transdifferentiate into other lineages. These studies identified H3K4me2 as a central epigenetic mechanism controlling lineage identity and cell-specific specialized functions. Our findings may have broad implications for the understanding of mechanisms controlling multiple plastic cell type behaviors and functions in various pathophysiological processes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35465051" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179217" }, "primaryId" : "GEO:GSE179217", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179217" } ] }, "title" : "H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis [CUT&Tag_H3K4me2_FLAG]", "dateAssigned" : "2021-06-30T00:00:00.000-05:00", "summary" : "Epigenetic control of lineage-specific gene expression is essential for cell differentiation, acquisition of specialized functions, and tissue homeostasis. Here, we uncovered a unique epigenetic pathway critical for governing lineage identity in cells presenting milieu-dependent phenotypic modulation in adult organisms, by using vascular smooth muscle cells (SMC) as a model of highly specialized and differentiated cell type retaining phenotypic plasticity. We found that the histone modification H3K4me2 is essential for the maintenance of vascular SMC lineage identity and functions by performing H3K4me2 demethylation selectively on a SMC lineage-specific subset of genes. Removal of H3K4me2 on the myocardin-regulated genes led to a marked loss of contractility and alteration in SMC adaptive response capacities during vascular remodeling. Rather than presenting intrinsic gene activation properties, H3K4me2 serves as a stable preferential hub for the dynamic recruitment of the DNA methylcytosine dioxygenase Ten-Eleven Translocation 2 (TET2). Besides the SMC contractile apparatus, the H3K4me2/TET2 complex controls the expression of miR-145, a central microRNA promoting SMC differentiation and participation in vascular remodeling. Finally, H3K4me2 editing induced a profound loss of SMC lineage identity and gain of plasticity, characterized by the redistribution of H3K4me2 on genes associated with stemness and developmental programs and the greater ability of H3K4me2 edited SMC to transdifferentiate into other lineages. These studies identified H3K4me2 as a central epigenetic mechanism controlling lineage identity and cell-specific specialized functions. Our findings may have broad implications for the understanding of mechanisms controlling multiple plastic cell type behaviors and functions in various pathophysiological processes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35465051" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179218" }, "primaryId" : "GEO:GSE179218", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179218" } ] }, "title" : "H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis [CUT&Tag_HA-TET2]", "dateAssigned" : "2021-06-30T00:00:00.000-05:00", "summary" : "Epigenetic control of lineage-specific gene expression is essential for cell differentiation, acquisition of specialized functions, and tissue homeostasis. Here, we uncovered a unique epigenetic pathway critical for governing lineage identity in cells presenting milieu-dependent phenotypic modulation in adult organisms, by using vascular smooth muscle cells (SMC) as a model of highly specialized and differentiated cell type retaining phenotypic plasticity. We found that the histone modification H3K4me2 is essential for the maintenance of vascular SMC lineage identity and functions by performing H3K4me2 demethylation selectively on a SMC lineage-specific subset of genes. Removal of H3K4me2 on the myocardin-regulated genes led to a marked loss of contractility and alteration in SMC adaptive response capacities during vascular remodeling. Rather than presenting intrinsic gene activation properties, H3K4me2 serves as a stable preferential hub for the dynamic recruitment of the DNA methylcytosine dioxygenase Ten-Eleven Translocation 2 (TET2). Besides the SMC contractile apparatus, the H3K4me2/TET2 complex controls the expression of miR-145, a central microRNA promoting SMC differentiation and participation in vascular remodeling. Finally, H3K4me2 editing induced a profound loss of SMC lineage identity and gain of plasticity, characterized by the redistribution of H3K4me2 on genes associated with stemness and developmental programs and the greater ability of H3K4me2 edited SMC to transdifferentiate into other lineages. These studies identified H3K4me2 as a central epigenetic mechanism controlling lineage identity and cell-specific specialized functions. Our findings may have broad implications for the understanding of mechanisms controlling multiple plastic cell type behaviors and functions in various pathophysiological processes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35465051" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179301" }, "primaryId" : "GEO:GSE179301", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179301" } ] }, "title" : "Mesenchymal stem cells exert renoprotection via extracellular vesicle-mediated modulation of M2 macrophages and spleen-kidney network.", "dateAssigned" : "2021-07-01T00:00:00.000-05:00", "summary" : "Adipose-derived mesenchymal stem cells (ASCs) have shown therapeutic potentials against refractory diseases. However, the detailed therapeutic mechanisms remain unclear. Here, we report the therapeutic actions of human ASCs in nephritis, focusing on cellular dynamics and multi-organ networks. Intravenously-administered ASCs accumulated in spleen but not kidneys. Nevertheless, ASCs increased M2 macrophages and Tregs in kidneys and drove strong renoprotection. Splenectomy abolished these therapeutic effects. ASC-derived extracellular vesicles (EVs) were transferred to M2 macrophages, which entered the bloodstream from spleen. EVs induced the transcriptomic signatures of hyperpolarization and PGE2 stimulation in M2 macrophages and ameliorated glomerulonephritis. ASCs, ASC-derived EVs, and EV-transferred M2 macrophages enhanced Treg induction. These findings suggest that EV transfer from spleen-accumulated ASCs to M2 macrophages and subsequent modulation of renal immune-environment underlie the renoprotective effects of ASCs. Our results provide new insights into the therapeutic actions of ASCs, focusing on EV-mediated modulation of macrophages and the spleen-kidney immune network.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35902687" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179370" }, "primaryId" : "GEO:GSE179370", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179370" } ] }, "title" : "Effect of bromodomain inhibitors on dopamine D1R induced gene expression in striatal neurons", "dateAssigned" : "2021-07-02T00:00:00.000-05:00", "summary" : "The dopamine D1R is Gs coupled GPCR which is expressed in striatal neurons and stimulates gene expression upon activation by dopamine or other agonists. In this work we investigated the role of the BET protein bromodomain containing protein 4 (Brd4) in mediating D1R-dependent gene expression in rat striatal neurons. Here we report the results of 3 RNA sequencing experiments. In Experiment 1 we treated primary striatal neurons with the D1R-selective agonist SKF-81297 alone or in combination with the non-selective BET inhibitor JQ1 for 60 minutes to assess the effect of BET inhibition on acute D1R-dependent gene expression. In Experiment 2, we treated primary striatal neurons with the D1R-selective agonist SKF-81297 alone or in combination with the BET bromodomain 2 selective inhibitor iBD2 for 60 minutes to determine the contribution of BD2 specifically to D1R-dependent gene expression. In Experiment 3 we treated primary striatal neurons with the D1R-selective agonist SKF-81297 alone or in combination with the non-selective BET inhibitor JQ1 for 24 hours to assess the effect of prolonged BET inhibition on basal gene expression and D1R-dependent gene expression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179378" }, "primaryId" : "GEO:GSE179378", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179378" } ] }, "title" : "A single dose of lysergic acid diethylamide influences gene expression patterns within the mammalian brain [array]", "dateAssigned" : "2021-07-03T00:00:00.000-05:00", "summary" : "We have undertaken the first comprehensive analysis of gene expression influenced by acute LSD administration in the mammalian brain to elucidate the mechanism of action of this class of drugs. We have identified a number of genes that are predicted to be involved in the processes of synaptic plasticity, glutamatergic signaling and cytoskeletal architecture. Understanding these molecular events will lead to new insights into the etiology of disorders whose behavioral symptoms resemble the temporary effects of hallucinogenic drugs, and also may ultimately result in new therapies.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34729786" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179379" }, "primaryId" : "GEO:GSE179379", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179379" } ] }, "title" : "Chronic LSD alters gene expression profiles in the mPFC relevant to schizophrenia [RNA-seq]", "dateAssigned" : "2021-07-03T00:00:00.000-05:00", "summary" : "Results: We observed widespread changes in the neurogenetic state of treated animals four weeks after cessation of LSD treatment. QPCR was used to validate a subset of gene expression changes observed with RNA-Seq, and confirmed a significant correlation between the two methods. Functional clustering analysis indicates differentially expressed genes are enriched in pathways involving neurotransmission (Drd2, Gabrb1), synaptic plasticity (Nr2a, Krox20), energy metabolism (Atp5d, Ndufa1) and neuropeptide signaling (Npy, Bdnf), among others. Many processes identified as altered by chronic LSD are also implicated in the pathogenesis of schizophrenia, and genes affected by LSD are enriched with putative schizophrenia genes. Our results provide a relatively comprehensive analysis of mPFC transcriptional regulation in response to chronic LSD, and indicate that the long-term effects of LSD may bear relevance to psychiatric illnesses, including schizophrenia.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34729786" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179383" }, "primaryId" : "GEO:GSE179383", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179383" } ] }, "title" : "Deciphering the conserved dynamic transcriptional signature and regulatory software governing neuronal fate commitment", "dateAssigned" : "2021-07-03T00:00:00.000-05:00", "summary" : "The transcriptional program underlying neuronal apoptosis and survival has to date been partially characterized. However, the complete spectrum of genes/proteins as well as the ‘regulatory software’ controlling neuronal fate decisions remain almost entirely unknown. Here, for the first time, we characterized the earliest molecular events following the induction of neuronal apoptosis and its rescue by three potent anti-apoptotic growth factors (GFs), in order to identify key genes and upstream regulators primarily responsible for driving execution of these processes. A core set of 175 survival-related genes (SRGs) with opposite transcriptional signatures between apoptosis and GF-mediated survival was identified. Promoter motif analysis of SRGs revealed a repertoire of intrinsic upstream regulators that may drive the apoptotic/survival switch, with Hoxd9 predicted to be the master regulator. Finally, the clinical implication of SRGs in the pathogenesis of neurological and neuropsychiatric diseases, here emerged, suggested their potential utility as targets for treating these severe disorders.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34831459" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179400" }, "primaryId" : "GEO:GSE179400", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179400" } ] }, "title" : "Quantitative transcriptome analysis of the repair mechanism of AKBA on the treatment of rat sciatic nerve injury", "dateAssigned" : "2021-07-03T00:00:00.000-05:00", "summary" : "The data obtained through differential mRNA expression analysis showed that 258 genes were significantly differentially expressed at the mRNA level in the AKBA group relative to in the model group . These genes included 189 upregulated genes and 69 downregulated genes. A total of 355 genes, including 194 upregulated genes and 161 downregulated genes, were significantly differentially expressed at the mRNA level in the AKBA group relative to in the sham operation group . A total of 410 genes, among which 171 were upregulated and 239 were downregulated, were significantly differentially expressed at the mRNA level in the sham operation group relative to in the model group. The results showed that significantly differentially expressed genes in the AKBA and model control groups were enriched in 193 pathways. The the highest enrichment the phagosome pathways.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35662229" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179405" }, "primaryId" : "GEO:GSE179405", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179405" } ] }, "title" : "Effect of Soluble Guanylyl Cyclase Stimulator Compound 1 on Renal function in ZSF-1 model of diabetic nephropathy", "dateAssigned" : "2021-07-03T00:00:00.000-05:00", "summary" : "Diabetic nephropathy is associated with endothelial dysfunction and oxidative stress, in which nitric oxide-soluble guanylate cyclase-cyclic guanosine monophosphate (NO-sGC-cGMP) signaling pathway is impaired. We hypothesize that sGC stimulator, Compound 1, can enhance NO signaling, reduce proteinuria in diabetic nephropathy pre-clinical model with diminished NO-bioavailability and increased oxidized sGC. We therefore, evaluated the effect of sGC stimulator Compound 1 on renal effect in obese ZSF1 rats. Materials and Methods: The sGC stimulator Compound 1, the standard of care agent enalapril, and combination of Compound 1 with enalapril was administered chronically to ZSF1 rats for 6 months. Mean arterial pressure, heart rate, creatinine clearance for estimate glomerular filtration rate (eGFR), urinary protein excretion to creatinine ratio (UPCR), and urinary albumin excretion ratio (UACR) were determined during the study. Histopathology of glomerular and interstitial lesions were assessed at the completion of the study. Results: While both Compound 1 and Enalapril significantly reduced blood pressure the combination of Compound 1 and enalapril normalized blood pressure level. Compound 1 improved eGFR and reduced UPCR and UACR. Combination of enalapril and Compound 1 resulted in marked reduction in UPCR and UACR and improved GFR. Conclusion: The sGC stimulator Compound 1 as a monotherapy slowed renal disease progression and the combination of sGC stimulator with enalapril provided a greater renal protection in a rodent model of diabetic nephropathy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179446" }, "primaryId" : "GEO:GSE179446", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179446" } ] }, "title" : "Integrative multi-omics approach for mechanism of humidifier disinfectant-associated lung injury [rat]", "dateAssigned" : "2021-07-05T00:00:00.000-05:00", "summary" : "Inhalation of toxic chemicals, including recent e-cigarettes, often cause life-threatening lung injury. Although exposure to polyhexamethylene guanidine (PHMG)-containing humidifier disinfectant (HD) has been identified as a cause of fatal lung injury, the mechanism underlying HD-associated lung injury (HDLI) is unknown. The present study evaluated global changes in gene expression in lung tissues from patients with PHMG-induced HDLI, and compared gene expression changes in PHMG-induced rat lung tissues. Significantly different expressions in lung tissues between patients with HDLI and unaffected controls were observed. Furthermore, several fibrosis-associated overlapping genes (such as MMP2 and COL1A2) shared between humans with HDLI and rats exposed to PHMG were identified. Interactome network analysis predicted different pathways between children and adults with HDLI: the TGFβ/SMAD signaling pathway was central in adults, whereas other pathways, including integrin signaling, were associated with HDLI in children. Further interactome network analysis revealed that Rap1 and CCKR signaling pathways were significantly enriched in HDLI compared with idiopathic pulmonary fibrosis as well as their recapitulation in the lung tissues of rats exposed to PHMG. Our results suggest that MMP2-mediated different mechanisms between children and adults may be associated with PHMG-induced HDLI development, and Rap1 and CCKR pathways appear to be crucial.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34841713" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179878" }, "primaryId" : "GEO:GSE179878", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179878" } ] }, "title" : "mRNA sequencing analysis on cardiofibroblasts exposed to reduced graphene oxide (rGO) Nanomaterials", "dateAssigned" : "2021-07-11T00:00:00.000-05:00", "summary" : "In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to rGO on cardiofibroblasts (CFs) cells. We performed mRNA sequencing experiments using CFs cells exposed to rGO for 24h.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34485415" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179945" }, "primaryId" : "GEO:GSE179945", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE179945" } ] }, "title" : "Glomerular Transcriptome from Experimental Nephrotic Syndrome Model and Treatment with PPARgamma Agonists", "dateAssigned" : "2021-07-12T00:00:00.000-05:00", "summary" : "Nephropathy was induced with puromycin amino-nucleoside (PAN) in Wistar rats and treated with daily treatments of Pioglitazone (Pio) and GQ-16. Total glomerular RNA was isolated, and mRNA libraries were generated and subjected to sequencing using NovaSeq6000 SP. Injury with PAN resulted in 1089 DEGs compared to controls, and 26 of these DEGs were restored by both Pio and GQ-16 treatments, whereas 106 unique GQ-16 regulated DEGs and 17 unique Pio-regulated DEGs were identified (Fig. 4A). Overall, Pio and GQ-16 treatment resulted in 75 and 173 DEGs compared to PAN injury, which included 29 common and 190 distinct genes (Fig. 4A). Of the 29 common DEGs, 28 DEGs were down-regulated by both Pio and GQ-16 and only 1 DEG upregulated by both treatments, when compared to PAN (Fig. 4B). Of the 190 distinct DEGs identified between Pio and GQ-16 treatments, 41 were down-regulated and 5 up-regulated by Pio and 124 down-regulated and 20 up-regulated by GQ-16 treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35310946" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180054" }, "primaryId" : "GEO:GSE180054", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180054" } ] }, "title" : "Converging Effects of Three Different Endocrine Disrupters on Sox and Pou Gene Expression in Developing Rat Hippocampus: Possible Role of microRNA in Sex Differences", "dateAssigned" : "2021-07-13T00:00:00.000-05:00", "summary" : "Abstract. Transcriptomes of developing, early postnatal rat hippocampus were compared after gestational and lactational exposure to different environmental chemicals exhibiting endocrine activity (endocrine disrupters) at doses impairing memory in adult offspring: Aroclor 1254 (PCB mixture) and bisphenol A, 5 or 0.5 mg/kg administered in chow, and chlorpyrifos, 3 or 1 mg/kg injected subcutaneously. All three chemicals exhibited a common effect on Sox6, Sox11, Pou2f2/Oct2, and Pou3f2/Brn2 in male hippocampus at the higher dose level. Additional Sox and Pou genes were affected by two treatments. Real time RT PCR in samples not used for transcriptomics confirmed the transcriptomics data and showed a comparable expression change for bisphenol A also at the lower dose. No changes were seen in female hippocampus. In the case of Sox6, gene network analyses indicated that miR-24 may be involved in the sexual dimorphism. This miR, which represses Sox6 and is repressed by estrogen receptor-alpa in other tissues, was downregulated by all chemicals in male but not female hippocampus. Sox6 expression levels of individual hippocampus samples (FPKM) were inversely correlated with expression levels of Pvalb, a downstream target of Sox6 and marker of an interneuron subpopulation, but not with markers of Sox6-independent interneuron subpopulations, Nos1 and 5HT3aR, indicating a selective effect on a hippocampal interneuron subpopulation. Effects on interneuron development are further suggested, in males, by changes in Nrg1 and Erbb4 expression controlling interneuron migration. Our investigation disclosed genes involved in cell-autonomous regulation of developmental processes as potential targets of endocrine disrupters. If corroborated by additional studies, they may serve as markers of early developmental effects in regulatory test development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34858468" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180160" }, "primaryId" : "GEO:GSE180160", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180160" } ] }, "title" : "Rat colonic tissue transcriptome with dietary intervention by freeze-dried baby spinach (10% w/w in AIN-93 diet)", "dateAssigned" : "2021-07-15T00:00:00.000-05:00", "summary" : "Polyposis in rat colon (Pirc) model harbors an Apc mutation and mimics human Familial Adenomatous Polyposis (FAP), allowing for intervention studies (e.g., PMID: 27706811, PMID: 30643017). RNA-sequencing of adenomatous polyps and normal colon identified genes altered by dietary spinach consumption.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34494932" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180354" }, "primaryId" : "GEO:GSE180354", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180354" } ] }, "title" : "Altered Genome-Wide Hippocampal Gene Expression Profiles Following Early Life Lead Exposure and their Potential for Reversal by Environmental Enrichment", "dateAssigned" : "2021-07-19T00:00:00.000-05:00", "summary" : "Developmental lead (Pb) exposure results in persistent cognitive/behavioral impairments as well as an elevated risk for developing a variety of diseases in later life. The quality of the environment can modify negative influences from Pb exposure. How the interaction between Pb and quality of the environment influences gene expression pattern in the brain affecting the development treajectory is unexplored. We used RNA-seq to examine how the interaction between developmental Pb exposure and living in an enriched versus a non-enriched environment affects genome-wide gene expression pattern in Hippocampus (HIPP) CA1.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35879375" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180609" }, "primaryId" : "GEO:GSE180609", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180609" } ] }, "title" : "Mutations of the histone linker H1-4 in neurodevelopmental disorders and functional characterization of neurons expressing C-terminus frameshift mutant H1.4 ", "dateAssigned" : "2021-07-21T00:00:00.000-05:00", "summary" : "Rahman syndrome (RMNS) is a rare genetic disorder characterized by mild to severe intellectual disability, hypotonia, anxiety, autism spectrum disorder, vision problems, bone abnormalities, and dysmorphic facies. De novo heterozygous mutations in H1-4 encoding the linker histone H1.4 are found in individuals with RMNS; however, the underlying mechanisms causing significantly impaired neurodevelopment are not understood. So far, all neurodevelopmental associated mutations in H1-4 are small insertions or deletions that create a shared frameshift, resulting in a H1.4 protein that is both truncated and possessing an abnormal C-terminus frameshifted tail (H1.4 CFT). To expand understanding of mutations and phenotypes associated with mutant H1-4, we identified additional and new DNA variants at both the C- and N-terminus of H1.4. The clinical features of mutations identified at the C-terminus are consistent with other reports that strengthen the support of pathogenicity of H1.4 CFT. However, the pathogenicity of disrupting variants at the N-terminus could not be determined. To understand how H1.4 CFT may disrupt brain function, we exogenously expressed wildtype or H1.4 CFT protein in primary rat hippocampal neurons and assessed neuronal structure and function. Genome-wide transcriptome analysis revealed ~400 genes altered specifically in the presence of H1.4 CFT. Neuronal genes downregulated by H1.4 CFT were enriched for functional categories involved in synaptic communication and neuropeptide signaling. Neurons expressing H1.4 CFT showed reduced activity on extracellular electrode arrays, indicating that these transcriptional changes were sufficient to disrupt physiological neuronal function. These data are the first to characterize the consequence of H1.4 CFT in neurons. Our data provide initial insights into causes of neurodevelopmental impairments associated with these frameshift mutations in the C-terminus of H1.4 and highlight the need for future studies on the function of normal histone H1.4 in neurons.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180643" }, "primaryId" : "GEO:GSE180643", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180643" } ] }, "title" : "Effect of volume overload on right ventricular remodeling in neonatal SD rats", "dateAssigned" : "2021-07-22T00:00:00.000-05:00", "summary" : "We reported the RNAseq analyses of right ventricualr free wall myocardium in neonatal volume overload (VO) SD rat. VO was induced by the fistula between abdominal aorta and inferior vena cava (AVF) within 24 hours postnatally (P1). RNAseq analyses of RV free wall at P7 from VO and sham-operated rat revealed that there were 454 differentially expressed genes between VO and sham group at P7. GO analysis showed that in the VO and sham comparison, the upregulated genes mainly mediated immune system response and the downregulated genes mainly mediated apoptotic process at P7. VO has no effect to neonatal right ventricular cardiomyocyte proliferation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34869688" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180673" }, "primaryId" : "GEO:GSE180673", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180673" } ] }, "title" : "The mRNA profile from rats ventral prostate submitted to maternal low protein diet", "dateAssigned" : "2021-07-22T00:00:00.000-05:00", "summary" : "Methods: Ventral Prostate mRNA profiles of 21- and 540-day-old control rats (CTR) and gestational and lactational low protein diet rats (GLLP) were generated by deep sequencing, in triplicate, using Illumina HiSeq-2500.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36499183" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180674" }, "primaryId" : "GEO:GSE180674", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180674" } ] }, "title" : "The miRNA profile from rats ventral prostate submitted to maternal low protein diet", "dateAssigned" : "2021-07-22T00:00:00.000-05:00", "summary" : "Methods: Ventral prostate microRNA profiles of 21- and 540-day-old control rats (CTR) and gestacional and lactacional low protein diet rats (GLLP) were generated by deep sequencing, in triplicate, using Illumina HiSeq-2500.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36499183" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180993" }, "primaryId" : "GEO:GSE180993", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180993" } ] }, "title" : "Activity-dependent history in hippocampal neurons dictates temporal dynamics of homeostatic synaptic scaling", "dateAssigned" : "2021-07-28T00:00:00.000-05:00", "summary" : "Neural circuits utilize a host of homeostatic plasticity mechanisms, including synaptic scaling, to maintain stability in circuits undergoing experience-dependent remodeling necessary for information processing. During synaptic scaling, compensatory adaptations in synaptic strength are induced after chronic manipulations in neuronal firing, but our understanding of this process is largely limited to its initial induction. How these homeostatic synaptic adaptations evolve when activity renormalizes and their impact on subsequent homeostatic compensation are both poorly understood. To examine these issues, we investigated whether a previous history of homeostatic scaling in networks of cultured hippocampal neurons altered their subsequent homeostatic responses to chronic activity manipulations. Unexpectedly, we found that a history of synaptic scaling strongly suppressed future scaling to the same, and even opposite, activity challenges. This history-dependent suppression was specific for future homeostatic compensation, as networks with a prior scaling history showed no deficits in the chemical induction of long-term potentiation (cLTP), a Hebbian form of synaptic plasticity. Hippocampal neurons with a prior scaling history exhibited normal engagement of activity-dependent signaling during subsequent activity challenges (as assessed by examination of the ERK/MAPK pathway) but demonstrated widespread alterations in activity-dependent transcriptional", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180996" }, "primaryId" : "GEO:GSE180996", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE180996" } ] }, "title" : "Identification of altered blood microRNAs in a rat model of Parkinson’s disease by Custom \"Brain Specific miRNA\" Open Array Real-time PCRpanel", "dateAssigned" : "2021-07-28T00:00:00.000-05:00", "summary" : "12 week male wistar rats were exposed with rotenone (2.5mg/kg b.wt.) and control rats exposed with vehicle (corn oil) intraperetonially for two months. Animals were sacrifised at the end of the experiment and blood was isolated and stored at -80°C in RNALater until further analysis.RNA (including small RNAs) was extracted by Ribopure Blood RNA Isolation Kit by Thermo Fisher as suggested protocol by manufacturer. A custom Taqman OpenArray panel was used to profile the miRNAs expression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181033" }, "primaryId" : "GEO:GSE181033", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181033" } ] }, "title" : "Serum Circulating Proteins from Pediatric Dilated Cardiomyopathy Patients Cause Pathologic Remodeling and Cardiomyocyte Stiffness [RNA-Seq]", "dateAssigned" : "2021-07-28T00:00:00.000-05:00", "summary" : "Dilated cardiomyopathy (DCM) is the most common form of cardiomyopathy and main indication for heart transplantation in children. Therapies specific to pediatric DCM remains limited due to lack of a disease model. Our previous study showed that treatment of neonatal rat ventricular myocytes (NRVMs) with non-failing or DCM pediatric patient serum activates the fetal gene program (FGP). Here we show that serum treatment with Proteinase K prevents activation of the FGP, whereas RNase treatment exacerbates it, suggesting that circulating proteins, but not circulating microRNAs, promote these pathological changes. Evaluation of the protein secretome showed that midkine (MDK) is up-regulated in DCM serum, and NRVM treatment with MDK activates the FGP. Changes in gene expression in serum-treated NRVMs, evaluated by next-generation RNA sequencing (RNA-Seq), indicates extracellular matrix remodeling and focal adhesion pathways are upregulated in pediatric DCM serum and serum-treated NRVMs, suggesting alterations in cellular stiffness. Cellular stiffness was evaluated by Atomic Force Microscopy, which showed an increase in stiffness in DCM serum-treated NRVMs. Of the proteins increased in DCM sera, secreted frizzled related protein 1 (sFRP1) was a potential candidate for the increase in cellular stiffness, and sFRP1 treatment of NRVMs recapitulated the increase in cellular stiffness observed in response to DCM-serum treatment. Our results show that serum circulating proteins promote pathological changes in gene expression and cellular stiffness, and circulating miRNAs are protective against pathological changes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34383712" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181092" }, "primaryId" : "GEO:GSE181092", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181092" } ] }, "title" : "Non-coding small RNA expression analysis of rat pancreatic acinar cells(AR42J) treated with sodium taurocholate", "dateAssigned" : "2021-07-29T00:00:00.000-05:00", "summary" : "Acute pancreatitis (AP) is a common digestive disorder with high morbidity and mortality. At present, the pathogenic mechanisms of AP remain unclear. Pancreatic acinar intracellular trypsinogen activation is considered to be an important cause of AP and is an important event in the early stages of AP. The activation of trypsinogen is a key factor for the pancreas to maintain normal function and that the abnormal activation of trypsinogen in pancreatic acinar cells is an initiating factor for the occurrence of AP. In the past decade, microRNA-related research results suggest that small non-coding RNAs play an important role in AP. Recently, endogenous transfer RNA-derived small RNA (tsRNA), a newly identified non-coding small RNA, is reported to be associated with multiple diseases. tsRNAs can be broadly classified into two main groups: tiRNAs (tRNA halves) and tRFs (tRNA-derived fragments). tiRNAs are produced by specific cleavage in the anticodon loop under various stress conditions (29-50 nucleotides). tRFs are separated to 4 subtypes by their sites of origin in pre-tRNA or mature tRNA, and generally shorter than tiRNAs (16-28 nucleotides). Similar to the function of microRNA, tsRNA can inhibit their functions by binding to target genes. However, the role of tsRNA in regulating AP pathogenesis has not been investigated. In this experiment, sodium taurocholate was used to treat the rat pancreatic acinar cell (AR42J) to establish the AP-related intracellular activation of trypsinogen model. Then we used RNA sequencing to identify the differentially expressed non-coding small RNAs including microRNA and tsRNA in the cell model.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181255" }, "primaryId" : "GEO:GSE181255", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181255" } ] }, "title" : "Increased sinusoidal pressure impairs liver endothelial mechanosensing pathways uncovering specific plasma biomarkers of portal hypertension.", "dateAssigned" : "2021-07-31T00:00:00.000-05:00", "summary" : "Abstract: Background and aims: Portal hypertension (PH) is the most frequent and severe clinical syndrome associated to chronic liver disease (CLD), defined by a pathological increase in the hepatic venous pressure gradient (HVPG). Considering the known mechanobiological effects of hydrostatic pressure and shear stress on endothelial cells, we hypothesized that PH could not only be a consequence of, but significantly influence the phenotype of liver sinusoidal endothelial cells (LSECs) during disease progression. The aim of this study was to investigate the effects of pathological hydrodynamic pressure on LSECs and to identify endothelial-derived biomarkers of PH. Methods: Primary LSECs were cultured under normal or increased hydrodynamic pressure within a pathophysiological range (1 vs 12 mmHg) using a microfluidic liver-on-a-chip device. RNAseq was used to identify pressure-sensitive genes, which were validated in liver biopsies from two independent cohorts of CLD patients with PH (n=73) vs subjects without PH (n=23). Biomarker discovery was performed in plasma from a third independent cohort of 64 patients (46 with PH vs 18 w/o). Results: Transcriptomic analysis revealed a marked deleterious effect of pathological pressure in LSECs and identified chromobox 7 (CBX7) as a key transcription factor diminished by pressure. Hepatic CBX7 downregulation was validated in patients with PH and significantly correlated with HVPG. MicroRNA 181a-5p was identified as pressure-induced upstream regulator of CBX7. Analysis of two downstream targets of CBX7, ECAD and SPINK1, were found increased in the bloodstream of patients with PH and were highly predictive of PH and clinically significant PH, with a sensitivity of 91.3% and 91.4% respectively. Conclusions: We describe the detrimental effects of increased hydrodynamic pressure on the sinusoidal endothelium, identify CBX7 as a pressure-sensitive transcription factor, and propose that the combination of two of its reported products could be used as plasma biomarkers of PH.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37151732" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181268" }, "primaryId" : "GEO:GSE181268", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181268" } ] }, "title" : "Sex-Dependent Changes of miRNA Levels in the Hippocampus of Adrenalectomized Rats Following Acute Corticosterone Administration", "dateAssigned" : "2021-08-01T00:00:00.000-05:00", "summary" : "We explored sex-biased effects of the primary stress glucocorticoid hormone corticosterone on the miRNA expression profile in the rat hippocampus. Adult adrenalectomized (ADX) female and male rats received a single corticosterone (10 mg/kg) or vehicle injection and after 6 h, hippocampi were collected for miRNA, mRNA and Western blot analyses. miRNA profiling microarrays showed a basal sex-biased miRNA profile in ADX rat hippocampi. Additionally, acute corticosterone administration triggered a sex-biased differential expression of miRNAs derived from genes located in several chromosomes and clusters on the X and 6 chromosomes. Putative promoter analysis unveiled that most corticosterone-responsive miRNA genes contained motifs for either direct or indirect glucocorticoid actions in both sexes. The evaluation of transcription factors indicated that almost 50 % of miRNA genes sensitive to corticosterone in both sexes was under glucocorticoid receptor regulation. Transcription factor-miRNA regulatory network analyses identified several transcription factors that regulate, activate or repress miRNA expression. Validated target mRNA analysis of corticosterone-responsive miRNAs showed a more complex miRNA-mRNA interaction network in males compared to females. Enrichment analysis revealed that several hippocampal-relevant pathways were affected in both sexes, such as neurogenesis and neurotrophin signaling. The evaluation of selected miRNA targets from these pathways displayed a strong sex difference in the hippocampus of ADX-vehicle rats. Corticosterone treatment did not change the levels of the miRNA targets and their corresponding tested proteins. Our data indicate that corticosterone exerts a sex-biased effect on hippocampal miRNA expression, which may engage in sculpting the basal sex differences observed at higher levels of hippocampal functioning.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34339164" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181275" }, "primaryId" : "GEO:GSE181275", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181275" } ] }, "title" : "RNA-seq profiling of colon and ileum tissues from the UC Davis Type 2 Diabetes Mellitus Rat Model", "dateAssigned" : "2021-08-01T00:00:00.000-05:00", "summary" : "The RNA-seq analysis continues our work profiling the the gastrointestinal tract of the UC Davis Type 2 Diabetes Mellitus (UCD-T2DM) Rat. Male UCD-T2DM rats (age ~170 days) were included in this study if either recently diagnosed as diabetic (n=6, RD, nonfasting glucose > 300 mg/dl) or 3-month post-onset of diabetes (n=6, D3M). A set of younger non-diabetic UCD-T2DM rats were also studied as a non-diabetic comparison (n=6, ND, age ~70 days).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34806320" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181296" }, "primaryId" : "GEO:GSE181296", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181296" } ] }, "title" : "Identification of differential gene expression profile in rats showing risk-averse and risk-seeking preferences in rat gambling task (rGT)", "dateAssigned" : "2021-08-02T00:00:00.000-05:00", "summary" : "In the present study, we examined using next-generation sequencing (NGS) whether there are differences in gene expression profiles in the brain when rats make different choices toward risk in rGT.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181362" }, "primaryId" : "GEO:GSE181362", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181362" } ] }, "title" : "Transcriptome Analysis Reviewed a Two-step Transformation of VSMCs to Macrophage-like Cells", "dateAssigned" : "2021-08-03T00:00:00.000-05:00", "summary" : "We report the transcriptome profiles of rat vascular smooth muscle cells (rVSMCs) treated by cholesterol loading or NOTCH inhibitor DAPT through RNA-Seq. rVSMCs were resistant to cholesterol loading alone that only promoted limited inflammatory responses. DAPT treatment alone also resulted in limited gene expression changes related with VSMC differentiations. Interestingly, cholesterol loading supplemented with DAPT resulted in significant changes of gene expression in rVSMCs and promoted VSMC-to-macrophage-like cell transformations.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35255257" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181380" }, "primaryId" : "GEO:GSE181380", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181380" } ] }, "title" : "Effect of Hirudin,Curcumin or Buyang Huanwu Formulas Exposure on Gene Expression of UUO rats", "dateAssigned" : "2021-08-03T00:00:00.000-05:00", "summary" : "We performed RNA-Seq analysis to investigate the gene expression patterns in the kidneys of rats with unilateral ureteral obstruction (UUO) treated with hirudin, curcumin or Buyang Huanwu Formula(BHF).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34621173" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181512" }, "primaryId" : "GEO:GSE181512", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181512" } ] }, "title" : "Next-generation sequencing facilitates quantitative analysis of rat BMSCs in soft or stiff SA hydrogel", "dateAssigned" : "2021-08-05T00:00:00.000-05:00", "summary" : "Conclusions: Our results present the detailed analysis of MSCs transcriptomes cultured in soft (2 kPa) and stiff (18 kPa) matrix, and found that matrix stiffness dominated multiple mRNA pathways in MSCs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181972" }, "primaryId" : "GEO:GSE181972", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181972" } ] }, "title" : "scRNA-seq analysis (well-based) of pharmacological HCN channel block with ZD7288 on rat primary cortical neuronal stem cells", "dateAssigned" : "2021-08-12T00:00:00.000-05:00", "summary" : "We analysed transcriptomic changes of single cell transcriptomes from primary rat cortical neuronal stem cells (NSC) after pharmacologically blocking HCN channels with ZD7288 compared to untreated NSC. This well-based scRNA-seq aproach revealed a pronounced cell cycle arrest in G1 phase of ZD7288 treated (HCN blocked) NSC.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34429357" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181979" }, "primaryId" : "GEO:GSE181979", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE181979" } ] }, "title" : "scRNA-seq analysis (drop-seq) of pharmacological HCN channel block with ZD7288 on rat primary cortical neuronal stem cells", "dateAssigned" : "2021-08-12T00:00:00.000-05:00", "summary" : "We analysed transcriptomic changes of single cell transcriptomes from primary rat cortical neuronal stem cells (NSC) after pharmacologically blocking HCN channels with ZD7288 compared to untreated NSC. This drop-seq scRNA-seq aproach showed accumulation of ZD7288 treated cells in G1 phase and confirmed our previous findings from a well-based scRNA-seq approach with cell cycle arrest in G1 after HCN channel block.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34429357" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182042" }, "primaryId" : "GEO:GSE182042", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182042" } ] }, "title" : "lncRNA-sequencing in a rat model of hypoxic pulmonary hypertension (HPH)", "dateAssigned" : "2021-08-13T00:00:00.000-05:00", "summary" : "lncRNA sequencing for 6 samples of the HPH (10% fractional inspired oxygen) and the control(N, 21% fractional inspired oxygen) groups.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34996349" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182054" }, "primaryId" : "GEO:GSE182054", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182054" } ] }, "title" : "m7G-MeRIP-sequencing in a rat model of hypoxic pulmonary hypertension (HPH)", "dateAssigned" : "2021-08-13T00:00:00.000-05:00", "summary" : "m7G-MeRIP-sequencing for 6 samples of the HPH (10% fractional inspired oxygen) and the control(N, 21% fractional inspired oxygen) groups.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34996349" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182360" }, "primaryId" : "GEO:GSE182360", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182360" } ] }, "title" : "Penetrating ballistic brain injury produces acute alterations in sleep and circadian-related genes in the rodent cortex: A preliminary study", "dateAssigned" : "2021-08-18T00:00:00.000-05:00", "summary" : "We performed transcriptional profiling in an established rodent model of penetrating ballistic brain injury (PBBI) in conjunction with continuous sleep pattern recording of the first 24 hours after injury. 12 adult male Sprague-Daley rats that were randomized to PBBI (n=6) or sham (n=6) groups, animals received a right unilateral frontal PBBI, then were sacrificed after 24 hours of EGG/EMG recording. Brains were harvested, underwent sectioning and cortical tissue samples were stored. RNA were isolated from tissue samples.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34777213" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182413" }, "primaryId" : "GEO:GSE182413", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182413" } ] }, "title" : "MiR-221/222 suppression induced by activation of the cAMP/PKA/CREB1 pathway is required for cAMP-induced bidirectional differentiation of glioma cells.", "dateAssigned" : "2021-08-19T00:00:00.000-05:00", "summary" : "Factors that increase cAMP levels can induce lineage-specific differentiation of glioma cells into astrocyte-like cells. However, the differentiation pattern and underlying mechanisms remain unclear. Here, we find that cAMP/PKA/CREB1-induced miR-221/222 suppression contributes to the neuron-like differentiation of gliomas. cAMP agonists selectively induced neuron- and astrocyte-like but not oligodendrocyte-like differentiation of C6 glioma cells. PKA inhibitors and CREB1 knockout blocked neuron-like differentiation of glioma cells. cAMP inhibited miR-221/222 in a PKA/CREB1 dependent manner. Importantly, both in vitro and in vivo assays demonstrated that transcriptional suppression of miR-221/222 is required for neuronal differentiation of glioma cells. Our findings suggest that increasing cAMP levels can induce bidirectional differentiation of glioma cells. Furthermore, the miR-221/222 cluster acts as an epigenetic brake during glioma differentiation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182422" }, "primaryId" : "GEO:GSE182422", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182422" } ] }, "title" : "AP-1 activation mediates postnatal cardiomyocyte maturation", "dateAssigned" : "2021-08-19T00:00:00.000-05:00", "summary" : "Mammalian cardiomyocytes rapidly mature after birth, with hallmarks such as cell-cycle exit, binucleation, and metabolic switch to oxidative phosphorylation of lipids. The causes and transcriptional programs regulating cardiomyocyte maturation are not fully understood yet. Thus, we performed single cell RNA-seq of neonatal and postnatal day 7 rat hearts to identify the key factors for this process and found AP-1 as a key factor to regulate cardiomyocyte maturation. To find the mechanism of AP-1 during cardiomyocyte maturation, we performed RNA-seq analysis of neonatal rat ventricular cardiomyocytes and found Ap-1 promote cardiomyocyte maturation by regulating cardiomyocyte metabolism.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182481" }, "primaryId" : "GEO:GSE182481", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182481" } ] }, "title" : "Effects of zinc ions and HrasG12V-activated signaling on gene expression of rat embryonic fibroblasts maintained in serum-free media", "dateAssigned" : "2021-08-19T00:00:00.000-05:00", "summary" : "To identify intracellular events affected by HrasG12V and zinc ion availability, gene expression profiling was performed with Rat-1·RasValA1, a stably transfected cell line where oncogenic mutant HrasG12V is expressed under the control of an IPTG-inducible promoter. Rat-1·RasValA1 cells were treated for 24 h with or without 5 mM IPTG in serum-free DMEM in the presence or absence of ZnCl2 supplementation at 3 microM. Total RNA was purified for gene expression profiling with microarray.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35212861" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182498" }, "primaryId" : "GEO:GSE182498", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182498" } ] }, "title" : "MiR-221/222 suppression induced by activation of the cAMP/PKA/CREB1 pathway is required for cAMP-induced bidirectional differentiation of glioma cells [miRNA]", "dateAssigned" : "2021-08-20T00:00:00.000-05:00", "summary" : "Factors that increase cAMP levels can induce lineage-specific differentiation of glioma cells into astrocyte-like cells. However, the differentiation pattern and underlying mechanisms remain unclear. Here, we find that cAMP/PKA/CREB1-induced miR-221/222 suppression contributes to the neuron-like differentiation of gliomas. cAMP agonists selectively induced neuron- and astrocyte-like but not oligodendrocyte-like differentiation of C6 glioma cells. PKA inhibitors and CREB1 knockout blocked neuron-like differentiation of glioma cells. cAMP inhibited miR-221/222 in a PKA/CREB1 dependent manner. Importantly, both in vitro and in vivo assays demonstrated that transcriptional suppression of miR-221/222 is required for neuronal differentiation of glioma cells. Our findings suggest that increasing cAMP levels can induce bidirectional differentiation of glioma cells. Furthermore, the miR-221/222 cluster acts as an epigenetic brake during glioma differentiation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182559" }, "primaryId" : "GEO:GSE182559", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182559" } ] }, "title" : "miRNA sequencing in liver of rats exposed to glyphosate, MON 52276, and a mixture of pesticides", "dateAssigned" : "2021-08-23T00:00:00.000-05:00", "summary" : "Small RNAs have emerged as a promising new type of biomarker to monitor health status and track the development of diseases. Here we report changes in the levels of small RNAs in the liver of rats exposed to a mixture (MIX) of six pesticides frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole), and glyphosate (G50) (50 mg/kg bw/day), or its representative EU commercial herbicide formulation Roundup MON 52276 (R50) at the same glyphosate equivalent doses in comparison to a control group (CON).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34850229" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182642" }, "primaryId" : "GEO:GSE182642", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182642" } ] }, "title" : "Exploring Relevant mRNAs and miRNAs in Injured Urethral Tissues of Rats with High-Throughput Sequencing [RNA-seq]", "dateAssigned" : "2021-08-24T00:00:00.000-05:00", "summary" : "Acute urethral injuries caused by urethral endoscopy and other mechanical injuries are the main reasons for secondary infection and late urethral stricture. However, there are no studies to explore the transcriptomic changes in urethral injury and the molecular mechanism of urethral injury, which is important for the treatment and cure of urethral injury. Therefore, we used RNA-seq and sRNA-seq profiles from normal and injured urethral tissues to identify and characterize differentially expressed mRNAs and miRNAs. In total, we found 166 differentially expressed mRNAs, of which 69 were upregulated, and 97 were downregulated in injured urethral tissues. The differentially expressed mRNAs were mainly involved in the positive regulation of epithelial cell differentiation, focal adhesion, cell adhesion molecules, protein activation cascade, complement activation, complement and coagulation cascades, and chemokine-mediated signaling pathway. Additionally, we found six upregulated and four downregulated miRNAs, respectively, in the injured urethral tissues. Notably, their target genes were involved in the vascular endothelial growth factor receptor 2 binding, PI3k-Akt signaling pathway, and Notch signaling pathway. In summary, our results suggest that the cell damage response induced by mechanical injury activates the pathological immune response in a variety of ways in injured urethral tissues.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35627209" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182675" }, "primaryId" : "GEO:GSE182675", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182675" } ] }, "title" : "The expression level of miRNAs in Control-EXO and RIPC-EXO", "dateAssigned" : "2021-08-24T00:00:00.000-05:00", "summary" : "To explore the possibility of miRNA(s) contributing to the cardioprotection induced by plasma exosomes at the late phase of RIPC, we performed a miRNA profiling assay (763 rat miRNAs) comparing the differences between RIPC-exo and Control-exo using Illumina HiSeq 2500 high-throughput sequencing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34917657" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182706" }, "primaryId" : "GEO:GSE182706", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182706" } ] }, "title" : "Algesic activity of the human coronavirus OC43 derived peptide", "dateAssigned" : "2021-08-24T00:00:00.000-05:00", "summary" : "The human coronavirus OC43 is responsible for 15-30% of seasonal “common cold” infections with typically mild respiratory symptoms. We demonstrated that the coronavirus OC43 derived small peptide encoded by the viral p65 proteins may exhibit molecular mimicry with the pro-algesic fragment of Myelin Basic Protein (MBP). After intrasciatic injection, the p65-derived peptide induced robust pain hypersensitivity in rats lasting for up to 21 days. Transcriptomic analysis at day 21 revealed extensive spinal up-regulation of pro-nociceptive genes. Strikingly, genome-wide isoform switching due to activation of transcriptional start sites and alternative splicing events has occurred. We hypothesized that the coronavirus-derived peptides can dysregulate MBP function in the PNS/CNS and promote neuropathic chronic pain. Our findings offer paradigm-shifting mechanistic understanding of the viral origin of idiopathic neurological effects including chronic neuropathic pain, a condition currently refractory to therapeutic treatment. This new knowledge will lead to new diagnostic, prognostic, and therapeutic approaches to benefit patients with chronic pain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35466531" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182796" }, "primaryId" : "GEO:GSE182796", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182796" } ] }, "title" : "Astrocyte-selective transduction with AAV5 viral vector does not exacerbate astrogliosis or alter tissue immune responses following spinal injury", "dateAssigned" : "2021-08-25T00:00:00.000-05:00", "summary" : "To investigate the effect of transgene expression within astrocytes upon the immunological state of the contused cord, we injected the astrocyte-selective AAV5-GfaABC1D-dYFP reporter vector into an animal model of moderate contusive spinal cord injury. Bulk RNA microarrays were used to assess transcriptomic changes of the perilesional tissue.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182860" }, "primaryId" : "GEO:GSE182860", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182860" } ] }, "title" : "DEN-induced rat model reproduces key features of human hepatocellular carcinoma", "dateAssigned" : "2021-08-26T00:00:00.000-05:00", "summary" : "Using RNA-seq analysis, we study a DEN-induced HCC rat model during fibrosis progression and HCC development with special focus on liver inflammatory microenvironment. RNA-seq results show that DEN-induced liver tumors in rat model share remarkable molecular characteristics with human HCC, especially with HCC associated with high proliferation. In conclusion, our study provides detailed insight into the hepatocarcinogenesis in a commonly used model of HCC, facilitating the future use of this model for preclinical testing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35805134" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182931" }, "primaryId" : "GEO:GSE182931", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182931" } ] }, "title" : "Time-restricted feeding prevents deleterious metabolic effects of circadian disruption through epigenetic control of β-cell function [RNAseq]", "dateAssigned" : "2021-08-27T00:00:00.000-05:00", "summary" : "Circadian rhythm disruption (CD) is associated with dysregulation of glucose homeostasis and Type 2 diabetes mellitus (T2DM). While the link between CD and T2DM remains unclear, there is accumulating evidence that disruption of fasting/feeding cycles mediates CD-induced metabolic dysfunction. Herein we utilized an approach encompassing analysis of behavioral, physiological, transcriptomic, and single-cell epigenomic effects of CD and consequences of restoration of fasting/feeding cycles through time-restricted feeding (tRF) in mice. Results show that CD perturbs glucose homeostasis through disruption of pancreatic β-cell function and loss of circadian β-cell transcriptional and epigenetic control. In contrast, restoration of fasting/feeding cycle prevented CD-mediated metabolic dysfunction by reestablishing circadian regulation of glucose tolerance, β-cell function, β-cell transcriptional profile, and reestablishment of proline and acidic amino acid-rich basic leucine zipper (PAR-bZIP) transcription factor activity in β-cells. This study provides mechanistic insights into beneficial effects of tRF and its role in prevention of β-cell failure in T2DM.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34910509" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182933" }, "primaryId" : "GEO:GSE182933", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182933" } ] }, "title" : "Time-restricted feeding prevents deleterious metabolic effects of circadian disruption through epigenetic control of β-cell function [ChIPseq]", "dateAssigned" : "2021-08-27T00:00:00.000-05:00", "summary" : "Circadian rhythm disruption (CD) is associated with dysregulation of glucose homeostasis and Type 2 diabetes mellitus (T2DM). While the link between CD and T2DM remains unclear, there is accumulating evidence that disruption of fasting/feeding cycles mediates CD-induced metabolic dysfunction. Herein we utilized an approach encompassing analysis of behavioral, physiological, transcriptomic, and single-cell epigenomic effects of CD and consequences of restoration of fasting/feeding cycles through time-restricted feeding (tRF) in mice. Results show that CD perturbs glucose homeostasis through disruption of pancreatic β-cell function and loss of circadian β-cell transcriptional and epigenetic control. In contrast, restoration of fasting/feeding cycle prevented CD-mediated metabolic dysfunction by reestablishing circadian regulation of glucose tolerance, β-cell function, β-cell transcriptional profile, and reestablishment of proline and acidic amino acid-rich basic leucine zipper (PAR-bZIP) transcription factor activity in β-cells. This study provides mechanistic insights into beneficial effects of tRF and its role in prevention of β-cell failure in T2DM.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34910509" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182947" }, "primaryId" : "GEO:GSE182947", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE182947" } ] }, "title" : "Exploring Relevant mRNAs and miRNAs in Injured Urethral Tissues of Rats with High-Throughput Sequencing [miRNA-seq]", "dateAssigned" : "2021-08-27T00:00:00.000-05:00", "summary" : "Acute urethral injuries caused by urethral endoscopy and other mechanical injuries are the main reasons for secondary infection and late urethral stricture. However, there are no studies to explore the transcriptomic changes in urethral injury and the molecular mechanism of urethral injury, which is important for the treatment and cure of urethral injury. Therefore, we used RNA-seq and sRNA-seq profiles from normal and injured urethral tissues to identify and characterize differentially expressed mRNAs and miRNAs. In total, we found 166 differentially expressed mRNAs, of which 69 were upregulated, and 97 were downregulated in injured urethral tissues. The differentially expressed mRNAs were mainly involved in the positive regulation of epithelial cell differentiation, focal adhesion, cell adhesion molecules, protein activation cascade, complement activation, complement and coagulation cascades, and chemokine-mediated signaling pathway. Additionally, we found six upregulated and four downregulated miRNAs, respectively, in the injured urethral tissues. Notably, their target genes were involved in the vascular endothelial growth factor receptor 2 binding, PI3k-Akt signaling pathway, and Notch signaling pathway. In summary, our results suggest that the cell damage response induced by mechanical injury activates the pathological immune response in a variety of ways in injured urethral tissues.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35627209" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183025" }, "primaryId" : "GEO:GSE183025", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183025" } ] }, "title" : "Excessive Branched Chain Amino Acid Accumulation Creates an Unfavourable Myocardial Milieu that Inhibits the Cardioprotective Effects of Implanted Mesenchymal Stem Cells in Ischemic Heart Injury [RNA-Seq]", "dateAssigned" : "2021-08-30T00:00:00.000-05:00", "summary" : "Myocardial infarction (MI) causes cardiac metabolic reprogramming and results in robust changes in intramyocardial metabolite composition, but little is known about how these metabolic changes influence the fate of implanted stem cells. We found that excessive branched chain amino acid (BCAA) accumulation, a metabolic signature of the post-infarcted heart, created an unfavorable milieu inhibiting the retention and cardioprotection of intramyocardially-delivered mesenchymal stem cells (MSCs). BCAA at pathological levels sensitized MSCs to the acquisition of a injured phenotype by suppressing the histone H3K9 trimethylation (H3K9me3) modification. Furthermore, a novel mTORC1/DUX4/KDM4E axis was identified as the cause of the H3K9me3 loss and adverse phenotype acquisition induced by BCAA. Enhancing BCAA catabolism in MSCs via genetic or pharmacological approaches improved their adaptation to the extracellular BCAA milieu and strengthened their cardioprotective efficacy. These findings reveal a critical role of myocardial metabolic reprogramming in regulating the fate and cardioprotection of implanted MSCs after MI.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183027" }, "primaryId" : "GEO:GSE183027", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183027" } ] }, "title" : "Excessive Branched Chain Amino Acid Accumulation Creates an Unfavourable Myocardial Milieu that Inhibits the Cardioprotective Effects of Implanted Mesenchymal Stem Cells in Ischemic Heart Injury [CUT&Tag]", "dateAssigned" : "2021-08-30T00:00:00.000-05:00", "summary" : "Myocardial infarction (MI) causes cardiac metabolic reprogramming and results in robust changes in intramyocardial metabolite composition, but little is known about how these metabolic changes influence the fate of implanted stem cells. We found that excessive branched chain amino acid (BCAA) accumulation, a metabolic signature of the post-infarcted heart, created an unfavorable milieu inhibiting the retention and cardioprotection of intramyocardially-delivered mesenchymal stem cells (MSCs). BCAA at pathological levels sensitized MSCs to the acquisition of a injured phenotype by suppressing the histone H3K9 trimethylation (H3K9me3) modification. Furthermore, a novel mTORC1/DUX4/KDM4E axis was identified as the cause of the H3K9me3 loss and adverse phenotype acquisition induced by BCAA. Enhancing BCAA catabolism in MSCs via genetic or pharmacological approaches improved their adaptation to the extracellular BCAA milieu and strengthened their cardioprotective efficacy. These findings reveal a critical role of myocardial metabolic reprogramming in regulating the fate and cardioprotection of implanted MSCs after MI.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183109" }, "primaryId" : "GEO:GSE183109", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183109" } ] }, "title" : "The Xiaogu San Attenuates Pain and Cartilage Damage in Rats with Monosodium Iodoacetate Induced Osteoarthritis", "dateAssigned" : "2021-08-31T00:00:00.000-05:00", "summary" : "Methods: A total of 24 Sprague Dawley rats were evenly and randomly divided into three separate groups including the normal control (NC), OA and XGS groups. MIA (50 μL, 10 mg/mL) was injected into the left knee joints of the rats to induce OA. After 7 days, The rats of XGS group were given XGS (0.45 g) that was externally applied to the left knee joint, were fixed with gauze and continuously administered XGS for 28 days. Morphological changes in tissues and organs were examined using H&E staining. Biochemical indicators were measured using an automatic biochemical analyzer. Inflammatory cytokines were detected using ELISA kits and immunohistochemistry. RNA-based high-throughput sequencing (RNA-seq) was performed to detect differential expression of mRNAs in normal and MIA–induced OA rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34629040" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183110" }, "primaryId" : "GEO:GSE183110", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183110" } ] }, "title" : "ETV2 regulates PARP-1 binding protein to induce ER stress-mediated cell death in tuberin-deficient cells", "dateAssigned" : "2021-08-31T00:00:00.000-05:00", "summary" : "We used microarrays to discern the potential difference in Syk inhibition and mTORC1-inhibition pathways. The goal was to investigate regulatory pathways or targets of Syk inhibition to induce cytocidal response in Tsc2-deficient cells, independent of its crosstalk with mTORC1 signaling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35181635" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183172" }, "primaryId" : "GEO:GSE183172", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183172" } ] }, "title" : "Deciphering responses of the fetal suprachiasmatic nuclei to the rhythmic maternal signals using omics approach", "dateAssigned" : "2021-09-01T00:00:00.000-05:00", "summary" : "We report circadian (time series, circadian time 0, 3, 6, 9, 12, 18, 21h) transcriptomic analysis of mouse fetal (embryonic day 17) suprachiasmatic nuclei (SCN) from either sham operarated ad libitum fed mothers (group A) or from SCN-lesioned mothers on resctricted feeding regime. The analysis revealed low amplitude rhythms in the fetal SCN driven by maternal SCN and/or maternal feeding behavior.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35609026" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183174" }, "primaryId" : "GEO:GSE183174", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183174" } ] }, "title" : "Cadherin-12 regulates neurite outgrowth through PKA/Rac1/Cdc42 pathway in cortical neurons", "dateAssigned" : "2021-09-01T00:00:00.000-05:00", "summary" : "Cadherins play an important role in tissue homeostasis, as they are responsible for cell-cell adhesion during embryogenesis, tissue morphogenesis, and differentiation. In this study, we identified Cadherin-12 (CDH12), which encodes a type II classical cadherin, as a gene to promote neurite outgrowth in a vitro model consist of neurons with differentiated intrinsic growth ability. First, the effects of CDH12 on neurons were evaluated by RNA interference, and the result indicated that the knock down of CDH12 expression restrained the axon extension of E18 neurons. The transcriptome profile of the neurons with or without siCDH12 treatment revealed a set of pathways positively correlated with the effect of CDH12 on neurite outgrowth. We further revealed that CDH12 affected Rac1/Cdc42 phosphorylation in PKA dependent manner by testing with H-89 and 8-Bromo-cAMP sodium salt. Moreover, we investigated the expression of CDH12 in brain, spinal cord, and dorsal root ganglion during development by using immunofluorescence staining. Thereafter, we explored the effects of CDH12 on neurite outgrowth in vivo. A zebrafish model of CDH12 knockdown was established by using NgAgo-gDNA system and registered the vital role of CDH12 in peripheral neurogenesis. In summary, our study is the first to report the effect of CDH12 on axonal extension in vitro and in vivo and we provided a preliminary explanation for the mechanism.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34820384" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183339" }, "primaryId" : "GEO:GSE183339", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183339" } ] }, "title" : "RNA sequencing of lung tissue from Angiotensin2/TRV023/losartan treated MCT rats", "dateAssigned" : "2021-09-03T00:00:00.000-05:00", "summary" : "We report the application of RNA sequencing in lung tissues of MCT rats, that were treated with Angiotensin 2 or TRV023 or Losartan to study their effects on Pulmonary hypertension. We received FPKM data of each gene from each group of MCT rats. The gene expression of the study MCT rats were normalized to control MCT rat. The differentially expressed genes in Angiotensin 2 and TRV023 treated MCT rats, confirmed that like Angiotensin 2, TRV023 is also involved in vascular remodelling and lead to worsening of pulmonary hypertension.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183386" }, "primaryId" : "GEO:GSE183386", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183386" } ] }, "title" : "Molecular profiling in the Habenula of Rat Chronic Restaint Stress Model", "dateAssigned" : "2021-09-03T00:00:00.000-05:00", "summary" : "Chronic stressful situations contribute to the risk of developing depression. Using Genome-wide gene expression analysis, we analyzed the habenula transcriptome of rats exposed to chronic restraint stress for 14 days. We selected 379 differentially expressed genes (DEGs) affected by chronic stress. From 379 DEGs, neuroactive ligand-receptor interaction, cAMP signaling pathway, circadian entrainment and synaptic signaling on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, response to corticosteroid, positive regulation of lipid transport, anterograde trans-synaptic signaling, chemical synapse transmission on Gene Ontology (GO) pathway analysis was identified as significantly enriched pathways. We made a protein-protein interaction network of DEGs and analyzed subclusters, and neuroactive ligand-receptor interaction, circadian entrainment, and cholinergic synapse-related clusters were identified. To validate the findings, quantitative RT-PCR was done for significant genes. Identified DEGs and pathways could be important factors modulating habenular response to stress and lead to behavioral change. These data identify key molecular targets involved in chronic stress-induced depression within habenula and provides a valuable resource for future study.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35534192" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183460" }, "primaryId" : "GEO:GSE183460", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183460" } ] }, "title" : "Expression data from normo- and hypoosmotic perfused rat liver [120min]", "dateAssigned" : "2021-09-05T00:00:00.000-05:00", "summary" : "We used microarrays to detail differential gene expression in perfused rat liver after 180 min under normo- and hypoosmotic condition.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35287291" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183461" }, "primaryId" : "GEO:GSE183461", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183461" } ] }, "title" : "Expression data from normo- and hypoosmotic perfused rat liver [180min]", "dateAssigned" : "2021-09-05T00:00:00.000-05:00", "summary" : "We used microarrays to detail differential gene expression in perfused rat liver after 180 min under normo- and hypoosmotic condition.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35287291" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183503" }, "primaryId" : "GEO:GSE183503", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183503" } ] }, "title" : "Development of Specific Therapy Against Right Ventricular Failure (in vitro analysis)", "dateAssigned" : "2021-09-06T00:00:00.000-05:00", "summary" : "Right ventricular (RV) failure plays a critical role in any type of heart failure. However, there is no specific therapy developed for RV failure. To understand RV failure, we focused on the RV specific genes. Global gene expression analysis showed that alternative complement pathway-related genes including C3 and Cfd were significantly upregulated in right ventricle in murine heart. We generated the RV failure by right ventricle-specific pressure overload model mice, pulmonary artery constriction (PAC), which induces RV failure around 14 days. After administration of C3a receptor (C3aR) antagonist, RV function was dramatically improved PAC-induced RV dysfunction in wild type mice. To investigate the role of C3a to cardiomyocyte, C3a recombinant protein was administerd to neonatal rat ventricular myocytes (NRVMs), the results that several MAP kinesis were phosphorylated by C3a. In turn, to identify the key expressed genes as downstream of C3a in NRVMs, global gene expression analysis was performed in vitro.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36109509" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183591" }, "primaryId" : "GEO:GSE183591", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183591" } ] }, "title" : "Transcriptional study of the temporal evolution after severe traumatic spinal cord injury (SCI) and neural progenitor cells (NPCs)-transplantation intervention.", "dateAssigned" : "2021-09-07T00:00:00.000-05:00", "summary" : "This transcriptional profile analysis of total RNA samples from spinal cord homogenates of adult rats (Sprague Dawley) provides tissular (tought not cell-type specific) information of the critical time points after the injury from 1 to 8 weeks (acute, sub-acute and early-chronic and late-chronic stages) which conferred a wide temporal coverage making it ideal for studying the temporal dynamics of SCI. Furthermore, we have evaluated the impact of intramedullary acute or subacute transplantation of NPCs over the transcriptional regulation of the spinal cord tissue in order to define the functional outcomes of the NPCs therapy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35904607" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183705" }, "primaryId" : "GEO:GSE183705", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183705" } ] }, "title" : "Transcriptomic changes and toxicologic potential of per/polyflourinated alkyl substances (pfas) in laboratory animals via gavage", "dateAssigned" : "2021-09-08T00:00:00.000-05:00", "summary" : "The US EPA has identified a number of PFAS and other chemicals of high priority to States and Regional EPA offices that have no available in vivo toxicology data. Based on the list of data-poor chemicals and availability of the chemicals, four were selected for 5-day hepatic and renal transcriptomic assessments in male and female Hsd: Sprague Dawley (SD) rats. These data will be used for determining provisional pathway-based transcriptomic BMDs for use in human health risk estimations. Traditional toxicological endpoints (e.g. organ weights and clinical chemistry) have been added to the studies to provide additional contextualizaing information (i.e., phenotypic anchoring).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183839" }, "primaryId" : "GEO:GSE183839", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183839" } ] }, "title" : "Single cell transcriptomics and chromatin accessibility profiling elucidate the kidney protective mechanism of mineralocorticoid receptor antagonism [snRNA-seq]", "dateAssigned" : "2021-09-09T00:00:00.000-05:00", "summary" : "Mineralocorticoids play a critical role in maintaining sodium and potassium homeostasis and pathophysiological processes including hypertrophy, inflammation and fibrosis. Mineralocorticoid antagonists (MRAs) have shown to protect from kidney and heart disease, however, their molecular mechanism of action is poorly understood. Here we performed single nuclei and bulk transcriptomics and chromatin accessibility analysis to characterize the mode of kidney protection by steroidal and non-steroidal MRA treatment in a rat model of mineralocorticoid-induced cardiorenal end-organ damage. We define mineralocorticoid sensitive cell types and gene network in the kidney. We show that in diseased kidneys specific proximal tubule cells develop an injured profibrotic phenotype expressing Spp1 and Il34. Nonsteroidal finerenone protects from profibrotic differentiation of proximal tubule cells. Profibrotic gene signature can classify human kidney tissue samples and predict prognosis. Our multi-omics approach elucidates target cell types and potential mechanisms of renal protection by finerenone.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37906287" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183840" }, "primaryId" : "GEO:GSE183840", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183840" } ] }, "title" : "Single cell transcriptomics and chromatin accessibility profiling elucidate the kidney protective mechanism of mineralocorticoid receptor antagonism [snATAC-seq]", "dateAssigned" : "2021-09-09T00:00:00.000-05:00", "summary" : "Mineralocorticoids play a critical role in maintaining sodium and potassium homeostasis and pathophysiological processes including hypertrophy, inflammation and fibrosis. Mineralocorticoid antagonists (MRAs) have shown to protect from kidney and heart disease, however, their molecular mechanism of action is poorly understood. Here we performed single nuclei and bulk transcriptomics and chromatin accessibility analysis to characterize the mode of kidney protection by steroidal and non-steroidal MRA treatment in a rat model of mineralocorticoid-induced cardiorenal end-organ damage. We define mineralocorticoid sensitive cell types and gene network in the kidney. We show that in diseased kidneys specific proximal tubule cells develop an injured profibrotic phenotype expressing Spp1 and Il34. Nonsteroidal finerenone protects from profibrotic differentiation of proximal tubule cells. Profibrotic gene signature can classify human kidney tissue samples and predict prognosis. Our multi-omics approach elucidates target cell types and potential mechanisms of renal protection by finerenone.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37906287" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183841" }, "primaryId" : "GEO:GSE183841", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183841" } ] }, "title" : "Single cell transcriptomics and chromatin accessibility profiling elucidate the kidney protective mechanism of mineralocorticoid receptor antagonism [bulk RNA-seq]", "dateAssigned" : "2021-09-09T00:00:00.000-05:00", "summary" : "Mineralocorticoids play a critical role in maintaining sodium and potassium homeostasis and pathophysiological processes including hypertrophy, inflammation and fibrosis. Mineralocorticoid antagonists (MRAs) have shown to protect from kidney and heart disease, however, their molecular mechanism of action is poorly understood. Here we performed single nuclei and bulk transcriptomics and chromatin accessibility analysis to characterize the mode of kidney protection by steroidal and non-steroidal MRA treatment in a rat model of mineralocorticoid-induced cardiorenal end-organ damage. We define mineralocorticoid sensitive cell types and gene network in the kidney. We show that in diseased kidneys specific proximal tubule cells develop an injured profibrotic phenotype expressing Spp1 and Il34. Nonsteroidal finerenone protects from profibrotic differentiation of proximal tubule cells. Profibrotic gene signature can classify human kidney tissue samples and predict prognosis. Our multi-omics approach elucidates target cell types and potential mechanisms of renal protection by finerenone.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37906287" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183857" }, "primaryId" : "GEO:GSE183857", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE183857" } ] }, "title" : "Angiotensin II-induced long non-coding RNA Alivec regulates chondrogenesis in vascular smooth muscle cells", "dateAssigned" : "2021-09-09T00:00:00.000-05:00", "summary" : "We used microarrays to investigate Alivec-mediated global gene expression and identified distinct classes of up- and down-regulated genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34685676" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184026" }, "primaryId" : "GEO:GSE184026", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184026" } ] }, "title" : "A critical role for thrombin in regulating chondrocytes catabolism through RNA-Seq and experimental validation", "dateAssigned" : "2021-09-13T00:00:00.000-05:00", "summary" : "Conclusions: Thrombin stimulated the proliferation and promoted the morphology transformation towards fibrotic chondrocytes. Thrombin improved the chondrocytes’ catabolism by regulating the expression of the key enzymes which were responsible for ECMsynthesis. Meanwhile thrombin increased the expression of MMPs and chemokines that aimed at extracellular ECM degradation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184067" }, "primaryId" : "GEO:GSE184067", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184067" } ] }, "title" : "Exosomal microRNA sequencing in Tongxinluo pretreated and non-treated MSC-derived exosomes", "dateAssigned" : "2021-09-14T00:00:00.000-05:00", "summary" : "In order to investigate the specific mechanisms underlying the cardioprotective effects of Tongxinluo pretreated MSC-derived exosomes (MSCTXL-Exo) in cardiac repair, we performed microRNA sequencing on exosomes secreted from Tongxinluo pretreated MSCs and non-treated MSCs to identify differentially expressed miRNA. We found that 18 miRNAs were identified to be upregulated and 25 miRNAs downregulated (over 2-fold change) in MSCTXL-Exo compared to MSC-Exo.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184095" }, "primaryId" : "GEO:GSE184095", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184095" } ] }, "title" : "Breast cancer prevention by short-term inhibition of TGFβ signaling", "dateAssigned" : "2021-09-14T00:00:00.000-05:00", "summary" : "Cancer prevention has a profound impact on cancer-associated mortality and morbidity. We previously identified TGFβ signaling as a candidate regulator of mammary epithelial cells associated with breast cancer risk. Here, we show that short-term TGFBR inhibitor (TGFBRi) treatment of peripubertal ACI inbred and Sprague Dawley outbred rats induces lasting changes and prevents estrogen- and carcinogen-induced mammary tumors, respectively. We identify TGFBRi-responsive cell populations by single cell RNA-sequencing, including a unique epithelial subpopulation designated secretory basal cells (SBCs) with progenitor features. We detect SBCs in normal human breast tissues and find them to be associated with breast cancer risk. Interactome analysis identifies SBCs as the most interactive cell population and the main source of insulin-IGF signaling. Accordingly, inhibition of TGFBR and IGF1R decrease proliferation of organoid cultures. Our results reveal a critical role for TGFβ in regulating mammary epithelial cells relevant to breast cancer and serve as a proof-of-principle cancer prevention strategy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36476730" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184120" }, "primaryId" : "GEO:GSE184120", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184120" } ] }, "title" : "Mechanisms of Sinoatrial Node Dysfunction in Heart Failure with Preserved Ejection Fraction", "dateAssigned" : "2021-09-14T00:00:00.000-05:00", "summary" : "RNA sequencing from sinoatrial node tissue was performed to identify transcriptomic changes in Dahl salt-sensitive rats fed with normal salt diet (0.4% NaCl, control group) or high-salt diet (8% NaCl, HFpEF group) for 11 weeks. Transcriptomic profiling revealed numerous changes in multiple disease-associated genes in HFpEF, which is functionally related to the observed physiological impairments and structural remodeling.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34905696" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184280" }, "primaryId" : "GEO:GSE184280", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184280" } ] }, "title" : "Deciphering the role of 3D genome organization in breast cancer susceptibility (Hi-C)", "dateAssigned" : "2021-09-16T00:00:00.000-05:00", "summary" : "Cancer risk by environmental exposure is modulated by an individual’s genetics and age at exposure. This age-specific period of susceptibility is referred to as a “Window of Susceptibility” (WOS). Radiation exposures poses a high breast cancer risk for women between the early childhood and young adult stage and is reduced in the mid-30s. Rats have a similar WOS for developing breast cancer. Previous studies have identified a looping interaction between a genomic region in the mammary carcinoma susceptibility Mcs5c locus and a known cancer gene, PAPPA. However, the global role of three-dimensional organization in the WOS is not known. Therefore, we generated Hi-C and RNA-seq data in rat mammary epithelial cells within and outside WOS. We compared the temporal changes in chromosomal looping to those in expression and find that interactions that have significantly higher counts within WOS are significantly enriched for genes upregulated in WOS. To systematically identify higher-order changes in 3D genome organization, we developed an approach that combines network enhancement to smooth the Hi-C matrices followed by multitask non-negative matrix factorization (NMF) to identify clusters of interacting loci. We found that large-scale topological re-organizations are enriched for differential interactions within and outside the WOS timepoints. Finally, we mapped previously published breast-cancer associated human GWAS variants to rat loci and identified the corresponding rat ortholog gene interacting with the loci. Many of the associated rat genes participate in differential interactions, recapitulate the human SNP- gene interactions and are associated with breast cancer. Our results suggest that WOS-specific changes in 3D genome organization are linked to transcriptional changes that may increase susceptibility to breast cancer.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35087569" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184284" }, "primaryId" : "GEO:GSE184284", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184284" } ] }, "title" : "Deciphering the role of 3D genome organization in breast cancer susceptibility (RNA-Seq)", "dateAssigned" : "2021-09-16T00:00:00.000-05:00", "summary" : "Cancer risk by environmental exposure is modulated by an individual’s genetics and age at exposure. This age-specific period of susceptibility is referred to as a “Window of Susceptibility” (WOS). Radiation exposures poses a high breast cancer risk for women between the early childhood and young adult stage and is reduced in the mid-30s. Rats have a similar WOS for developing breast cancer. Previous studies have identified a looping interaction between a genomic region in the mammary carcinoma susceptibility Mcs5c locus and a known cancer gene, PAPPA. However, the global role of three-dimensional organization in the WOS is not known. Therefore, we generated Hi-C and RNA-seq data in rat mammary epithelial cells within and outside WOS. We compared the temporal changes in chromosomal looping to those in expression and find that interactions that have significantly higher counts within WOS are significantly enriched for genes upregulated in WOS. To systematically identify higher-order changes in 3D genome organization, we developed an approach that combines network enhancement to smooth the Hi-C matrices followed by multitask non-negative matrix factorization (NMF) to identify clusters of interacting loci. We found that large-scale topological re-organizations are enriched for differential interactions within and outside the WOS timepoints. Finally, we mapped previously published breast-cancer associated human GWAS variants to rat loci and identified the corresponding rat ortholog gene interacting with the loci. Many of the associated rat genes participate in differential interactions, recapitulate the human SNP- gene interactions and are associated with breast cancer. Our results suggest that WOS-specific changes in 3D genome organization are linked to transcriptional changes that may increase susceptibility to breast cancer.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35087569" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184294" }, "primaryId" : "GEO:GSE184294", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184294" } ] }, "title" : "N6-methyladenosine RNA methylome analyses in cyclophosphamide-treated neonatal rat cardiac myocytes.", "dateAssigned" : "2021-09-16T00:00:00.000-05:00", "summary" : "To identify N6-methyladenosine RNA methylome in cyclophosphamide-treated neonatal rat cardiac myocytes (NRCMs), MeRIP-seq of NRCMs treated with cyclophosphamide (CYP) or solvent control (DMSO) were performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34820430" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184308" }, "primaryId" : "GEO:GSE184308", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184308" } ] }, "title" : "The synthetic triterpenoid RTA-408 limits radiation damage to normal tissue", "dateAssigned" : "2021-09-16T00:00:00.000-05:00", "summary" : "Results: In the first experiment, 40 rats were divided into the three groups and underwent treatment accordingly. The average flap necrosis was 20% (95% CI, 16-45%) in the radiation control group, 3% (95% CI, 0-11%) in the non-irradiated control, and 3% (95% CI, 0.2-10%) in the radiation group treated with RTA-408. Vascular density was preserved in the treatment group as compared to the radiated control. Nine rats were included in the second experiment, and transcriptome analyses in the treatment group revealed robust activation of antioxidant pathways with induced expression of genes associated with hypoxia and adipogenesis/angiogenesis. Conclusions: Administration of RTA-408 during radiation treatment in a rat model resulted in transcriptome changes which appear to mitigate the toxic effects of radiation, preserving capillary networks and improving flap survival and tissue healing after subsequent surgery. Such reductions in toxicity may have broad implications for functional outcomes and salvage surgery following therapeutic irradiation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34709651" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184319" }, "primaryId" : "GEO:GSE184319", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184319" } ] }, "title" : "The astroglial and stem cell functions of adult rat folliculostellate cells", "dateAssigned" : "2021-09-16T00:00:00.000-05:00", "summary" : "The mammalian pituitary gland is a complex organ consisting of hormone-producing cells, anterior lobe folliculostellate cells (FSCs), posterior lobe pituicytes, vascular pericytes and endothelial cells, and Sox2-expressing stem cells. We present single-cell RNA sequencing and immunohistofluorescence analyses of pituitary cells of adult female rats with a focus on the transcriptomic profiles of nonhormonal cell types. Samples obtained from whole pituitaries and separated anterior and posterior lobe cells contained all expected pituitary resident cell types and lobe-specific vascular cell subpopulations. FSCs and pituicytes expressed S100B, ALDOC, EAAT1, ALDH1A1, and VIM genes and proteins, as well as other astroglial marker genes, some common and some cell type-specific. We also found that the SOX2 gene and protein were expressed in ~15% of pituitary cells, including FSCs, pituicytes, and a fraction of hormone-producing cells, arguing against its stem cell specificity. FSCs comprised two Sox2-expressing subclusters; FS1 contained more cells but lower genetic diversity, while FS2 contained proliferative cells, shared genes with hormone-producing cells, and expressed genes consistent with stem cell niche formation, regulation of cell proliferation and stem cell pluripotency, including the Hippo and Wnt pathways. FS1 cells were randomly distributed in the anterior and intermediate lobes, while FS2 cells were localized exclusively in the marginal zone between the anterior and intermediate lobes. These data indicate the identity of the FSCs as anterior pituitary-specific astroglia, with FS1 cells representing differentiated cells equipped for classical FSC roles and FS2 cells exhibiting additional stem cell-like features.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35058881" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184410" }, "primaryId" : "GEO:GSE184410", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184410" } ] }, "title" : "Mouse DNA methylation atlas using Infinium Mouse Methylation Beadchips", "dateAssigned" : "2021-09-19T00:00:00.000-05:00", "summary" : "Design, annotation, and technical and biological validation of the MouseMethylation Beadchips (MM285) platform. Application of the mouse array for tissue and tumor epigenetics, comparative epigenomics, genomic imprinting, epigenetic inhibitors, PDX assessment, backcross tracing, and epigenetic clocks.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36617464" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184413" }, "primaryId" : "GEO:GSE184413", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184413" } ] }, "title" : "Mechanotherapy promotes extracellular matrix remodeling in aged rat muscle recovering from disuse by reprogramming intercellular communication", "dateAssigned" : "2021-09-19T00:00:00.000-05:00", "summary" : "A mechanistic understanding of the age-related impairment to skeletal muscle regrowth following disuse atrophy as well as therapies to augment recovery in the aged are currently lacking. Mechanotherapy in the form of cyclic compressive loading has been shown to benefit skeletal muscle under a variety of paradigms, but not during the recovery from disuse in aged muscle. To determine whether mechanotherapy promotes extracellular matrix (ECM) remodeling, a critical aspect of muscle recovery after atrophy, we performed single cell RNA sequencing (scRNA-seq) of gastrocnemius muscle cell populations, stable isotope tracing of intramuscular collagen, and histology of the ECM in adult and aged rats recovering from disuse, with and without mechanotherapy. ECM remodeling-related gene expression in fibro-adipose progenitor cells (FAPs) was absent in aged compared to adult muscle following 7 days of recovery, and instead were enriched in chemoattractant genes. There was a significantly lower expression of genes related to phagocytic activity in aged macrophages during recovery, despite enriched chemokine gene expression of numerous stromal cell populations, including FAPs and endothelial cells. Mechanotherapy reprogrammed the transcriptomes of both FAPs and macrophages in aged muscle recovering from disuse to restore ECM-and phagocytosis-related gene expression, respectively. Stable isotope labeling of intramuscular collagen and histological evaluation confirmed mechanotherapy-mediated remodeling of the ECM in aged muscle recovering from disuse. In summary, our results highlight mechanisms underlying age-related impairments during the recovery from disuse atrophy and promote mechanotherapy as an intervention that reprograms the muscle transcriptional environment more similar to that of adult skeletal muscle.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36895061" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184441" }, "primaryId" : "GEO:GSE184441", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184441" } ] }, "title" : "G3bp1-miR-1 axis regulates cardiomyocyte hypertrophy", "dateAssigned" : "2021-09-20T00:00:00.000-05:00", "summary" : "We examine the role of G3bp1, a RNA binding protein and site specific endoribonuclease in gene expression in isolated neonatal cardiomyocytes. RNAseq data from cardiomyocytes were infected with adenoviruses expressing shRNA against G3bp1 (ad-siG3bp1) or Luciferase (ad-siLUC, control) showed significant decrease in transcript abudnnace of cardiac-enriched genes involved in Calcium handling, contraction, action potential and sacromere function. On the other hand increase was observed in genes that regulate Hippo, TNF and TGFb signaling. Knockdown of G3bp1 inhibited endothelin-1 induced cardiomyocyte hypertrophy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35017014" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184493" }, "primaryId" : "GEO:GSE184493", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184493" } ] }, "title" : "The effect of moderate-intensity treadmill exercise on the transcription of peripheral blood mononuclear cells in ovariectomized rats", "dateAssigned" : "2021-09-20T00:00:00.000-05:00", "summary" : "Conclusion: Moderate-intensity treadmill exercise may improve the body composition and bone mass of the OVX group by upregulating CCL2 and other genes of the PBMC. The results also showed that the PBMCs in the peripheral blood can be a useful tool for monitoring the effect of exercise on bone health in postmenopausal osteoporosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34777002" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184649" }, "primaryId" : "GEO:GSE184649", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184649" } ] }, "title" : "Calycosin as a novel PI3K activator reduces inflammation and fibrosis in heart failure through AKT-IKK/STAT3 axis", "dateAssigned" : "2021-09-23T00:00:00.000-05:00", "summary" : "Conclusion: Cal improves cardiac function against HF by inhibiting cardiomyocytes inflammation and fibroblasts fibrosis via activation of the PI3K-AKT pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35264961" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184674" }, "primaryId" : "GEO:GSE184674", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184674" } ] }, "title" : "Gene expression profiling of age-related changes in coronary arterioles following intravenous stromal vascular fraction using RNA-seq", "dateAssigned" : "2021-09-23T00:00:00.000-05:00", "summary" : "The goal of this study is to examine age-related changes in the beta-1 adrenergic receptor dependent vasodilaiton in coronary microvessels from young, old, and old rats treated intravenously with stromal cells isolated from adipose tissue (SVF). We have shown that an aged coronary microvasculature has impaired vasodilation to adrenergic agonists and that a single treatment of SVF cells ameliorates the impaired vasodilation but the therapeutic mechanism is unknown.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36018760" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184693" }, "primaryId" : "GEO:GSE184693", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184693" } ] }, "title" : "The protective role of hydrogen sulfide and its impact on gene expression profiling in rat model of COPD", "dateAssigned" : "2021-09-23T00:00:00.000-05:00", "summary" : "To investigate the role of H2S in Chronic obstructive pulmonary disease (COPD), a rat model of COPD was established by cigarette smoking (CS) and intratracheal instillation of lipopolysaccharide (LPS). Rats were randomly divided into 4 groups: Control, CS+LPS, CS+LPS+NaHS and CS+LPS+propargylglycine (PPG). Transcription profiling of lung tissue comparing Control with CS+LPS, CS+LPS with CS+LPS+NaHS, and CS+LPS with CS+LPS+PPG. The goal was to determine the impact of H2S on gene expression profiling in rat model of COPD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35340205" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184823" }, "primaryId" : "GEO:GSE184823", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184823" } ] }, "title" : "The effect of Uphill and Downhill treadmill Running on the transcription of peripheral blood mononuclear cells in young male SD rats", "dateAssigned" : "2021-09-27T00:00:00.000-05:00", "summary" : "Thirty-six male Sprague-Dawley rats were randomly assigned to a control group and both running groups of uphill and downhill (n = 12). Bone mineral density (BMD), bone mineral content (BMC) and bone microstructure of the femur were measured. PBMCs were extracted and the gene expression profile of mRNA detected.Gene Ontology and KEGG pathway analysis were used.The results showed exercise mainly activated the biological processes and cellular pathways involved in immune, inflammation and osteoclast differentiation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184844" }, "primaryId" : "GEO:GSE184844", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184844" } ] }, "title" : "Calcitriol ameliorates damage in high-salt diet-induced hypertension: evidence of communication with the gut–kidney axis", "dateAssigned" : "2021-09-27T00:00:00.000-05:00", "summary" : "Several studies have established a link between high-salt diet, inflammation, and hypertension. Vitamin D supplementation has shown anti-inflammatory effects in many diseases; gut microbiota is also associated with a wide variety of cardiovascular diseases, but potential role of vitamin D and gut microbiota in high-salt diet-induced hypertension remains unclear. Therefore, we used rats with hypertension induced by a high-salt diet as the research object and analyzed the transcriptome of their tissues (kidney and colon) and gut microbiome to conduct an overall analysis of the gut–kidney axis. We aimed to confirm the effects of high salt and calcitriol on the gut–kidney immune system and the composition of the intestinal flora. We demonstrate that consumption of a high-salt diet results in hypertension and inflammation in the colon and kidney and alteration of gut microbiota composition and function. High-salt diet-induced hypertension was found to be associated with seven microbial taxa and mainly associated with reduced production of the protective short-chain fatty acid butyrate. Calcitriol can reduce colon and kidney inflammation, and there are gene expression changes consistent with restored intestinal barrier function. The protective effect of calcitriol may be mediated indirectly by immunological properties. Additionally, the molecular pathways of the gut microbiota-mediated BP regulation may be related to circadian rhythm signals, which needs to be further investigated. An innovative association analysis of the microbiota may be a key strategy to understanding the association between gene patterns and host.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34894804" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184929" }, "primaryId" : "GEO:GSE184929", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184929" } ] }, "title" : "From Bench to Bedside and Back: Improving the Safety of GalNAc-siRNA Conjugates Using GNA-Destabilized Seed-Pairing", "dateAssigned" : "2021-09-28T00:00:00.000-05:00", "summary" : "Preclinical mechanistic studies have pointed towards RNAi-mediated off-target effects as a major driver of hepatotoxicity for GalNAc-siRNA conjugates. Here we demonstrate that a single glycol nucleic acid (GNA) modification can substantially reduce siRNA seed-mediated binding to off-target transcripts while maintaining on-target activity. In siRNAs with established off-target effects leading to hepatotoxicity, these Enhanced Stabilization Chemistry plus (ESC+) designs exhibit a substantially improved therapeutic window in rat. We utilized this strategy to improve the safety of ALN-HBV, which exhibited dose-dependent, transient, and asymptomatic alanine aminotransferase elevations in healthy volunteers.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35736224" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184940" }, "primaryId" : "GEO:GSE184940", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184940" } ] }, "title" : "The integrated single cell RNAseq analysis of bone marrow cells produced by mouse-mouse intraspecies blastocyst complementation and mouse-rat interspecies blastocyst complementation", "dateAssigned" : "2021-09-28T00:00:00.000-05:00", "summary" : "We report the application of single cell RNAseq analysis of bone marrow cells from mouse-mouse intraspecies blastocyst complementation and mouse-rat interspecies blastocyst complementation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36178184" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184959" }, "primaryId" : "GEO:GSE184959", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE184959" } ] }, "title" : "THAP1 is cell type dependent regulator of SP1 family crucial for dystonic syndromes in human and rat [Striatum_RNA-seq]", "dateAssigned" : "2021-09-28T00:00:00.000-05:00", "summary" : "THAP1 is a transcription factor and its mutations are responsible for DYT6 dystonia. However, how THAP1 mutations lead to these gene expression alterations and whether the gene expression changes are also reflected in the brain of THAP1 patients are still unclear. In this study we used epigenetic and transcriptomic approaches combined with multiple model systems to uncover the function of THAP1 and the potential pathogenesis of DYT6 dystonia. THAP1 mutations lead to dysregulation of genes mainly through regulation of SP1 family members, SP1 and SP4, in a cell type dependent manner.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36417521" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185140" }, "primaryId" : "GEO:GSE185140", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185140" } ] }, "title" : "Gene expression analyses of three early phases of osteogenic, adipogenic, and chondrogenic differentiation of rat bone marrow mesenchymal stem cells", "dateAssigned" : "2021-10-01T00:00:00.000-05:00", "summary" : "To further reveal key mRNAs deciding osteogenic, adipogenic, and chondrogenic differentiation of rat bone marrow mesenchymal stem cells (BMSCs) in early phases, we have employed next-generation high-throughput transcriptome sequencing to detect the expression of mRNA in rat BMSCs during differentiation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35223983" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185147" }, "primaryId" : "GEO:GSE185147", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185147" } ] }, "title" : "The effect of curcumin/ZNPs hydrogel on the transcription of gingiva in rats with periodontitis", "dateAssigned" : "2021-10-01T00:00:00.000-05:00", "summary" : "Conclusions: Our study represents the first detailed analysis of gingival transcriptomes of rats treated by Cur/ZnO gel, with biologic replicates, generated by RNA-seq technology.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185195" }, "primaryId" : "GEO:GSE185195", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185195" } ] }, "title" : "Gene expression profiling of the nucleus accumbens and dorsolateral striatum in a two-hit model combining maternal immune activation and peripubertal stress in rats", "dateAssigned" : "2021-10-02T00:00:00.000-05:00", "summary" : "Substance use disorders are more prevalent in schizophrenia, worsening its course and prognosis. Here, we used a double-hit rat model, combining maternal immune activation (MIA) and peripubertal stress (PUS), to study cocaine addiction and the underlying neurobehavioral alterations. We injected lipopolysaccharide (LPS) or saline on gestational days 15 and 16 to pregnant rats. Their male offspring were then subjected to unpredictable stress during adolescence. When rats reached adulthood, we studied their cocaine addiction-like behavior, impulsivity and conditioning processes, and several aspects of brain structure and function by MRI, PET and RNAseq. MIA facilitated the acquisition of cocaine self-administration but PUS reduced cocaine intake, an effect that was reversed by MIA. MIA increased motivation for cocaine and revearsed the effects of PUS during extended access. Incubation of seeking was unaffected. Neither hit alone nor their combination impacted pavlovian or instrumental learning or impulsiveness. At the brain level, PUS reduced hippocampal volume and hyperactivated the dorsal subiculum. When combined, both hits altered the structure and function of the dorsal striatum increasing its volume and interferring with glutamatergic dynamics. MIA alone had no effect on the gene expression of the nucleus accumbens but, when combined with PUS, modulated specific genes that could account for the decreased cocaine intake. PUS had a profund effect on the dorsal striatal transcriptome however, this was obliterated when PUS occurred in animals with MIA. These results describe a complex interplay between MIA and stress on neurodevelopment and in the susceptibility to develop cocaine addiction.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185278" }, "primaryId" : "GEO:GSE185278", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185278" } ] }, "title" : "Effective control of neuropathic pain by interrupting C/EBPβ-CLEC7A cross-talk-mediated NLRP3 inflammasome-dependent pyroptosis", "dateAssigned" : "2021-10-04T00:00:00.000-05:00", "summary" : "In this study, we used microarrays to detect the global gene expression in spinal cord of rats in sham group and CCI model group(an animal model of neuropathic pain), and the differentially expressed genes between diseases and control group were obtained.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185368" }, "primaryId" : "GEO:GSE185368", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185368" } ] }, "title" : "RNA-Seq of rat cardiac fibroblasts depleted for Yap and Wwtr1 ", "dateAssigned" : "2021-10-05T00:00:00.000-05:00", "summary" : "Primary neonatal rat cardiac fibroblasts were isolated and subjected to siRNA mediated Yap and/or Wwtr1 knockdown", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36998974" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185538" }, "primaryId" : "GEO:GSE185538", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185538" } ] }, "title" : "Single-nucleus chromatin accessibility and RNA-seq reveal impaired brain development in prenatal e-cigarette exposed neonatal rats", "dateAssigned" : "2021-10-07T00:00:00.000-05:00", "summary" : "We studied the influence of maternal vaping on rat neonates' brain development, using single nucleus -ATAC-seq (snATAC-seq) and -RNA-seq (snRNA-seq) technologies. We found that maternal vaping distorted neuronal lineage differentiation by promoting excitatory neuron and inhibiting lateral ganglionic eminence derived inhibitory neuron differentiation. Maternal vaping also diminished microglia population in rat developing brain. Functional enrichment revealed that the distorted neuronal differentiation and reduced microglia population were associated with disrupted brain calcium homeostasis and signaling. Our findings raise the concern that maternal vaping may cause adverse long-term brain damage to the offsprings. In addition, we proposed a set of brain cell specific chromatin accessibility markers for identifying rat brain cells directly from snATAC-seq data.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35874099" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185542" }, "primaryId" : "GEO:GSE185542", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185542" } ] }, "title" : "Inhibiting L-type calcium channel promotes cardiomyocyte proliferation through activating canonical Wnt signaling pathway", "dateAssigned" : "2021-10-08T00:00:00.000-05:00", "summary" : "We performed RNA-Seq analysis of neoatal rat ventricular cardiomyocytes (NRVCs) and human pluripotent stem cells derived cardiomyocytes (hPSC-CMs) which were treated with Nimodipine (NM) to investigate the moleclular mechanism of inhibiting L-type calcium channel (LTCC) to promote cardiomyocyte proliferation.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185573" }, "primaryId" : "GEO:GSE185573", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185573" } ] }, "title" : "Rat oocyte epigenomes", "dateAssigned" : "2021-10-08T00:00:00.000-05:00", "summary" : "The rat is a widely used model for human physiology and psychology. However, due to their longer gestation periods and husbandry costs relative to mice, as well as the availability of superior molecular techniques to manipulate the mouse genome, relatively few genome-wide studies have been conducted in the rat. As such, a comprehensive analysis of genomic imprinting, which impacts complex traits such as growth and behaviour, has yet to be conducted in the rat. Towards this end, we systematically profiled embryonic and extra-embryonic tissue gene expression and DNA methylation with allele-specific resolution. We identified 14 embryonic and 26 extra-embryonic imprinted genes in the rat. Comparative analyses with mouse revealed that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes in the extra-embryonic embryo are conserved in Muridae, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel candidate non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extra-embryonic imprinting. Cross-species analysis of novel rat imprinted genes with mouse and human revealed multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the birth of ZFP57 binding motifs and the insertion of endogenous retroviral promoters. Thus, characterization of the rat imprintome provides insights into the conservation of imprinted gene expression and the etiology of species-specific imprinting.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36918927" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185574" }, "primaryId" : "GEO:GSE185574", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185574" } ] }, "title" : "Rat and mouse imprintomes (allele-specific transcriptomes)", "dateAssigned" : "2021-10-08T00:00:00.000-05:00", "summary" : "The rat is a widely used model for human physiology and psychology. However, due to their longer gestation periods and husbandry costs relative to mice, as well as the availability of superior molecular techniques to manipulate the mouse genome, relatively few genome-wide studies have been conducted in the rat. As such, a comprehensive analysis of genomic imprinting, which impacts complex traits such as growth and behaviour, has yet to be conducted in the rat. Towards this end, we systematically profiled embryonic and extra-embryonic tissue gene expression and DNA methylation with allele-specific resolution. We identified 14 embryonic and 26 extra-embryonic imprinted genes in the rat. Comparative analyses with mouse revealed that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes in the extra-embryonic embryo are conserved in Muridae, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel candidate non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extra-embryonic imprinting. Cross-species analysis of novel rat imprinted genes with mouse and human revealed multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the birth of ZFP57 binding motifs and the insertion of endogenous retroviral promoters. Thus, characterization of the rat imprintome provides insights into the conservation of imprinted gene expression and the etiology of species-specific imprinting.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36918927" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185600" }, "primaryId" : "GEO:GSE185600", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185600" } ] }, "title" : "Hyperbaric oxygen therapy after mid-cervical spinal contusion injury", "dateAssigned" : "2021-10-09T00:00:00.000-05:00", "summary" : "Hyperbaric oxygen (HBO) therapy is frequently used to treat peripheral wounds or decompression sickness. Evidence suggests that HBO therapy can provide neuroprotection and has an anti-inflammatory impact after neurologic injury including spinal cord injury (SCI). Our primary purpose was to conduct an unbiased, genome-wide screening of mRNA expression changes in the injured spinal cord after HBO therapy. A mRNA gene array was used to evaluate samples taken from the contused region of the spinal cord following a lateralized mid-cervical contusion injury in adult female rats. HBO therapy consisted of daily, 1-hour sessions (3.0 ATA, 100% O2) initiated on the day of SCI. Gene set enrichment analyses indicated that HBO upregulated genes in pathways associated with electron transport, mitochondrial function, and oxidative phosphorylation, and downregulation genes in pathways associated with inflammation (including cytokines and NF-B) and apoptotic signaling. In a separate cohort, spinal cord histology was performed to verify whether the HBO treatment impacted neuronal cell counts or inflammatory markers. Compared to untreated rats, there was increased NeuN positive cells in the spinal cord of HBO treated rats (p=0.007). Further, staining for anti-ionized calcium binding adaptor protein (Iba-1, a microglial marker) was reduced after HBO (p=0.028). We conclude that HBO therapy, initiated shortly after SCI and continued for 10-days, can alter the molecular signature of the lesioned spinal cord in a manner consistent with an anti-inflammatory and neuroprotective impact.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35152735" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185633" }, "primaryId" : "GEO:GSE185633", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185633" } ] }, "title" : "NQO1 regulates expression and alternative splicing of apoptotic genes associated with Alzheimer's disease in PC-12 cells", "dateAssigned" : "2021-10-11T00:00:00.000-05:00", "summary" : "Quinone oxidoreductase I (NQO1), an important antioxidant enzyme which plays an important role in monitoring cellular redox state, was altered in the brain tissues of Alzheimer’s disease (AD) patients. In addition to its traditional antioxidant effect, NQO1 is also a multifunctional RNA-binding protein (RBP) in post-transcriptional regulation. However, NQO1 in AD pathology by acting as an RBP is not studied. In the present study, the RBP functions of NQO1 in rat PC12 cells, a cell line widely used in neurological disease studies, were investigated using siRNA knock-down (KD) and following whole transcriptome (RNA-seq) analysis. Reduced levels of NQO1 led to a significant increase in cellular apoptosis, compared with control cells. Notably, RNA-seq analysis of the transcriptome of PC12 cells by NQO1-KD revealed that genes in certain apoptosis pathways, were under global transcriptional and alternative splicing regulation. Quantitative RT-PCR confirmed the NQO1-regulated transcription of apoptotic genes Cryab, Lgmn , Ngf, Apoe, Brd7, Stat3, and alternative splicing of Bin1, Picalm, Fyn. These NQO1-regulated genes have been found to be closely related to AD pathogenesis. Our findings suggest that NQO1 acts as an RBP and participates in the pathology of AD by regulating expression and alternative splicing of genes involved in apoptosis. The results of present study extend our understanding of the cellular and molecular mechanisms in AD pathogenesis, which might contribute to the development of novel therapeutic targets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37002649" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185636" }, "primaryId" : "GEO:GSE185636", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185636" } ] }, "title" : "Gene expression profiles of primary myocardial cells treated with LPS and transfected siMETTL3 in rats", "dateAssigned" : "2021-10-11T00:00:00.000-05:00", "summary" : "Methyltransferase-like 3 (METTL3) is the m6A methyltransferase which binds to METTL14 and wilms tumour 1-associated protein (WTAP) to form a complex catalyzing the m6A modification, the most abundant epitranscriptomic modification in eukaryotic mRNAs. And it has been demonstrated that m6A methylation mediated by METTL3 to be essential for inflammatory responses. To identify the messenger RNA (mRNA) profile in the primary myocardial cells that were treated with lipopolysaccharide (LPS) and/or small interference siMETTL3, six groups of primary myocardial cells were used for analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185699" }, "primaryId" : "GEO:GSE185699", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185699" } ] }, "title" : "NAP1L5 is required for translation activation during cardiomyocyte hypertrophy", "dateAssigned" : "2021-10-12T00:00:00.000-05:00", "summary" : "Pathological growth of cardiomyocytes during hypertrophy is characterized by excess protein synthesis; however, the regulatory mechanism remains largely unknown. Using a neonatal rat ventricular myocyte (NRVMs) model, here we find that the expression of nucleosome assembly protein 1 like 5 (Nap1l5) is upregulated in phenylephrine (PE)-induced hypertrophy. Knockdown of Nap1l5 expression by siRNA significantly blocks cell size enlargement and pathological gene induction after PE treatment. In contrast, Adenovirus-mediated Nap1l5 overexpression significantly aggravates the pro-hypertrophic effects of PE on NRVMs. RNA-seq analysis reveals that Nap1l5 knockdown reverses the pro-hypertrophic transcriptome reprogramming after PE treatment. Whereas immune response is dominantly enriched in the upregulated genes, oxidative phosphorylation, cardiac muscle contraction and ribosome related pathways are remarkably enriched in the down-regulated genes. Although PRC2 and PRC1 are involved in Nap1l5-mediated gene regulation, Nap1l5 does not directly alter the levels of global histone methylations. However, puromycin incorporation assay shows that Nap1l5 is both necessary and sufficient to drive the increased protein synthesis rate in cardiomyocyte hypertrophy. This is attributable to a direct regulation of ribosome assembly by Nap1l5. Our findings demonstrate a previously unrecognized role of Nap1l5 in translation control during cardiac hypertrophy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34977198" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185702" }, "primaryId" : "GEO:GSE185702", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185702" } ] }, "title" : "Enhanced glucose metabolism through activation of HIF-1α covers the energy demand in a rat embryonic heart primordium after heartbeat initiation.", "dateAssigned" : "2021-10-12T00:00:00.000-05:00", "summary" : "The initiation of heartbeat is an essential step in cardiogenesis in the heart primordium, but it remains unclear how intracellular metabolism responds to increased energy demands after heartbeat initiation. In this study, embryos in Wistar rats at embryonic day 10, at which heartbeat begins in rats, were divided into two groups by the heart primordium before and after heartbeat initiation and their metabolic characteristics were assessed. Metabolome analysis revealed that increased levels of ATP, a main product of glucose catabolism, and reduced glutathione, a by-product of the pentose phosphate pathway, were the major determinants in the heart primordium after heartbeat initiation. Glycolytic capacity and ATP synthesis-linked mitochondrial respiration were significantly increased, but subunits in complexes of mitochondrial oxidative phosphorylation were not upregulated in the heart primordium after heartbeat initiation. Hypoxia-inducible factor (HIF)-1α was activated and a glucose transporter and rate-limiting enzymes of the glycolytic and pentose phosphate pathways, which are HIF-1α-downstream targets, were upregulated in the heart primordium after heartbeat initiation. These results suggest that the HIF-1α-mediated enhancement of glycolysis with activation of the pentose phosphate pathway, potentially leading to antioxidant defense and nucleotide biosynthesis, covers the increased energy demand in the beating and developing heart primordium.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34996938" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185805" }, "primaryId" : "GEO:GSE185805", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185805" } ] }, "title" : "The transcriptome data of primary microglia cells from contrl and over expression CYP11A1 rat's offspring", "dateAssigned" : "2021-10-13T00:00:00.000-05:00", "summary" : "NOT PROVIDED; REQUESTED", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35002603" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185931" }, "primaryId" : "GEO:GSE185931", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185931" } ] }, "title" : "Long noncoding RNA expression profiles in brain ischemic tolerance by cerebral ischemic preconditioning", "dateAssigned" : "2021-10-14T00:00:00.000-05:00", "summary" : "In this study, cerebral cortical astrocytes and neurons of rats were co-cultured, the astrocytes of the co-cultured cell model pretreated by ischemic preconditioning (45 min of OGD) were subjected to lncRNA high-throughput sequencing (RNA-seq).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185935" }, "primaryId" : "GEO:GSE185935", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185935" } ] }, "title" : "The dsRBP Staufen2 governs RNP assembly of neuronal Argonaute proteins", "dateAssigned" : "2021-10-14T00:00:00.000-05:00", "summary" : "Here, we have characterized the role of the RNA-binding protein Staufen2, a potential Ago interactor, in RNP assembly. Staufen2 depletion resulted in the upregulation of Ago1/2 and the RISC effector proteins Ddx6 and Dcp1a. This upregulation was accompanied by the displacement of Ago2 from processing bodies, large RNPs implicated in RNA storage, and subsequent association of Ago2 with translating polysomes. Analysis of miRNA expression levels did not reveal changes of global miRNA abundance. In parallel, Staufen2 deficiency yielded decreased global translation. As the observed phenotype can be rescued by Ago1/2 knockdown, we propose a working model in which both Staufen2 and Ago proteins critically depend on each other and contribute to neuronal homeostasis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35687120" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185988" }, "primaryId" : "GEO:GSE185988", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE185988" } ] }, "title" : "Magnesium facilitates the healing of atypical femoral fractures: A single-cell transcriptomic study", "dateAssigned" : "2021-10-15T00:00:00.000-05:00", "summary" : "We reported the application of single-cell mRNA sequencing to identify a unique population of fibroblasts that exits in the fracture callus of bisphosphonate-treated rats. Such unique population of fibroblasts prevented fracture healing by secreting ECM. Further, it was found that these ECM-secreting fibroblasts were enriched for myeloid genes, suggesting a bone marrow orgin. After fractures were treated with local CGRP injection or Magnesium based biometal, such population of fibroblasts was cleared off, resulting in facilitated fracture healing of bisphosphonate-treated rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186026" }, "primaryId" : "GEO:GSE186026", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186026" } ] }, "title" : "Transcriptomic analyses of the anti-adipogenic and pro-osteoblastic effects of aspirin in rat bone mesenchymal stem cell", "dateAssigned" : "2021-10-16T00:00:00.000-05:00", "summary" : "Theoretically, the differentiation of mesenchymal stem cells (MSCs) into either adipocytic or osteoblastic phenotype can be deemed as a seesaw, where induction of one lineage comes at the expense of the other. Previously, researchers, including our team, found that aspirin promoted osteoblast differentiation of bone mesenchymal stem cells (BMSCs) whereas inhibiting adipogenic differentiation. However, the precise mechanisms, that is, which pathways, what biological process or key genes involved during this process, had not been systematically studied. In the present study, we tend to analyze the whole transcriptome of the anti-adipogenic and promote-osteoblastic effects of aspirin in BMSCs. Our results showed that aspirin’s presence restored or further strengthened the expression of an important part of the gene population repressed during adipogenesis or increased during osteogenesis. Besides, classical pathways related to osteogenic differentiation (p53 signaling pathway, focal adhesion, osteoclast differentiation, PI3K-Akt signaling pathway, MAPK signaling pathway, and Wnt signaling pathway) and the fat metabolism were also disturbed during the promote-osteoblastic and anti-adipogenic effects of aspirin. Therefore, our whole-genome transcriptomic results shed new light and open the door to more specific “omics” studies. Our results allow a better understanding of the anti-adipogenic and promote-osteoblastic effects of aspirin and pave the way to aspirin clinical use for the prevention and treatment of diseases like tissue defect and osteoporosis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186048" }, "primaryId" : "GEO:GSE186048", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186048" } ] }, "title" : "Transcriptomics study reveals the underlying molecular mechanisms of circadian gene Bmal1 in rat nucleus pulposus cells", "dateAssigned" : "2021-10-18T00:00:00.000-05:00", "summary" : "Intervertebral disc degeneration (IDD) is a major cause of low back pain (LBP), and the pathogenesis remains unknown. Recently, an autoregulating circadian rhythm was identiï¬�ed in intervertebral discs (IVDs), the abolition of which led to IDD. The genetic disruption of the mouse IVD molecular clock, speciï¬�cally through the disruption of Bmal1, predisposes mice to IDD. However, the precise role of circadian gene Bmal1 in IDD remain elusive. In this study, RNA-seq was used to determine differentially expressed genes (DEGs) in rat nucleus pulposus cells (NPCs) treated with Bmal1 shRNA or its negative control lentivirus. GO and KEGG pathway analysis were also performed. In general, 6900 DEGs was identified. The anabolic genes, such as col2a1 and acan, showed significantly decreased expression, whereas catabolic genes, such as MMP-3 and MMP-13, showed significantly upregulated expression. GO analysis was performed to annotate the functions of the DEGs. The DEGs were primarily associated with the processes of cell transcription, behaviour, signal transduction, biological regulation, and protein binding. KEGG pathway analysis revealed that Bmal1 was related to multiple signalling pathways, such as p53, Hedgehog, Wnt, PI3K-Akt, mTOR, Hippo and MAPK. This study, for the first time, analyzes the transcriptome of NPCs in response to Bmal1 diminished, indicating that circadian gene Bmal1 is involved in the establishment and progression of IDD through its wide effects on the viability and function of NPCs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186104" }, "primaryId" : "GEO:GSE186104", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186104" } ] }, "title" : "The effect of lithium and dexamethasone on fetal rat metatarsal bones transcriptome", "dateAssigned" : "2021-10-19T00:00:00.000-05:00", "summary" : "While dexamethasone impairs bone growth and adds to the development of osteoporosis, lithium enhances cell renewal. The aim of this project was to explore the genes and pathways affected by adding dexamethasone, lithium or both to the medium in which fetal rat metatarsal bones were cultivated. RNA sequencing and differential gene expression analysis were implemented to describe the transcriptome of the metatarsals. We identified significant opposite as well as independent effects of the substances on several cellular pathways. This may open up to identify the mechanisms of dexamethasone induced bone growth and structure impairment and possible preventive measures.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186158" }, "primaryId" : "GEO:GSE186158", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186158" } ] }, "title" : "Single-cell transcriptomic atlas reveals the evolution of immune cells and molecules across multiple vertebrate species", "dateAssigned" : "2021-10-19T00:00:00.000-05:00", "summary" : "We utilized single-cell RNA sequencing (scRNA-seq) to carry out comparative transcriptome analysis in various immune cells from the spleens across seven vertebrate species.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36871615" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186237" }, "primaryId" : "GEO:GSE186237", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186237" } ] }, "title" : "Therapeutic Interrupting C/EBPβ-Clec7a Cross-talk-mediated NLRP3 Inflammasome-dependent Pyroptosis for Relieving Neuropathic Pain", "dateAssigned" : "2021-10-20T00:00:00.000-05:00", "summary" : "Neuropathic pain (NP) is a complex chronic pain due to the nervous system damage or diseases.During NP development and progression, the neuroinflammation has been observed along the pain pathways from the spinal cord to the thalamus and the parietal cortex. It may be caused by the activation of glial cells, especially microglia, with production of cytokines and other inflammatory mediators within the central nervous system (CNS), especially in spinal cord. In this study, we used high-throughput RNA-seq technology to detect the global gene expression in spinal cord of rats in sham group and CCI model group(an animal model of neuropathic pain), and the differentially expressed genes between diseases and control group were obtained.Significant differentially expressed genes (DEGs) of the Sham vs. CCI groups were identified using the criteria of a fold change>1.5 and P value <0.05. Finally, we focused on C/EBPβ-Clec7a Cross-talk-mediated NLRP3 Inflammasome-dependent Pyroptosis pathway and further studied its role in neuropathic pain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186247" }, "primaryId" : "GEO:GSE186247", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186247" } ] }, "title" : "The difference of right and left ventricular remodeling caused by volume overload in neonatal SD rats", "dateAssigned" : "2021-10-20T00:00:00.000-05:00", "summary" : "We reported the RNAseq analyses of right ventricle (RV) and left ventricle (LV) in neonatal volume overload (VO) and sham-operated SD rat. VO was induced by the fistula between abdominal aorta and inferior vena cava (AVF) within 24 hours postnatally (P1). RNAseq analyses of RV and LV free wall of P7 from VO and sham-operated rat. It demonstrated that the 1806 differentially expressed genes (DEGs) between RV and LV at the neonatal stage were primarily enriched in GTPase mediating signal transduction, insulin signaling pathway and thyroid hormone signaling pathway. VO produced 3 more times DEGs in LV than RV . GO analysis of these DEGs demonstrated that in the top 150 enriched terms, the LV comparison and RV comparison shared 34 terms (22.7%) in common. These commonly enriched terms were primarily associated with GTPase mediating signal transduction. KEGG analysis of these DEGs demonstrated that in the top 30 enriched terms, the LV comparison and RV comparison shared 14 terms (46.7%) in common. And insulin signaling pathway and thyroid hormone signaling pathway are the top two enriched terms in common. Regarding the differently enriched GO terms, they were primarily associated with lipid metabolism and ion channel in RV and primarily associated nucleic acid metabolism in LV. The top two differently enriched KEGG terms were arrhythmogenic right ventricular cardiomyopathy (ARVC) and adipocytokine signaling pathway in RV while microRNAs in cancer and longevity regulating pathway in LV. These results were further confirmed by the determination of metabolites.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36552341" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186248" }, "primaryId" : "GEO:GSE186248", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186248" } ] }, "title" : "Therapeutic Effect of Histone Acetyltransferase Inhibitors on Galactose-Induced Cataract in Rats", "dateAssigned" : "2021-10-20T00:00:00.000-05:00", "summary" : "To identify the genes regulated by HAT inhibitors, we conducted microarray analysis of treated and untreated cataract samples.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36417410" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186492" }, "primaryId" : "GEO:GSE186492", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186492" } ] }, "title" : "Rat and mouse imprintomes (allele-specific DNA methylomes)", "dateAssigned" : "2021-10-24T00:00:00.000-05:00", "summary" : "The rat is a widely used model for human physiology and psychology. However, due to their longer gestation periods and husbandry costs relative to mice, as well as the availability of superior molecular techniques to manipulate the mouse genome, relatively few genome-wide studies have been conducted in the rat. As such, a comprehensive analysis of genomic imprinting, which impacts complex traits such as growth and behaviour, has yet to be conducted in the rat. Towards this end, we systematically profiled embryonic and extra-embryonic tissue gene expression and DNA methylation with allele-specific resolution. We identified 14 embryonic and 26 extra-embryonic imprinted genes in the rat. Comparative analyses with mouse revealed that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes in the extra-embryonic embryo are conserved in Muridae, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel candidate non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extra-embryonic imprinting. Cross-species analysis of novel rat imprinted genes with mouse and human revealed multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the birth of ZFP57 binding motifs and the insertion of endogenous retroviral promoters. Thus, characterization of the rat imprintome provides insights into the conservation of imprinted gene expression and the etiology of species-specific imprinting.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36918927" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186517" }, "primaryId" : "GEO:GSE186517", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186517" } ] }, "title" : "Metagenomics assessment of WKY and SHR rodents", "dateAssigned" : "2021-10-25T00:00:00.000-05:00", "summary" : "The microbiome plays a significant role in gut brain communication and is linked to several animal and human diseases. Hypertension is characterized by gut dysbiosis, and this study aimed to determine how the gut microbiome differed between male and female normotensive and hypertensive rodents. WKY is a genetic control for spontaneous hypertensive rats or SHR which is well documented to have elevated blood pressure at approximately 8 to 10 weeks. We compared the microbiome of normotensive and hypertensive rodents using a meta-genomics approach.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186615" }, "primaryId" : "GEO:GSE186615", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186615" } ] }, "title" : "Loss of m6A methyltransferase METTL5 promotes cardiac hypertrophy through translational control of SUZ12", "dateAssigned" : "2021-10-26T00:00:00.000-05:00", "summary" : "The methyltransferase-like5 (METTL5), which catalyzes m6A in 18S rRNA at position A1832, has been shown to regulate the efficient of mRNA translation in the differentiation of ES cell and the growth of cancer cells. It remains unknown that whether and how METTL5 regulates cardiac hypertrophy. In this study, we generated a mouse model (METTL5-cKO) with cardiac-specific abolishment of METTL5 in vivo. Loss function of METTL5 promotes pressure overload-induced cardiomyocyte hypertrophy and adverse remodeling. The regulatory function of METTL5 in hypertrophic growth of cardiomyocyte were further confirmed with both gain- and loss-of-function approaches in primary isolated cardiomyocytes. Mechanically, METTL5 was identified to modulate the mRNA translation of SUZ12, a core component of PRC2 complex, and further regulate the transcriptome shift during cardiac hypertrophy. Therefore, our study uncover an important translational regulator of cardiac hypertrophy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35295259" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186626" }, "primaryId" : "GEO:GSE186626", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186626" } ] }, "title" : "RNA sequencing in iAM-1 differentiated cells and RnSbk2 knockdown", "dateAssigned" : "2021-10-26T00:00:00.000-05:00", "summary" : "RNA sequencing in iAM-1 differentiated cells and RnSbk2 knockdown", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35587025" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186659" }, "primaryId" : "GEO:GSE186659", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186659" } ] }, "title" : "Comparison of toxicological effects and exposure levels between triclosan and its structurally similar chemicals using in vitro tests for read-across case study", "dateAssigned" : "2021-10-27T00:00:00.000-05:00", "summary" : "To improve prediction accuracy of read-across, we compared biological similarities between triclosan and its structurally similar chemicals including diclosan and 1-chloro-3-(4-chlorophenoxy) benzene. To elucidate and compare the potential mechanisms between them, we performed in vitro toxicogenomics with rat primary hepatocytes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186702" }, "primaryId" : "GEO:GSE186702", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186702" } ] }, "title" : "Integrated insight into the molecular mechanisms of selenium modulates MPP+ induced cytotoxicity in Parkinson’s disease model", "dateAssigned" : "2021-10-27T00:00:00.000-05:00", "summary" : "Parkinson’s disease (PD) is a common neurodegenerative disease, which associated with oxidative stress. Due to the antioxidant function of Selenium (Se), it may have a neuroprotective function in PD. Nevertheless, the Se involved and its role in the protective function is still unclear. 1-methyl-4-phenylpyridinium (MPP+), which inhibits mitochondrial respiration, is usually used to produce a reliable PD cellular model. In this study, we discovered that Se could modulate cytotoxicity in MPP+ induced PD model and used genome wide high throughput sequencing to capture the gene expression profiles of MPP+ treatment PC12 cells with or without Se. We identified 351 differentially expressed mRNAs (DEGs) and 14 differentially expressed long non-coding RNAs (DELs) in MPP+ group vs. normal control group, 244 DEGs and 27 DELs in Se + MPP+ group vs. MPP+ group. Functional annotation analysis of DEGs and DELs cis-target genes revealed that they were enriched in reactive oxygen species (ROS) metabolic process and mitochondrial control of apoptosis. Our data suggests that DEGs, Txnrd1, siglec1 and Klf2, and the DEL AABR07044454.1 cis-acting on target gene Cdkn1a, may act a protective function in PD model. For the first time, our study systematically demonstrated that mRNAs and lncRNAs induced by Se involved in neuroprotection in PD and provided new insight into how Se modulates cytotoxicity in MPP+ induced PD model.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186706" }, "primaryId" : "GEO:GSE186706", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186706" } ] }, "title" : "The Role of Sorting Nexin 17 in Cardiac Development", "dateAssigned" : "2021-10-27T00:00:00.000-05:00", "summary" : "Homozygous deletion of the SNX17 gene in rats resulted in mid-gestational embryonic lethality which was accompanied by congenital heart defects, including in the double-outlet right ventricle, atrioventricular and ventricular septal defects. To elucidate the potential mechanisms underlying development of cardiac OFT defects induced by SNX17 knockout, we performed RNA-seq analysis in cardiac outflow tract (OFT) tissues isolated from WT and HO embryos at E13.5. A total of 262 differentially expressed genes (DEGs) were identified between WT and HO samples, of which 94 and 168 were up-regulated and down-regulated, respectively. Analysis of biological functions of the DEGs, via Gene Ontology (GO), revealed that the up-regulated genes were mainly involved in heart development, and negative regulation of the intrinsic apoptotic pathway, while the down-regulated DEGs were associated with cell adhesion, extracellular organization, and negative regulation of the Wnt signaling pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34988124" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186726" }, "primaryId" : "GEO:GSE186726", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186726" } ] }, "title" : "Next-generation sequencing facilitates quantitative analysis of rat BMSCs in fast, medium or slow stress relaxation SA hydrogel", "dateAssigned" : "2021-10-27T00:00:00.000-05:00", "summary" : "To identify genes and the molecular pathways involved in the regulation of mesenchymal stem cells (MSCs) exposure to various matrix viscoelasticity, we performed RNA-sequence of MSCs in fast stress relaxation (FAST), medium stress relaxation (MEDIUM) and slow stress relaxation (SLOW) matrix.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186840" }, "primaryId" : "GEO:GSE186840", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186840" } ] }, "title" : "Prenatal Adversity Alters the Epigenetic Profile of the Prefrontal Cortex: Sexually Dimorphic Effects of Prenatal Alcohol Exposure and Food-related Stress", "dateAssigned" : "2021-10-29T00:00:00.000-05:00", "summary" : "Prenatal adversity or stress can have long-term consequences on developmental trajec-tories and health outcomes. Although the biological mechanisms underlying these effects are poorly understood, epigenetic modifications, such as DNA methylation, have the potential to link early-life environments to alterations in physiological systems, with long-term functional impli-cations. We investigated the consequences of two prenatal insults, prenatal alcohol exposure (PAE) and food-related stress, on DNA methylation profiles of the rat brain during early devel-opment. As these insults can have sex-specific effects on biological outcomes, we analyzed epige-nome-wide DNA methylation patterns in prefrontal cortex, a key brain region involved in cogni-tion, executive function, and behavior, of both males and females. We found sex-dependent and sex-concordant influences of these insults on epigenetic patterns. These alterations occurred in genes and pathways related to brain development and immune function, suggesting that PAE and food-related stress may reprogram neurobiological/physiological systems partly through central epigenetic changes, and may do so in a sex-dependent manner. Such epigenetic changes may re-flect the sex-specific effects of prenatal insults on long-term functional and health outcomes and may have important implications for understanding possible mechanisms underlying fetal alco-hol spectrum disorder and other neurodevelopmental disorders.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34828381" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186972" }, "primaryId" : "GEO:GSE186972", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186972" } ] }, "title" : "Small RNA profiling of differentiated and de-differentiated vascular smooth muscle cell", "dateAssigned" : "2021-11-02T00:00:00.000-05:00", "summary" : "We report the application of small RNA sequencing for high-throughput profiling of small RNA under 75 bp in vascular smooth muscle cell. By a reading depth of 30M and single stranded sequencing, we generated the small RNA signature on differentiated and de-differentiated vascular smooth muscle cell induced by PDGF-BB and H3K4me2 editing. We found that PDGF-BB and H3K4me2 editing induced de-differentiation modulated miRNA profile significantly, which was demonstrated at least in part responsible for modulated vascular smooth muscle cell phenotype.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35465051" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186989" }, "primaryId" : "GEO:GSE186989", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186989" } ] }, "title" : "Comprehensive transcriptome analysis of heart tissues in the sugen/hypoxia rats with/without treatment of chrysin", "dateAssigned" : "2021-11-02T00:00:00.000-05:00", "summary" : "Pulmonary arterial hypertension (PAH) is a progressive disease characterized by pulmonary vascular remodeling leading to increased pulmonary vascular resistance and right ventricular (RV) hypertrophy, resulting in RV failure. RV dysfunction is a complex process that leads to cardiomyocyte hypertrophy, fibrosis, inflammation, angiogenesis, and metabolic changes. In patient with PAH, the adaptation of the RV to high pulmonary arterial pressures is the most important determinant of prognosis. However, the underlying molecular mechanism of adverse RV remodeling and dysfunction is poorly understood, and there are no currently approved therapies that improve RV function. Chrysin (5,7-dihydroxyflavone) is a phytochemical, which is a flavonoid widely present in plant sources. In various experimental models chrysin has shown to exert cardio-protective effects through its antioxidant and anti-inflammatory effects. In this study, we performed a comprehensive analysis of gene expression changes in heart tissues of rats under hypoxic conditions with chrysin treatment using RNA sequencing (RNA-seq).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35315498" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186990" }, "primaryId" : "GEO:GSE186990", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186990" } ] }, "title" : "CircPan3 Promotes the Ghrelin System and Chondrocyte Autophagy by Sponging miR-667-5p During Rat Osteoarthritis Pathogenesis [RNA-seq]", "dateAssigned" : "2021-11-02T00:00:00.000-05:00", "summary" : "This study aimed to investigate the potential roles of circRNAs in regulating osteoarthritis (OA)-related ghrelin synthesis, autophagy induction, and the relevant molecular mechanisms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34869311" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186992" }, "primaryId" : "GEO:GSE186992", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186992" } ] }, "title" : "CircPan3 Promotes the Ghrelin System and Chondrocyte Autophagy by Sponging miR-667-5p During Rat Osteoarthritis Pathogenesis [circRNA-Seq]", "dateAssigned" : "2021-11-02T00:00:00.000-05:00", "summary" : "This study aimed to investigate the potential roles of circRNAs in regulating osteoarthritis (OA)-related ghrelin synthesis, autophagy induction, and the relevant molecular mechanisms.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34869311" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186996" }, "primaryId" : "GEO:GSE186996", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE186996" } ] }, "title" : "Comprehensive transcriptome analysis of lung tissues in the sugen/hypoxia rats with/without treatment of chrysin or trimetazidine", "dateAssigned" : "2021-11-02T00:00:00.000-05:00", "summary" : "Pulmonary arterial hypertension (PAH) is a debilitating progressive disease characterized by high blood pressure in the pulmonary artery. Chrysin (5,7-dihydroxyflavone) is a phytochemical, which is a flavonoid widely present in plant sources. It is known that right ventricular dysfunction is the worst mortality predictor in patient with PAH. Recent studies have shown that chrysin improves hemodynamic parameters including right ventricular pressure, right ventricular hypertrophy, and pulmonary vascular remodeling in a rat model of chronic hypoxia-induced pulmonary hypertension. On the other hand, trimetazidine (TMZ) is an anti-ischemic agent widely used in the treatment of coronary artery disease. It has been reported that trimetazidine therapy for 3 months on top of standard PAH regime significantly improve right ventricular ejection fraction and functional capacity in patient with PAH. However, the effects of chrysin or trimetazidine on gene expression in lung of patient with PAH. Here, we performed that a comprehensive analysis of gene expression changes in lung tissues of sugen-received rats under hypoxic conditions, which is a model of PAH with chrysin or trimetazidine treatment using RNA sequencing (RNA-seq).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE187005" }, "primaryId" : "GEO:GSE187005", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE187005" } ] }, "title" : "ATF4 Protects the Heart from Failure by Antagonizing Oxidative Stress", "dateAssigned" : "2021-11-02T00:00:00.000-05:00", "summary" : "Cellular redox control is maintained by generation of reactive oxygen/nitrogen species balanced by activation of antioxidative pathways. Disruption of redox balance leads to oxidative stress, a central causative event in numerous diseases including heart failure. Redox control in the heart exposed to hemodynamic stress, however, remains to be fully elucidated. Here, we show that production of cardiomyocyte NADPH (nicotinamide adenine dinucleotide phosphate), a key factor in redox regulation, is decreased in pressure overload-induced heart failure. As a consequence, the level of reduced glutathione is downregulated, a change associated with cardiac cell death, fibrosis, and cardiomyopathy. We report that the pentose phosphate pathway (PPP) and mitochondrial serine/glycine/folate metabolic signaling, two major NADPH-generating pathways in the cytosol and mitochondria, respectively, are induced in the heart by pressure overload. We identify ATF4 (activating transcriptional factor 4) as an upstream transcription factor controlling the expression of multiple enzymes in these two pathways. Consistent with this, joint pathway analysis (JPA) of transcriptomic and metabolomic data reveals that ATF4 preferably controls oxidative stress and redox-related pathways. Overexpression of ATF4 in cardiomyocytes in culture leads to a significant increase in NADPH-producing enzymes whereas silencing of ATF4 decreases their expression. Further, stable isotope tracer experiments reveal that ATF4 overexpression in vitro strongly augments metabolic flux within these two pathways. In vivo, cardiomyocyte-specific deletion of ATF4 exacerbates cardiomyopathy in the setting of pressure overload and accelerates the development of heart failure, attributable, at least in part, to an inability to increase the expression of NADPH-generating enzymes. Taken together, our findings reveal that ATF4 plays a critical role in cardiac homeostasis under conditions of hemodynamic stress by governing both cytosolic and mitochondrial production of NADPH.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35574856" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE187602" }, "primaryId" : "GEO:GSE187602", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE187602" } ] }, "title" : "Adult Neurogenesis of the Median Eminence Contributes to Structural Reconstruction and Recovery of Body Fluid Metabolism in Hypothalamic Self-Repair", "dateAssigned" : "2021-11-03T00:00:00.000-05:00", "summary" : "Conclusions:We revealed that RNA-seq based transcriptome characterization would expedite genetic network analyses of hypothalamic ME and permit the dissection of complex biologic functions during the process of central diabetes insipidus after PEL surgery.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188210" }, "primaryId" : "GEO:GSE188210", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188210" } ] }, "title" : "Transcriptome profiling of cardiomyocytes treated with antiretroviral drugs", "dateAssigned" : "2021-11-04T00:00:00.000-05:00", "summary" : "The use of antiretroviral therapy (ART) improved the life expectancy of HIV patients through the suppression of HIV propagation in host. However, recent studies suggest that long-term use of ART induces comorbid conditions and heart failure in surviving HIV patients. The mechanism associated with the antiretroviral drugs (ARVs) induced cardiotoxicity and heart failure is not clear. In this study, we performed an RNA sequencing with ARV drugs-treated neonatal rat ventricular cardiomyocytes to explore drugs-induced cardiotoxicity. RNA-sequencing data analysis identified 1756 differentially expressed genes (padj<0.05) in cardiomyocytes. Out of 1756 genes, 701 genes were upregulated, and 1055 genes were downregulated in drug-treated cardiomyocytes. Functional enrichment analysis of differentially expressed genes was performed using clusterProfiler R and ingenuity pathway analysis. Our study showed that upregulated genes were linked with the biological processes associated with apoptosis, cellular movement or locomotion, cellular stress, and immune response. In contrast, down-regulated genes were involved in cell division and metabolism. Interestingly, we also found that ARV drugs treatment significantly upregulates the expression of a set of genes involved in cardiac enlargement and hypertrophy in the heart. Collectively, ARVs treatment in cardiomyocytes induces cardiotoxicity through differentially regulation of pathological genes expression in cardiomyocytes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34943964" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188231" }, "primaryId" : "GEO:GSE188231", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188231" } ] }, "title" : "MCLR-elicited hepatic fibrosis and carcinogenic gene expression changes persist in rats with diet-induced nonalcoholic steatohepatitis through a 4-week recovery period", "dateAssigned" : "2021-11-04T00:00:00.000-05:00", "summary" : "Nonalcoholic steatohepatitis (NASH) causes liver extracellular matrix (ECM) remodeling and is a risk factor for fibrosis and hepatocellular carcinoma (HCC). Microcystin-LR (MCLR) is a hepatotoxin produced by fresh-water cyanobacteria that causes a NASH-like phenotype, liver fibrosis, and is also a risk factor for HCC. The focus of the current study was to investigate and compare hepatic recovery after cessation of MCLR exposure in healthy versus NASH animals. Male Sprague-Dawley rats were fed either a control or a high fat/high cholesterol (HFHC) diet for eight weeks. Animals received either vehicle or 30 µg/kg MCLR (i.p: 2 weeks, alternate days). Animals were euthanized at one of three time points: at the completion of the MCLR exposure period and after 2 and 4 weeks of recovery. Histological staining suggested that after four weeks of recovery the MCLR-exposed HFHC group had less steatosis and more fibrosis compared to the vehicle-exposed HFHC group and MCLR-exposed control group. RNA-Seq analysis revealed dysregulation of ECM genes after MCLR exposure in both control and HFHC groups that persisted only in the HFHC groups during recovery. After 4 weeks of recovery, MCLR hepatotoxicity in pre-existing NASH persistently dysregulated genes related to cellular differentiation and HCC. These data demonstrate impaired hepatic recovery and persistent carcinogenic changes after MCLR toxicity in pre-existing NASH.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188336" }, "primaryId" : "GEO:GSE188336", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188336" } ] }, "title" : "The effect of trimethylamine N-oxide on the metabolism of visceral white adipose tissue in spontaneously hypertensive rat", "dateAssigned" : "2021-11-06T00:00:00.000-05:00", "summary" : "Male SHRs and normotensive Wistar-Kyoto(WKY) rats were purchased from Vital River (Vital River Laboratory Animal Technology Co., Ltd, Beijing, China). Briefly, eightteen SHRs aged seven to eight weeks old were randomly assigned to one of three groups: water group (drinking tap water), water containing 333 mg/L or 1g/L TMAO group (TMAO, product number: T1362, Tokyo Chemical Industry, Japan). Six WKY rats of the same age were used as normotensive controls. In this study, WKY rats (n=6), SHR (n=6), and SHR treated with 1g/L TMAO (n=6) were uesd for experiments.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35975941" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188348" }, "primaryId" : "GEO:GSE188348", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188348" } ] }, "title" : "Transcriptomic response in the heart and kidney to different types of antihypertensive drug administration [heart]", "dateAssigned" : "2021-11-06T00:00:00.000-05:00", "summary" : "To unravel antihypertensive drug-induced gene expression changes that are potentially related to the amelioration of end-organ damages, we performed in vivo phenotypic evaluation and transcriptomic analysis on the heart and the kidney, with administration of antihypertensive drugs to two inbred strains of (i.e., hypertensive and normotensive) rats. We chose to use six antihypertensive classes: enalapril (angiotensin converting enzyme inhibitor), candesartan (angiotensin receptor blocker), hydrochlorothiazide (diuretics), amlodipine (calcium-channel blocker), carvedilol (vasodilating beta-blocker) and hydralazine. In the tested rat strains, four of six drugs, including two renin-angiotensin system (RAS) inhibitors, were effective for BP lowering, whereas the remaining two drugs were not. Besides BP lowering, there appeared to be some inter-drug heterogeneity in phenotypic changes, such as suppressed body weight (Bw) gain and Bw-adjusted heart weight reduction. For the transcriptomic response, a considerable number of genes showed prominent mRNA expression changes either in a BP-dependent or BP-independent manner with substantial diversity between the target organs. Noticeable changes of mRNA expression were induced particularly by RAS blockade, e.g., for genes in the natriuretic peptide system (Nppb and Corin) in the heart and for those in the RAS/ kallikrein-kinin system (Ren and rat Klk1 paralogs) and those related to calcium ion binding (Calb1 and Slc8a1) in the kidney. The heart data comprises of this submission and part of ArrayExpress E-MTAB-9244.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34879704" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188349" }, "primaryId" : "GEO:GSE188349", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188349" } ] }, "title" : "Transcriptomic response in the heart and kidney to different types of antihypertensive drug administration [kidney]", "dateAssigned" : "2021-11-06T00:00:00.000-05:00", "summary" : "To unravel antihypertensive drug-induced gene expression changes that are potentially related to the amelioration of end-organ damages, we performed in vivo phenotypic evaluation and transcriptomic analysis on the heart and the kidney, with administration of antihypertensive drugs to two inbred strains of (i.e., hypertensive and normotensive) rats. We chose to use six antihypertensive classes: enalapril (angiotensin converting enzyme inhibitor), candesartan (angiotensin receptor blocker), hydrochlorothiazide (diuretics), amlodipine (calcium-channel blocker), carvedilol (vasodilating beta-blocker) and hydralazine. In the tested rat strains, four of six drugs, including two renin-angiotensin system (RAS) inhibitors, were effective for BP lowering, whereas the remaining two drugs were not. Besides BP lowering, there appeared to be some inter-drug heterogeneity in phenotypic changes, such as suppressed body weight (Bw) gain and Bw-adjusted heart weight reduction. For the transcriptomic response, a considerable number of genes showed prominent mRNA expression changes either in a BP-dependent or BP-independent manner with substantial diversity between the target organs. Noticeable changes of mRNA expression were induced particularly by RAS blockade, e.g., for genes in the natriuretic peptide system (Nppb and Corin) in the heart and for those in the RAS/ kallikrein-kinin system (Ren and rat Klk1 paralogs) and those related to calcium ion binding (Calb1 and Slc8a1) in the kidney. This submission includes the kidney data.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34879704" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188399" }, "primaryId" : "GEO:GSE188399", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188399" } ] }, "title" : "The molecular profile and ability to promote axon regeneration after peripheral nerve injury by Repair Schwann cells is distinctly different from that for developing Schwann cells", "dateAssigned" : "2021-11-08T00:00:00.000-06:00", "summary" : "Since Schwann cells (SCs) support axonal growth at development as well as after peripheral nerve injury (PNI), developing SCs might be able to promote axon regeneration after PNI. The purpose of the current study was to elucidate the capability of developing SCs to induce axon regeneration after PNI. SC precursors (SCPs), immature SCs (ISCs), repair SCs (RSCs) from injured nerves, and non-RSCs from intact nerves were tested by grafting into acellular region of rat sciatic nerve with crush injury. Both of developing SCs completely failed to support axon regeneration, whereas both of mature SCs, especially RSCs, induced axon regeneration. Further, RSCs but not SCPs promoted neurite outgrowth of adult dorsal root ganglion neurons. Transcriptome analysis revealed that the gene expression profiles were distinctly different between RSCs and SCPs. These findings indicate that developing SCs are markedly different from mature SCs in terms of functional and molecular aspects and that RSC is a viable candidate for regenerative cell therapy for PNI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35091563" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188425" }, "primaryId" : "GEO:GSE188425", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188425" } ] }, "title" : "A pulmonary vascular model from endothelialized whole organ scaffolds", "dateAssigned" : "2021-11-08T00:00:00.000-06:00", "summary" : "We introduce a novel in vitro platform that could simulate key native pulmonary vascular phenotypes and functions, and shows the potential of using the bioengineered whole organ as a platform for disease modeling. Since it is becoming clear that vascular endothelium and the coagulation cascade are adversely affected in some COVID19 patients, such an engineered organ system may play an important role in dissecting disease mechanisms and treatments.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34869270" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188520" }, "primaryId" : "GEO:GSE188520", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188520" } ] }, "title" : "Integrative Transcriptomic and Proteomic Analysis Reveals Mechanisms of Silica-induced Pulmonary Fibrosis in Rats", "dateAssigned" : "2021-11-10T00:00:00.000-06:00", "summary" : "To explore proteomic and transcriptomic changes in rat model of silicosis, transcriptomic analysis by microarray and tandem mass tags (TMT)-based proteomic analysis were performed to reveal the expression of mRNAs and proteins in lung tissues. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied to analyze the alterated genes and proteins. The integrated analysis was performed between transcriptome and proteome. Furthermore, the data were further verified by RT-qPCR and parallel reaction monitoring (PRM). In total, 244 differentially expressed proteins (DEPs) showed the same trend as that of the corresponding differentially expressed genes (DEGs) (named DEPs/DEGs). GM2a, CHI3L1, LCN2 and GNAI1, which were validated consistently by RT-qPCR and PRM, are involved in the extracellular matrix (ECM) and inflammation contributed to fibrosis in silicosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34991559" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188540" }, "primaryId" : "GEO:GSE188540", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188540" } ] }, "title" : "Pathway-focused (Ostegenesis) gene expression analysis of healthy, injured and treated rat entheses samples", "dateAssigned" : "2021-11-10T00:00:00.000-06:00", "summary" : "In the present study, a defect was created in the patellar enthesis of a rat model, and treatment was provided using two versions of a biphasic silk fibroin scaffold showing two different transition morphology between the phases. The study included two scaffold-treated groups, two control groups, and one native/healthy group. For the scaffold-treated groups, the defect was treated by implanting one of the two versions of the biphasic scaffolds. One scaffold showed a mixed/interconnected transition zone between the tendon and bony part of the construct (S-MT) while the transition in the other scaffold was abrupt (S-AT). Two control groups were included. In the first group, a defect was created in the patellar enthesis and the tendon was sutured back over the defect and to the bone. In the second group, a transversal cut was performed at the tendon part of the enthesis and sutured back. Samples were collected (n=8) per group at two time points (4 weeks and 12 weeks) after the surgery. Healthy (contralateral) samples were used as reference. The Qiagen Osteogenesis Pathway-focused PCR array was utilized to profile the expression of relevant osteogenic, chondrogenic, and tenogenic genes in samples from healthy, injured and treated patellar entheses samples.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188604" }, "primaryId" : "GEO:GSE188604", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188604" } ] }, "title" : "Tormentic Acid Ameliorates Hepatic Fibrosis in vivo by Inhibiting Glycerophospholipids Metabolism and PI3K/Akt/mTOR and NF-κB Pathways: Based on Transcriptomics and Metabolomics", "dateAssigned" : "2021-11-11T00:00:00.000-06:00", "summary" : "This study aimed to investigate the effects and underlying mechanisms of tormentic acid (TA) on carbon tetrachloride (CCl4)-induced liver fibrosis in rats. The rats were intragastrically administered with 50% CCl4 for 9 weeks to induce hepatic fibrosis, followed by various agents for 6 weeks. Transcriptomic analysis was carried out to predict the potential targets, and then multiple examinations were performed to verify the prediction. The results showed that TA significantly alleviated liver injury and fibrosis, as evidenced by the ameliorative pathological tissue, low transaminase activity, and decreased collagen accumulation. Besides, TA markedly reduced hepatocyte apoptosis by regulating the expression of caspase-3 and Bcl-2 families. The transcriptomic analysis revealed 2,173 differentially expressed genes (DEGs) between the TA and model groups, which could be enriched in the metabolic pathways and the PI3K/Akt and NF-κB signaling pathways. The metabolomics analysis showed that TA could regulate the glycerophospholipid metabolism pathway by regulating the synthesis of phosphatidylserines, phosphatidylethanolamines and phosphatidylcholines. Moreover, the integrative analysis of the transcriptomics and metabolomics data indicated that TA inhibited the glycerophospholipid metabolism pathway by inhibiting the expression of LPCAT4, PTDSS2, PLA2G2A and CEPT1. In addition, the relevant signaling pathways analysis confirmed that TA inhibited HSCs activation by blocking the PI3K/Akt/mTOR pathway and ameliorated inflammatory injury by inhibiting the NF-κB pathway. In conclusion, TA significantly alleviates liver fibrosis in vivo by inhibiting the glycerophospholipid metabolism pathway and the PI3K/Akt/mTOR and NF-κB signaling pathways.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35359829" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188836" }, "primaryId" : "GEO:GSE188836", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE188836" } ] }, "title" : "Morphological, molecular and functional cardiac study during aging in animals submitted to gestational protein restriction", "dateAssigned" : "2021-11-15T00:00:00.000-06:00", "summary" : "Conclusion: The present study suggests that maternal protein restriction may lead to early heart disorders in the LP offspring compared to the NP group. We may hypothesize that rapid heart dysfunction is associated with heart fibrosis, myocardial cell hypertrophy and multiple gene expression abnormalities in the LP offspring.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36353510" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189080" }, "primaryId" : "GEO:GSE189080", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189080" } ] }, "title" : "Differential Expression Profile of MicroRNAs and Tight Junction in Lung Tissue of Rat with Mitomycin-C Induced Pulmonary Veno-Occlusive Disease", "dateAssigned" : "2021-11-18T00:00:00.000-06:00", "summary" : "Pulmonary veno-occlusive disease (PVOD) is characterized by increased pulmonary vascular resistance. Currently, there is a lack of effective treatment. It is of great significance to explore molecular targets for treatment of the disease. This study investigated the differentially expressed profile of miRNAs and tight junction in the lung tissue of rats with mitomycin-C induced PVOD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35252374" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189108" }, "primaryId" : "GEO:GSE189108", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189108" } ] }, "title" : "Transcriptomic analysis of engineered cardiac tissue in an oxygen gradient", "dateAssigned" : "2021-11-18T00:00:00.000-06:00", "summary" : "We report the use of RNA-seq for transcriptional analysis of engineered cardiac tissues cultured in microphysiological systems developed for tight control of oxygen levels, comparing normoxia, hypoxia, and a gradient divided into the normoxic side and hypoxic side.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36475790" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189190" }, "primaryId" : "GEO:GSE189190", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189190" } ] }, "title" : "A preclinical rat model of heart failure with preserved ejection fraction with multiple comorbidities", "dateAssigned" : "2021-11-19T00:00:00.000-06:00", "summary" : "As patients with heart failure with preserved ejection fraction (HFpEF) present with multiple comorbidities, we hypothesized, that metabolic syndrome in aging animals could lead to the development of diastolic dysfunction and HFpEF. HFpEF is a common complex morbid syndrome for which there are currently little evidence-based therapies. Obesity-prone rats were exposed to high-fat diet and compared to obesity-resistant rats fed with standard chow. Phenotyping of metabolic syndrome, associated with echocardiographic and cardiac hemodynamic measurements, was performed after 4 and 12 months. Blood and myocardial tissue sampling were performed for pathobiological evaluation. High-fat diet in obesity-prone rats elicited metabolic syndrome, characterized by increased body and abdominal fat weights, glucose intolerance and hyperlipidemia, as well as increased left ventricular (LV) systolic pressure (after 12 months). This was associated with LV diastolic dysfunction (assessed by increased LV end-diastolic pressure) and pulmonary hypertension (assessed by increased right ventricular systolic pressure). Echocardiography revealed significant concentric LV hypertrophy, while LV ejection fraction was preserved. LV remodeling was associated with cardiomyocyte hypertrophy, as well as myocardial and perivascular fibrosis. Circulating levels of soluble ST2 markedly increased in rats with HFpEF, while plasma NT-proBNP levels decreased. RNA-sequencing analysis identified clusters of genes implicated in fatty acid metabolism and calcium-dependent contraction as upregulated pathways in the myocardium of rats with HFpEF. High-fat diet during 12 months in obesity-prone rats led to the development of a relevant preclinical model of HFpEF with multiple comorbidities, suitable for investigating novel therapeutic interventions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35097026" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189192" }, "primaryId" : "GEO:GSE189192", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189192" } ] }, "title" : "circular RNA expression in the rat orbitofrontal cortex after self-administration of heroin or sucrose", "dateAssigned" : "2021-11-19T00:00:00.000-06:00", "summary" : "In this study we identified circular RNAs that are regulated in the orbitofrontal cortex after chronic heroin self-administration of a dosage of 0.03mg/kg/infusion or sucrose self-administration.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189337" }, "primaryId" : "GEO:GSE189337", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189337" } ] }, "title" : "Chronic sleep deprivation impaired bone formation in growing rats via down-regulating PI3K/AKT Signaling", "dateAssigned" : "2021-11-22T00:00:00.000-06:00", "summary" : "Background: This study aimed to assess the effects of chronic sleep deprivation (CSD) on bone metabolism in growing rats and the likely underlying mechanism. Methods: Twenty 5-week-old male Wistar rats and randomly divided into the CSD and normal control (NC) groups after one-week acclimatization. After a 6-week intervention of sleep deprivation, the left distal femurs of both groups were harvested for micro-computed tomography scans and histological analysis. Meanwhile, the right femur were measured the mRNA and protein expression via RNA sequencing and western blot. Serum bone turnover markers were evaluated at 0, 2, 4, and 6 weeks. Result: CSD impaired the bone growth, showing an imbalance of bone turnover status, dysphasia in the metaphysis growth plate, and deterioration of bone microarchitecture. Further, CSD suppressed bone formation, showing that the expression of osteogenesis-related proteins (col1α1 and osteocalcin) and mRNA (igf1, bglap, runx2, col1α1, pth1r) are down-regulated. Meanwhile, the potential of osteoblast differentiation of bone marrow-derived mesenchymal stem cells decreased in the CSD group. Differentially expressed genes were detected, and functional enrichment analyses revealed that the PI3K/AKT pathway was significantly down-regulated in the CSD group, which was further verified by the protein expression levels.Conclusion: These results suggest that CSD can significantly impaired bone health, and it may exert these effects in part by suppressing bone formation and osteoblast differentiation, and inactivating the PI3K/AKT signaling pathway.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189402" }, "primaryId" : "GEO:GSE189402", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189402" } ] }, "title" : "Differential expression profile of liver fibrosis rats induced by CCl4", "dateAssigned" : "2021-11-23T00:00:00.000-06:00", "summary" : "This study aimed to investigate the protective mechanisms of helenalin on hepatic fibrosis,Rats were intragastrically administrated with 50% CCl4 for 9 weeks to induce liver fibrosis, followed by various medicines for 6 weeks. The transcriptomic analysis was performed in liver tissues by RNA-seq.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36148946" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189509" }, "primaryId" : "GEO:GSE189509", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189509" } ] }, "title" : "Hyperbilirubinemia and phototherapy differentially alter hippocampal transcriptomic patterns in a Gunn rat model of neonatal hyperbilirubinemia.", "dateAssigned" : "2021-11-24T00:00:00.000-06:00", "summary" : "Neonatal hyperbilirubinemia (jaundice) is common in infants, with extremely preterm infants (EPT, <28 weeks gestational age) being at high risk for bilirubin-induced neurotoxicity, resulting in neurodevelopmental impairment. Hyperbilirubinemia is treated using phototherapy to lower unconjugated bilirubin levels. However, the benefits and risks of phototherapy in EPTs have not been well studied, and bilirubin at low levels may be protective as an antioxidant. Phototherapy is associated with markers of oxidative stress in the plasma, but the effects of phototherapy on the hippocampus (HPC) are not known. Bilirubin and insults associated with EPTs impair hippocampal development, a brain structure critical for cognitive function, but their underlying mechanisms remain unknown. The effects of hyperbilirubinemia and phototherapy on the HPC were studied using a Gunn rat model. Jaundiced (jj) and non-jaundiced (Nj) pups were subjected to phototherapy from postnatal day 4 (P4) through P6. The HPC was harvested and processed for RNA sequencing. Serum bilirubin levels were elevated in jj compared to Nj control rats. Phototherapy significantly lowered serum bilirubin levels in jj rats. Compared to Nj rats, 1294 genes were differentially expressed in the jj hippocampal transcriptome and mapped onto the nervous system development, inflammation, and ferroptosis signaling pathways. Phototherapy induces 3297 differentially-expressed genes (DEGs) in rat hippocampal transcriptome compared to untreated rats. These DEGs were annotated to pathways regulating synaptogenesis, long-term potentiation, and neurogenesis. Both hyperbilirubinemia and phototherapy altered expression of 407 genes, which mapped onto hippocampal plasticity functions, including neuritogenesis and long-term potentiation. Our study demonstrates a model for investigating molecular effects of hyperbilirubemia and phototherapy in an EPT-equivalent Gunn rat pup. Our data revealed the effects of hyperbilirubinemia and phototherapy on signaling pathways critical for hippocampal development and plasticity.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189593" }, "primaryId" : "GEO:GSE189593", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189593" } ] }, "title" : "m6A-modified transcripts in the context of MI", "dateAssigned" : "2021-11-26T00:00:00.000-06:00", "summary" : "Roles of m6A-modified mRNA transcripts in the context of MI were preliminarily verified. In the context of m6A methylation, three hub mRNAs were validated to impact the process of apoptosis/angiogenesis. Our study provided theoretical basis and innovative targets for treatment of MI and paved the way for future investigations aiming at exploring upstream epigenetic mechanisms of pathogenesis after MI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35155564" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189615" }, "primaryId" : "GEO:GSE189615", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189615" } ] }, "title" : "Effects of VNS on the NTS", "dateAssigned" : "2021-11-26T00:00:00.000-06:00", "summary" : "Chronic intermittent VNS was applied in sponteneously hypertensive rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37746712" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189640" }, "primaryId" : "GEO:GSE189640", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189640" } ] }, "title" : "Alteration of gene expression by diallyl trisulfide (DATS) administration in chemically-induced rat mammary tumors", "dateAssigned" : "2021-11-26T00:00:00.000-06:00", "summary" : "We report altered gene expression profiles by DATS in chemically-induced rat mammary tumors", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35419300" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189785" }, "primaryId" : "GEO:GSE189785", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189785" } ] }, "title" : "RNA sequencing analysis of the hippocampus reveals transcriptomic signatures of PTZ-kindled seizure rats and upon treatment of novel anti-convulsant chemical Q808", "dateAssigned" : "2021-11-29T00:00:00.000-06:00", "summary" : "The present study aimed to use RNA sequencing (RNA-seq) to reveal the gene transcriptomic profile of chronic PTZ-kindled seizure rats and the difference of the PTZ model rat before and after treatment with Q808.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35345815" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189797" }, "primaryId" : "GEO:GSE189797", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189797" } ] }, "title" : "RNAseq analysis of CD4+EGFP+ and CD8+EGFP+ regulatory T cells", "dateAssigned" : "2021-11-29T00:00:00.000-06:00", "summary" : "Gene-edited rats were generated in which EGFP was placed under the transcriptional control of the Foxp3 promoter. EGFP expression by CD4+ and CD8+ T cells allowed to define regulatory T cells (Treg) in both T cell compartments. This Foxp3-EGFP rats constitute a useful model to identify CD4+ and CD8+ natural and induced Treg. Transcriptomic analyses showed similarities but also differences among CD4+ and CD8+ EGFP+ cells, this being the first description of the transcriptomic profile in natural FOXP3+ CD8+ Treg.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36635667" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189809" }, "primaryId" : "GEO:GSE189809", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189809" } ] }, "title" : "The transcriptomic analysis of bladder tissue in a rat model of ketamine-induced bladder fibrosis", "dateAssigned" : "2021-11-29T00:00:00.000-06:00", "summary" : "We established the ketamine-induced cystitis (KIC) models in female Sprague-Dawley rats. The bladder of the ketamine group and the control group were obtained to perform transcriptome analysis.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189815" }, "primaryId" : "GEO:GSE189815", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189815" } ] }, "title" : "Single cell RNA-seq analysis of TBX18-driven reprogramming of ventricular myocytes to cardiac pacemaker cells", "dateAssigned" : "2021-11-29T00:00:00.000-06:00", "summary" : "Conclusion: Tgfβ signaling inhibition with a83-01 prevents against myofibroblast activation, cardiomyocytes apoptosis and inflammatory response induced by TBX18, and short term treatment of A8301 does not strongly interfere the reprogramming process and efficiency.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189845" }, "primaryId" : "GEO:GSE189845", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189845" } ] }, "title" : "The effect of FBS and cyclic mechanical stretch on serum starved mesenchymal stem cells", "dateAssigned" : "2021-11-29T00:00:00.000-06:00", "summary" : "Conclusions: Our RNA-seq data revealed that both CMS and FBS activates quiescent MSCs through regulating similar genes and pathways. miR-337 is one of the main factors that regulate MSC activation by targeting PI3K-Akt pathway.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189855" }, "primaryId" : "GEO:GSE189855", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189855" } ] }, "title" : "Transcriptomic profile of non-alcoholic fatty liver disease in rat induced by high-fat diet", "dateAssigned" : "2021-11-30T00:00:00.000-06:00", "summary" : "This study aimed to investigate the effect and underlying mechanism of Smilax china L.(SCL) on lipid metabolic disturbance in rats with non-alcoholic fatty liver disease (NAFLD). Rats were administrated with a high-fat diet (HFD) for 8 weeks to induce NAFLD, followed by SCL treatment for further 6 weeks.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189862" }, "primaryId" : "GEO:GSE189862", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189862" } ] }, "title" : "Uncovering the mechanisms-based quality control of traditional Chinese medicine against essential hypertension by network analysis and experimental validation", "dateAssigned" : "2021-11-30T00:00:00.000-06:00", "summary" : "A total of 4276 lncRNAs (1426 upregulated and 2850 down-regulated) and 9230 mRNAs (5187 upregulated and 4043 down-regulated) were differently expressed in SHR-C compared with WKY, whereas 265 lncRNAs (65 up-regulated and 200 down-regulated) and 267 mRNAs (132 upregulated and 135 down-regulated) were differently expressed after BSJY treatment (fold change >2. 0 and P value< 0. 05). Taking the intersection of the two sets, the analysis found that 8 lncRNAs and 35 mRNAs were upregulated, whereas 11 lncRNAs and 15 mRNAs were downregulated in the WKY vs. SHR-C group and SHR-Bh group (fold change > 2. 0 and P value < 0. 05). It showed the heatmap that were constructed using fold change, It showed the Volcano plots that were constructed using fold change values and P values and revealed the relationship between fold change and statistical significance.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189876" }, "primaryId" : "GEO:GSE189876", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189876" } ] }, "title" : "Dihydrocoumarin, an extract of Melilotus officinalis, inhibits IgE-dependent mast cell activation in vitro and in vivo", "dateAssigned" : "2021-11-30T00:00:00.000-06:00", "summary" : "In summary, dihydrocoumarin could suppress MC activation in vitro and in vivo through inhibiting the MAPKs and NF-kB pathways.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189881" }, "primaryId" : "GEO:GSE189881", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189881" } ] }, "title" : "next generation sequencing of icariin protection against contrast induced acute kidney injury", "dateAssigned" : "2021-11-30T00:00:00.000-06:00", "summary" : "This study aims to investigate the underlying mechanism of protective effect of icariin in contrast medium induced acute kidney injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189922" }, "primaryId" : "GEO:GSE189922", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189922" } ] }, "title" : "Single cell RNA-sequencing of rat gingva with diabetic periodontitis", "dateAssigned" : "2021-11-30T00:00:00.000-06:00", "summary" : "Using single cell-RNA sequencing, we reported structural and functional changes of gingival cellulome in diabetes-associated periodontitis, with the aim to identify distinct cell populations and functions involving in disease progression. We identified inflammation-related stromal and epithelial subpopulations that expanded in diabetes-associated periodontitis, creating distinct immune microenvironment that drives the progression of the disease.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37562294" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189942" }, "primaryId" : "GEO:GSE189942", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189942" } ] }, "title" : "Identification of AIA_H related genes and BHGZD therapeutic effect related genes. [array]", "dateAssigned" : "2021-12-01T00:00:00.000-06:00", "summary" : "To obtain AIA_H related genes [the significant differentially expressed genes (DEGs) of AIA_H model group vs. Normal control group] and BHGZD therapeutic effect related genes [DEGs of BHGZD treatment group vs. AIA_H model group], the microarray analysis was carried out.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35799788" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189964" }, "primaryId" : "GEO:GSE189964", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE189964" } ] }, "title" : "Intrinsic cardiac adrenergic (ICA) cells contribute to LPS-induced myocardial dysfunction", "dateAssigned" : "2021-12-01T00:00:00.000-06:00", "summary" : "The role of ICA cells in septic cardiomyopathy is unknown. Here we show that norepinephrine (NE) secretion from ICA cells is increased through activation of Toll-like receptor 4 (TLR4) to aggravate myocardial TNF-α production and dysfunction by lipopolysaccharide (LPS). In ICA cells, LPS activated TLR4-MyD88/TRIF-AP-1 signaling that promoted NE biosynthesis through expression of tyrosine hydroxylase, but did not trigger TNF-α production due to impairment of p65 translocation. Our findings suggest that ICA cells may be a potential therapeutic target for septic cardiomyopathy.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35079095" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190008" }, "primaryId" : "GEO:GSE190008", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190008" } ] }, "title" : "tsRNAs Are Potential Biomarkers of Acute Rejection in Vascularized Composite Allotransplantation", "dateAssigned" : "2021-12-02T00:00:00.000-06:00", "summary" : "Conclusion: In conclusion, it is speculated that tiRNA-1-34-Glu-CTC-1 plays an important role in VCA induced acute rejection by regulating CACNA1D gene in MAPK signaling pathway. This provides a new insight into the mechanism and therapeutic targets of acute rejection.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190020" }, "primaryId" : "GEO:GSE190020", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190020" } ] }, "title" : "1α,25-Dihydroxyvitamin D3 Regulates Packaging of microRNAs within Extracellular Matrix Vesicles and Their Release in the Matrix", "dateAssigned" : "2021-12-02T00:00:00.000-06:00", "summary" : "Growth plate chondrocytes are regulated by numerous factors and hormones as they mature during endochondral bone formation. Chondrocytes in the growth plate’s growth zone (GC cells) produce and export matrix vesicles (MVs) under the regulation of 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3]. 1α,25(OH)2D3 secreted by the cells acts on the MV membrane, releasing its contents. This study examined the regulatory role 1α,25(OH)2D3 has over the production and packaging of microRNA into MVs by GC cells and the ability to release microRNA from MVs once produced. We treated GC cells with 1α,25(OH)2D3 and then sequenced the microRNA in the cells and MVs. We also treated MVs with 1α,25(OH)2D3 and determined if the microRNA was released. To assess whether MVs can act directly with chondrocytes and if this is regulated by 1α,25(OH)2D3, we stained MVs with a membrane dye and treated GC cells with them. 1α,25(OH)2D3 regulated the production and packaging of microRNA into matrix vesicles. MVs did not release microRNA when treated with 1α,25(OH)2D3, indicating a heterogeneous MV population or a protective factor. Stained MVs were endocytosed by GC cells and this was increased with 1α,25(OH)2D3 treatment. This study adds new regulatory roles for 1α,25(OH)2D3 with respect to packaging and transport of MV microRNAs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36840756" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190146" }, "primaryId" : "GEO:GSE190146", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190146" } ] }, "title" : "Microarray expression profiling of the spiral ganglion of hearing and deafened rats", "dateAssigned" : "2021-12-03T00:00:00.000-06:00", "summary" : "The data are further described in Rahman MT, Bailey EM, Gansemer BM, Pieper AA, Manak JR, and Green SH. Anti-inflammatory compounds improve spiral ganglion neuron survival after aminoglycoside-induced hair cell loss in rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36697994" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190179" }, "primaryId" : "GEO:GSE190179", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190179" } ] }, "title" : "Transcriptome analysis revealed the symbiosis niche of 3D scaffolds to accelerate bone defect healing", "dateAssigned" : "2021-12-04T00:00:00.000-06:00", "summary" : "3D printed scaffolds have been shown to be superior in promoting tissue repair, but the cell-level specific regulatory network activated by 3D printing scaffolds with different material components to form a symbiosis niche have not been systematically revealed. Here, three typical 3D printed scaffolds, including natural polymer hydrogel (Gelatin-methacryloyl, GelMA), synthetic polymer material (Polycaprolactone, PCL) and bioceramic (β-tricalcium phosphate, β-TCP), were fabricated to explore the regulating effect of the symbiotic microenvironment during bone healing. Enrichment analysis showed that hydrogel promotes tissue regeneration and reconstruction by improving blood vessel generation by enhancing oxygen transport and red blood cell development. The PCL scaffold regulates cell proliferation and differentiation by promoting cellular senescence, cell cycle and DNA replication pathways, accelerating the process of endochondral ossification and the formation of callus. The β-TCP scaffold can specifically enhance the expression of osteoclast differentiation and extracellular space pathway genes to promote the differentiation of osteoclasts and promote the process of bone remolding. In these processes, specific biomaterial properties can be used to guide cell behavior and regulate molecular network in the symbiotic microenvironment to reduce the barriers of regeneration and repair.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35040587" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190203" }, "primaryId" : "GEO:GSE190203", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190203" } ] }, "title" : "Gut microbial metabolite trimethylamine N-oxide aggravates pulmonary hypertension", "dateAssigned" : "2021-12-05T00:00:00.000-06:00", "summary" : "Trimethylamine N-oxide (TMAO), a metabolite derived from intestine microbial flora, enhances vascular inflammation in a variety of cardiovascular disease, and the bacterial communities associated with trimethylamine N-oxide (TMAO) metabolism is higher in pulmonary hypertension (PH) patients. The effects of TMAO on PH, however, has not been elucidated. In the present study, we found that circulating TMAO is elevated in intermediate to high-risk PH patients when compared to healthy control or low-risk PH patients. In monocrotaline-induced rat PH models, circulating TMAO is elevated; and reduction of TMAO using 3,3-dimethyl-1-butanol (DMB) significantly decreased right ventricle systolic pressure, pulmonary vascular muscularization in both monocrotaline-induced rat PH and hypoxia induced mice PH models. RNA sequencing of rat lungs on DMB revealed significant suppression of pathways involved in cytokine-cytokine receptor interaction, and cytokine and chemokine signaling. Protein-protein interaction analysis of the differentially expressed transcripts regulated by DMB showed 5 hub genes with a strong connectivity of proinflammatory cytokines and chemokines including Kng1, Cxcl1, Cxcl2, CxcL6 and Il6. In vivo, TMAO significantly increased the expression of Kng1, Cxcl1, Cxcl2, CxcL6 and Il6 in bone marrow derived macrophage. And TMAO-treated conditioned medium from macrophage increased the proliferation and migration of pulmonary artery smooth muscle cells; but TMAO treatment did not change the proliferation or migration of pulmonary artery smooth muscle cells. In conclusion, our study demonstrates that TMAO is increased in severe PH, and the reduction of TMAO using DMB reduces pulmonary vascular muscularization and alleviates PH via suppressing the macrophage production of chemokines and cytokines.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190218" }, "primaryId" : "GEO:GSE190218", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190218" } ] }, "title" : "Roux-en-Y gastric bypass and caloric restriction but not gut hormone-based treatments profoundly impact the hypothalamic transcriptome in obese rats", "dateAssigned" : "2021-12-05T00:00:00.000-06:00", "summary" : "Background: The hypothalamus is an important brain region for the regulation of energy balance. Roux-en-Y gastric bypass (RYGB) surgery and gut hormone-based treatments are known to reduce body weight, but their effects on hypothalamic gene expression and signaling pathways are poorly studied. Methods: Diet-induced obese male Wistar rats were randomized into the following groups: RYGB, sham-operation, sham + body weight-matched (BWM) to the RYGB group, osmotic minipump delivering PYY3-36 (0.1mg/kg/day), liraglutide s.c. (0.4mg/kg/day), PYY3-36+liraglutide and saline. All groups (except BWM) were kept on a free choice of high- and low-fat diets. Four weeks after interventions, hypothalami were collected for RNA-sequencing. Results: While rats in the RYGB, BWM and PYY3-36+liraglutide groups had comparable reductions in body weight, only RYGB and BWM treatment had a major impact on hypothalamic gene expression. In these groups, hypothalamic leptin receptor expression as well as the JAK–STAT, PI3K-Akt and AMPK signaling pathways were upregulated. No significant changes could be detected in PYY3-36+liraglutide, liraglutide and PYY treated groups. Conclusions: Despite causing similar body weight changes compared to RYGB and BWM, PYY3-36+liraglutide treatment does not impact hypothalamic gene expression. Whether this striking difference is favorable or unfavorable to metabolic health in the long term requires further investigation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35010991" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190219" }, "primaryId" : "GEO:GSE190219", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190219" } ] }, "title" : "Developing high throughput single-cell single-nucleotide in situ pairwise sequencing for macromolecule spatail-omics", "dateAssigned" : "2021-12-05T00:00:00.000-06:00", "summary" : "To identified the method which can differentiate in situ SNP modification, we constructed an RNAseq library to identify SNPs in the C6 cell line and parent-specific SNPs in the PVN of C57. Design probes for these SNPs for in situ SNP detection and was applied to detect tumor driver genes mutation and allele specific expression of parental genes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190244" }, "primaryId" : "GEO:GSE190244", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190244" } ] }, "title" : "Transcriptome sequencing of SLC2A10 knock-down VSMCs", "dateAssigned" : "2021-12-06T00:00:00.000-06:00", "summary" : "shRNA was used to knock down SLC2A10 VSMCs. The effectiveness of gene interference was tested by qPCR. Transcriptome sequencing was performed and FASTQ files from RNA- seq experiments were clipped and trimmed. KEGG enrichment analysis on differently expressed genes was performed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190318" }, "primaryId" : "GEO:GSE190318", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190318" } ] }, "title" : "Genome-scale Screening in a Rat Haploid System Identifies Thop1 as a Modulator of Pluripotency Exit", "dateAssigned" : "2021-12-06T00:00:00.000-06:00", "summary" : "Rat embryonic stem cells (ESCs), which are widely studied, can self-renew and exhibit pluripotency in long-term culture, but the mechanism underlying how they exit pluripotency remains obscure. Rat haploid ESCs (haESCs) enable advances in the discovery of unknown functional genes owing to their homozygous and pluripotent characteristics. Herein, we performed genome-wide mutation using piggyBac transposons in rat haESCs and obtained differentiation-retarded mutants assisted by Rex1-GFP reporter selection. High-throughput sequencing analysis further revealed numerous insertions related to various pathways affecting random differentiation. Thereafter, deletion of Thop1 (one candidate gene in the screened list) arrested the differentiation of rat ESCs by inhibiting the phosphorylation of ERK1/2, whereas overexpression of Thop1 promoted rat ESCs exit from pluripotency. Our findings provide an ideal tool to study functional genomics in rats: a homozygous haploid system carrying a pluripotency reporter that facilitates robust discovery of the mechanisms involved in the self-renewal or pluripotency of rat ESCs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35274380" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190331" }, "primaryId" : "GEO:GSE190331", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190331" } ] }, "title" : "Expression data of miRNAs and lncRNAs from the lumbosacral spinal cord of fetal rats with anorectal malformations in embryonic day 17", "dateAssigned" : "2021-12-07T00:00:00.000-06:00", "summary" : "Many dysregulated miRNAs and lncRNAs as the primary factor could be play an important role in the development of lumbosacral spinal cord of fetal rats with anorectal malformations in embryonic day 17. High-throughput sequencing was utilized to reveal the expression of non-coding RNAs underlying the development of anorectal malformations.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190332" }, "primaryId" : "GEO:GSE190332", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190332" } ] }, "title" : "Expression data of miRNAs and lncRNAs from the lumbosacral spinal cord of fetal rats with anorectal malformations in embryonic day 19", "dateAssigned" : "2021-12-07T00:00:00.000-06:00", "summary" : "many dysregulated miRNAs and lncRNAs as the primary factor could be play an important role in the development of lumbosacral spinal cord of fetal rats with anorectal malformations in embryonic day 17.High-throughput sequencing was utilized to reveal the expression of non-coding RNAs underlying the development of anorectal malformations.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190334" }, "primaryId" : "GEO:GSE190334", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190334" } ] }, "title" : "Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones [RNA-seq]", "dateAssigned" : "2021-12-07T00:00:00.000-06:00", "summary" : "A Prader-willi syndrome (PWS) model of β-cell dysfunction", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37068109" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190336" }, "primaryId" : "GEO:GSE190336", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190336" } ] }, "title" : "Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones [ncRNA-Seq]", "dateAssigned" : "2021-12-07T00:00:00.000-06:00", "summary" : "A Prader-willi syndrome (PWS) model of β-cell dysfunction", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37068109" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190355" }, "primaryId" : "GEO:GSE190355", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190355" } ] }, "title" : "The effects of physical exercise training and / or human neural progenitor cell transplantation on the infarct area environment of stroke rats", "dateAssigned" : "2021-12-07T00:00:00.000-06:00", "summary" : "To detect the effects of physical exercise training and / or human neural progenitor cell transplantation on the infarct area environment of stroke rats, we conducted a genome-wide RNA sequencing and a gene ontology (GO) enrichment analysis of differentially expressed mRNAs in each group was performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35030322" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190472" }, "primaryId" : "GEO:GSE190472", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190472" } ] }, "title" : "Study on VEGF regulation mechanism of acupuncture improving endometrial receptivity in IVF-ET", "dateAssigned" : "2021-12-08T00:00:00.000-06:00", "summary" : "We find that the Endometrial Blood Vessel Generation is an important part ofthe establishment of Endometrial Receptivity. We have demonstrated inprevious experiments: Acupuncture in IVF-ET treatment can effectively improve Endometrial Receptivity and improve the pregnancy rate, therefore, we proposea VEGF signaling pathway in Acupuncture can improve Endometrial receptivity, thus improving the success rate of IVF-ET Hypothesis. Around the hypothesisintends to adopt the rat model of IVF-ET, through methods of acupuncture, acupuncture combined with blocker, research the related indexes effect performance that acupuncture on the VEGF signaling pathway in endometrial. Using experimental techniques such as Morphological observation, ELIAS, Immunohistochemistry, Real-time quantitative PCR, Methylation-sensitive high-resolution melting curve method(MS-HRM), to complete the research ofobserving the Effect of acupuncture interference IVF-ET, Blocking the impaction VEGF to the effect, the relationship VEGF or gene methylation inits receptors with effect. From the molecular level clarify the adverse effects and mechanism action that acupuncture will improve IVF-ET superovulation of endometrial receptivity, through adjust VEGF signaling pathway, to provide a scientific basis for acupuncture in IVF-ET treatment", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190480" }, "primaryId" : "GEO:GSE190480", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190480" } ] }, "title" : "Genome-scale Screening in a Rat Haploid System Identifies Thop1 as a Modulator of Pluripotency Exit II", "dateAssigned" : "2021-12-08T00:00:00.000-06:00", "summary" : "Rat embryonic stem cells (ESCs), which are widely studied, can self-renew and exhibit pluripotency in long-term culture, but the mechanism underlying how they exit pluripotency remains obscure. Rat haploid ESCs (haESCs) enable advances in the discovery of unknown functional genes owing to their homozygous and pluripotent characteristics. Herein, we performed genome-wide mutation using piggyBac transposons in rat haESCs and obtained differentiation-retarded mutants assisted by Rex1-GFP reporter selection. High-throughput sequencing analysis further revealed numerous insertions related to various pathways affecting random differentiation. Thereafter, deletion of Thop1 (one candidate gene in the screened list) arrested the differentiation of rat ESCs by inhibiting the phosphorylation of ERK1/2, whereas overexpression of Thop1 promoted rat ESCs exit from pluripotency. Our findings provide an ideal tool to study functional genomics in rats: a homozygous haploid system carrying a pluripotency reporter that facilitates robust discovery of the mechanisms involved in the self-renewal or pluripotency of rat ESCs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35274380" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190522" }, "primaryId" : "GEO:GSE190522", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190522" } ] }, "title" : "Identification of AIA_H related genes and BHGZD therapeutic effect related genes. [RNA-Seq]", "dateAssigned" : "2021-12-09T00:00:00.000-06:00", "summary" : "To obtain AIA_H related genes [the significant differentially expressed genes (DEGs) of AIA_H model group vs. Normal control group] and BHGZD therapeutic effect related genes [DEGs of BHGZD treatment group vs. AIA_H model group], the microarray analysis was carried out.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35799788" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190612" }, "primaryId" : "GEO:GSE190612", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190612" } ] }, "title" : "Transcriptional instability prevents dispersion of functional vomeronasal receptor genes [rat]", "dateAssigned" : "2021-12-09T00:00:00.000-06:00", "summary" : "Rodents perceive pheromones via vomeronasal receptors encoded by the Vr and Fpr gene superfamilies. The evolution of these latter is exceptionally dynamic. We report here that high numbers of V1r pseudogenes are scattered in mammalian genomes, contrasting with the clustered organization of functional V1r and Fpr genes. We also found that V1r pseudogenes are more likely to be expressed when located in a functional V1r gene cluster than when isolated. To explore the potential regulatory role played by the association of functional vomeronasal receptor genes with their clusters, we dissociated the mouse Fpr-rs3 from its native cluster via transgenesis. Singular and specific transgenic Fpr-rs3 transcription was observed in young vomeronasal neurons, but was only transient. Our data point to the existence of transcription stabilizing elements not coupled to vomeronasal gene units but rather associated with vomeronasal gene clusters, and thus explain the evolutionary conserved clustered organization of functional vomeronasal genes.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36383665" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190630" }, "primaryId" : "GEO:GSE190630", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190630" } ] }, "title" : "RNA-Sequencing of rats treated with Chinese herbal medicine Pulsatilla Chinensis", "dateAssigned" : "2021-12-10T00:00:00.000-06:00", "summary" : "Pulsatilla chinensis (PC) is a traditional Chinese medicinewith detoxification activities. It has been used for dysentery, vaginal trichomoniasis, bacterial infections and malignant tumor treatment. Gavage administration of PC in hyperlipidemia rats for 11 weeks resulted in obviously reduced serum total cholesterol, LDL-cholesterol and ameliorated fatty liver. So we wanted to further investigate the relationship between PC and lipid metabolism related pathways or genes", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190685" }, "primaryId" : "GEO:GSE190685", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190685" } ] }, "title" : "Nonwoven-based gelatin/polycaprolactone membrane loaded with ERK inhibitor U0126 for treatment of tendon defects", "dateAssigned" : "2021-12-10T00:00:00.000-06:00", "summary" : "Conclusion: Taken together, we have found U0126 promoted tenogenesis in TSPCs through activating GDF6, and NBM loaded with U0126 significantly promoted tendon defect healing, which provides a new treatment for tendon injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190744" }, "primaryId" : "GEO:GSE190744", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190744" } ] }, "title" : "High-throughput sequencing analyses of transcript changes in growth plates upon dexamethasone treatment", "dateAssigned" : "2021-12-13T00:00:00.000-06:00", "summary" : "Glucocorticoid-induced growth retardation (GIGR) is a common adverse effect of glucocorticoid treatment in pediatric patients. Accumulating evidence indicates that non-coding RNAs (ncRNAs) are involved in the pathogenesis of GIGR, but the roles of specific ncRNAs in growth remain largely unknown. In this study, we established an in vivo GIGR rat model by 7- or 14- day dexamethasone (Dex) treatment and performed high-throughput RNA sequencing to identify mRNAs, lncRNAs, circRNAs, and miRNAs differentially expressed in GIGR rats relative to control rats in the growth plates.High-throughput RNA sequencing identified 1718 mRNAs, 896 lncRNAs, 60 circRNAs, and 72 miRNAs with differing expression levels at 7d group. At 14d group, 1515 mRNAs, 880 lncRNAs, 46 circRNAs, and 55 miRNAs with differential expression were identified. Eight mRNAs were validated by RT-qPCR, with expression level differences consistent with RNA sequencing data. Function enrichment analyses indicate that the PI3K-Akt signaling pathway, NF-kappa B signaling pathway, and TGF-beta signaling pathway participated in the development of the GIGR. Then, ceRNA networks were constructed to investigate the potential molecular mechanisms of ncRNAs. These results provide new insights for exploring the molecular mechanisms underlying GIGR.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36684670" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190758" }, "primaryId" : "GEO:GSE190758", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190758" } ] }, "title" : "Human pluripotent stem cell-derived cardiomyocyte maturation both in vivo and in vitro", "dateAssigned" : "2021-12-13T00:00:00.000-06:00", "summary" : "We studied cardiomyocytes maturation through extended in vitro culture and also used the adult rat as a bioreactor,", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37028405" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190840" }, "primaryId" : "GEO:GSE190840", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190840" } ] }, "title" : "The Renin-Angiotensin System, High Inherent Aerobic Capacity, and Low Breast Cancer Risk", "dateAssigned" : "2021-12-13T00:00:00.000-06:00", "summary" : "Conclusions: This study found a biologically plausible heritable relationship linking mechanisms associated with aerobic capacity and the development of breast cancer. Through RNA-seq analyses, we identified AGT as a biomarker pointing to differences in the regulation of RAS as a candidate mediator linking aerobic capacity and breast cancer.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190858" }, "primaryId" : "GEO:GSE190858", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190858" } ] }, "title" : "JUN ChIP-seq in injured nerve", "dateAssigned" : "2021-12-14T00:00:00.000-06:00", "summary" : "ChIP-seq of c-JUN in injured rat peripheral nerve", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190863" }, "primaryId" : "GEO:GSE190863", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190863" } ] }, "title" : "Treatment of hepatocellular carcinoma with autologous platelets encapsulating sorafenib or lenvatinib: a novel therapy exploiting tumor-platelet interactions", "dateAssigned" : "2021-12-14T00:00:00.000-06:00", "summary" : "We investigated the effect of the drug encapsulation process on the degradation of resident mRNA inherited from megakaryocytes in platelets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34935134" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190893" }, "primaryId" : "GEO:GSE190893", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190893" } ] }, "title" : "Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation [DNA-Seq]", "dateAssigned" : "2021-12-14T00:00:00.000-06:00", "summary" : "Precise Hox gene expression is crucial for embryonic patterning. Local transcription factor binding and distal enhancer elements have emerged as the major regulatory modes controlling the initiation and maintenance of Hox gene expression. However, quantifying their relative contributions has remained elusive. Here, we introduce ‘synthetic regulatory reconstitution’, a novel conceptual framework for studying gene regulation and apply it to the mammalian HoxA cluster. To measure the HoxA intrinsic regulatory potential and distal enhancer contributions, we de novo synthesized and delivered variant rat HoxA clusters (130-170 kilobases each) to an ectopic location in the mouse genome. We find that a minimal HoxA cluster lacking distal enhancers induces the appropriate gene set and establishes distinct chromatin domains in response to patterning signals, while distal enhancers are required for full transcriptional output. These results suggest that the genomically compact Hox clusters contain all the information to decode patterning signals and maintain positional information", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190952" }, "primaryId" : "GEO:GSE190952", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE190952" } ] }, "title" : "Microarray expression profile and bioinformatics analysis of circular RNAs in the phenotypic switching of rat vascular smooth muscle cells: a preliminary study", "dateAssigned" : "2021-12-15T00:00:00.000-06:00", "summary" : "In order to further study the role of circular RNA in the phenotypic transformation of vascular smooth muscle cells (VSMCs), the differential expression profile of circRNA in the phenotypic transition of VSMCs induced by platelet-derived growth factor-BB (PDGF-BB) was screened using chip technology. Vascular smooth muscle cells from rat thoracic aorta were induced with 20ng/ml PDGF-BB as the experimental group and compared with the control group. After induction for 24 hours, the differentially expressed circRNA was screened by circular RNA chip.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE191141" }, "primaryId" : "GEO:GSE191141", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE191141" } ] }, "title" : "A nutriepigenetic pathway links diet to sensory plasticity", "dateAssigned" : "2021-12-17T00:00:00.000-06:00", "summary" : "RNAseq data related to the tongue epithelia of R.norvegicus rats fed either a chow and water diet or chow and water+30% sucrose", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE191287" }, "primaryId" : "GEO:GSE191287", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE191287" } ] }, "title" : "Transcriptome analysis of lung-derived MBP-specific T cells", "dateAssigned" : "2021-12-20T00:00:00.000-06:00", "summary" : "Transcriptome analysis of MBP-reactive T cells isolated from the lungs of wild type LEW/Crl rats (Rattus norvegicus) pre-treated with PBS or NEO on day 0 and day 1 after intratracheal immunization with MBP.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35197636" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192399" }, "primaryId" : "GEO:GSE192399", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192399" } ] }, "title" : "Gene expression of brain regions activated by sevoflurane and propofol", "dateAssigned" : "2021-12-21T00:00:00.000-06:00", "summary" : "We performed gene expression analysis using microarrays in the identified regions that have been related to the mechanisms of anesthetic action and side effects. Gene expression changes in these brain regions were determined for sevoflurane and propofol to understand the mechanisms that cause differences among anesthetics.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192411" }, "primaryId" : "GEO:GSE192411", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192411" } ] }, "title" : "Transcriptome analysis of spinal cord microglia and total spinal cord", "dateAssigned" : "2021-12-21T00:00:00.000-06:00", "summary" : "Transcriptome analysis of spinal cord microglia and total spinal cord from Lewis rats intratracheally treated with PBS, neomycin or vancomycin.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35197636" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192425" }, "primaryId" : "GEO:GSE192425", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192425" } ] }, "title" : "Liraglutide + PYY3-36 combination therapy mimics effects of Roux-en-Y bypass on early NAFLD whilst lacking-behind in metabolic improvements.", "dateAssigned" : "2021-12-21T00:00:00.000-06:00", "summary" : "Background: Non-alcoholic fatty liver disease (NAFLD) is common in the general population. Treatment options for NAFLD are very limited, GLP-1 analogues, however, seem to be effective. Roux-en-Y gastric bypass (RYGB) is highly effective in terms of body weight loss and improves histologic and metabolic markers of NAFLD. We directly compared the effects of RYGB and a treatment with liraglutide and/or peptide tyrosine tyrosine 3-36 (PYY3-36) on early NAFLD. Methods: High-fat diet (HFD)-induced obese male Wistar rats were randomized into 6 treatment groups: RYGB, sham-operation (Sham), liraglutide (0.4mg/kg/day), PYY3-36 (0.1mg/kg/day), li-raglutide+PYY3-36 and saline. Following intervention and after an observation period of 4 weeks liver samples were histologically evaluated, ELISAs and RT-qPCRs +RNA sequencing were per-formed. Results: RYGB and liraglutide+PYY3-36 induced a similar body weight loss and marked histological improvements with significantly less steatosis compared to sham/saline. However, only RYGB induced significant metabolic improvements and mRNA expression changes. Con-clusions: liraglutide+PYY3-36 combination therapy mimics the positive effects of RYGB on weight reduction and on hepatic steatosis, while its effects on insulin resistance and adipose tissue dys-function (adiponectin/leptin ratio) lack behind RYGB.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35160204" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192589" }, "primaryId" : "GEO:GSE192589", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192589" } ] }, "title" : "Developmental toxicity of Nafion byproduct 2 (NBP2) in the Sprague-Dawley rat", "dateAssigned" : "2021-12-24T00:00:00.000-06:00", "summary" : "Nafion byproduct 2 (NBP2; CAS: 749836-20-2; Product #: 6164-3-3J; Lot: 512400; SynQuest Laboratories Alachua, FL, USA) is a polyfluoroalkyl ether sulfonic acid that was recently detected in surface water, drinking water, and human serum samples from monitoring studies in North Carolina, USA. We orally exposed pregnant Sprague-Dawley rats to NBP2 from gestation day (GD) 14–18 (0.1–30 mg/kg/d), GD17-21, and GD8 to postnatal day (PND) 2 (0.3–30 mg/kg/d) to characterize maternal, fetal, and postnatal effects. GD14-18 exposures were also conducted with perfluorooctane sulfonate (PFOS) for comparison to NBP2, as well as data previously published for hexafluoropropylene oxide-dimer acid (HFPO-DA or GenX). NBP2 produced stillbirth (30 mg/kg), reduced pup survival shortly after birth (10 mg/kg), and reduced pup body weight (10 mg/kg). Histopathological evaluation identified reduced glycogen stores in newborn pup livers and hepatocyte hypertrophy in maternal livers at ≥ 10 mg/kg. Exposure to NBP2 from GD14-18 reduced maternal serum total T3 and cholesterol concentrations (30 mg/kg). Maternal, fetal, and neonatal liver gene expression was investigated using RT-qPCR pathway arrays, while maternal and fetal livers were also analyzed using TempO-Seq transcriptomic profiling. Overall, there was limited alteration of genes in maternal or F1 livers from NBP2 exposure with significant changes mostly occurring in the top dose group (30 mg/kg) associated with lipid and carbohydrate metabolism. Metabolomic profiling indicated elevated maternal bile acids for NBP2, but not HFPO-DA or PFOS, while all three reduced 3-indolepropionic acid. Maternal and fetal serum and liver NBP2 concentrations were similar to PFOS, but ∼10–30-fold greater than HFPO-DA concentrations at a given maternal oral dose. NBP2 is a developmental toxicant in the rat, producing neonatal mortality, reduced pup body weight, reduced pup liver glycogen, reduced maternal thyroid hormones, and altered maternal and offspring lipid and carbohydrate metabolism similar to other studied PFAS, with oral toxicity for pup loss that is slightly less potent than PFOS but more potent than HFPO-DA.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:34952357" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192633" }, "primaryId" : "GEO:GSE192633", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192633" } ] }, "title" : "Screening of genes differentiating transcriptional profiles of CIA rats at different NAMPT expression statuses", "dateAssigned" : "2021-12-27T00:00:00.000-06:00", "summary" : "We screened out differentially expressed genes between CIA rats and healthy controls at both NAMPT++ (CIA1) and NAMPT+ (CIA2) statuses.It was obvious that that high expression of NAMPT is linked to acute inflammation, as TLRs and its downstream MAPKs and NF-κB were identified as the most affected pathways in NAMPT++ samples compared with normal control. However, by the decrease of NAMPT expression, the pathological situation was not eased but became even more complicated. Energy metabolism (mainly lipid metabolism) was significantly altered at this status. Interestingly, many RA-related pathways emerged, such as TGF-β, IL-17, PI3K-AKT and osteoclast differentiation pathways. These results solidly support the hypothesis that NAMPT overexpression is an early event in CIA and directly affects the innate rather than adaptive immunity.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35111160" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192803" }, "primaryId" : "GEO:GSE192803", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192803" } ] }, "title" : "RNA-seq analysis of ipsilateral rat TGs on day 14 after CCI-ION or sham operation", "dateAssigned" : "2021-12-30T00:00:00.000-06:00", "summary" : "Nerve injury-induced changes in gene expression in primary sensory neurons, such as trigeminal ganglion (TG) neurons, play a critical role in the genesis of neuropathic pain. Therefore, understanding the molecular mechanisms underlying these changes in the TGs following peripheral nerve injury will enable us to develop a new avenue for managing trigeminal-mediated neuropathic pain. Studies have highlighted the involvement of miRNA-mediated modulation in a wide range of diseases, leading to the exploration of miRNA-based therapeutics as a potential treatment strategy. Here, in this RNA-seq database, we have found that microRNA-216a-3p (miR-216a-3p) and miR-32-5p (miR-32-5p), which are downregulated in injured TGs, are novel functional RNAs involved in regulating trigeminal-mediated neuropathic pain. Histone methylation-mediated miRNA downregulation in TG neurons regulates trigeminal neuropathic pain by targeting either STIM1 (H3K27me3/SOX10/miR-216a-3p/STIM1) or Cav3.2 (GR/miR-32-5p/Cav3.2) channels. Moreover, we found that miR-323-3p exhibited the most significant upregulation in the injured TG. Understanding the mechanistic role of the PRMT2/FOXA2/miR-323-3p/Kv2.1 signaling axis in sensory neurons may advance the discovery of novel therapeutic strategies for neuropathic pain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:39592234" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192885" }, "primaryId" : "GEO:GSE192885", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192885" } ] }, "title" : "Transcriptomic Analysis of Rat Cerebral Cortex Reveals the Potential Mechanism of Electroacupuncture Opening Blood Brain Barrier", "dateAssigned" : "2022-01-02T00:00:00.000-06:00", "summary" : "Therapeutic treatment options for central nervous system (CNS) diseases are greatly limited by the blood-brain barrier (BBB). Electroacupuncture (EA) can be used to induce an increase in BBB permeability on rats, providing a potential approach for the delivery of drugs from the systemic circulation into the brain. However, there remains a large gap in our knowledge regarding the impact of EA on brain gene expression. This work is focused on investigating the transcriptional changes of rat cerebral cortex following EA and expression changes in genes and bioinformatic analysis was performed. Our results provide a valuable resource that will guide mechanism research of EA opening BBB and other ways to mediate drug delivery into the brain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192910" }, "primaryId" : "GEO:GSE192910", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192910" } ] }, "title" : "High-Frequency Repetitive Transcranial Magnetic Stimulation (rTMS) Protects Against Ischemic Stroke by Inhibiting M1 Microglia Polarization through Let-7b-5p/HMGA2/NF-κB Signaling Pathway", "dateAssigned" : "2022-01-03T00:00:00.000-06:00", "summary" : "Modulating M1/M2 polarization is a potential therapy for treating ischemic stroke. Repetitive transcranial magnetic stimulation (rTMS) held the capacity to regulate astrocytic polarization, but little is known about rTMS effects on microglia. Therefore, the present study aimed to investigate whether and how rTMS influence microglia polarization in ischemic stroke models. The 10-Hz rTMS was applied to transient middle cerebral artery occlusion (MCAO) rats and oxygen and glucose deprivation/ reoxygenation injured BV2 cells. Western blot, immunofluorescence and ELISA were used to detect M1/M2 markers. High-throughput sequencing, RT-PCR and FISH staining were adopted to test microRNA changes. The 10-Hz rTMS inhibited ischemia/reperfusion induced M1 microglia and significantly increased let-7b-5p. HMGA2 was proved to be the target protein of let-7b-5p and its downstream NF-κB signaling pathway were inhibited by rTMS. Microglia culture medium (MCM) collected from rTMS treated microglia had low TNF-α but high IL-10 concentration, leading to reduced neural death, minor ischemic volumes and improved functional recovery of MCAO animals. However, knockdown of let-7b-5p by antagomir reversed rTMS effects on microglia. In conclusion, high-frequency rTMS could improve functional recovery through inhibiting M1 microglia polarization via regulating let-7b-5p/HMGA2/NF-κB signaling pathway in cerebral ischemic stroke models.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35927640" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192946" }, "primaryId" : "GEO:GSE192946", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192946" } ] }, "title" : "A druggable signaling hub of choroid plexus immune-secretory function", "dateAssigned" : "2022-01-03T00:00:00.000-06:00", "summary" : "Integrated multi-omics investigation of novel rat models of acquired hydrocephalus, Blood or bacteria in CSF trigger similar choroid plexus (ChP) immune-secretory responses, Crosstalk between ChP immune and epithelial cells drives CSF hypersecretion and ventriculomegaly, Repurposed systemic immunomodulators ameliorate acquired hydrocephalus, Identification of a druggable hub of ChP function relevant for multiple neurological diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36803604" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192979" }, "primaryId" : "GEO:GSE192979", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192979" } ] }, "title" : "mRNA sequencing of perilesional cortex and ipsilateral thalamus at 3-months after lateral fluid-percussion injury or sham-operation", "dateAssigned" : "2022-01-04T00:00:00.000-06:00", "summary" : "At 3-months after after traumatic brain injury, messenger RNA sequencing was performed on samples from ipsilateral thalamus and perilesional cortex of selected rats with the chronic inflammatory endophenotype, and sham-operated controls.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35052815" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192980" }, "primaryId" : "GEO:GSE192980", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE192980" } ] }, "title" : "Small RNA sequencing of perilesional cortex and ipsilateral thalamus at 3-months after lateral fluid-percussion injury or sham-operation", "dateAssigned" : "2022-01-04T00:00:00.000-06:00", "summary" : "At 3-months after after traumatic brain injury, small RNA sequencing was performed on samples from ipsilateral thalamus and perilesional cortex of selected rats with the chronic inflammatory endophenotype, and sham-operated controls.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193040" }, "primaryId" : "GEO:GSE193040", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193040" } ] }, "title" : "Integrative multi-omics landscape of fluoxetine action across 27 brain regions", "dateAssigned" : "2022-01-04T00:00:00.000-06:00", "summary" : "We constructed a comprehensive multi-omics map of the molecular effects of fluoxetine (an SSRI antidepressant), in 27 rat brain regions. We profiled gene expression (bulk RNA-seq, 210 datasets) and chromatin state (bulk chromatin immunoprecipitation sequencing (ChIP-seq) for the histone marker H3K27ac, 100 datasets) in a broad, unbiased panel of 27 brain regions across the entire rodent brain, in naive and fluoxetine-treated animals. We complemented this approach with single-cell RNA-seq (scRNA-seq) analysis of two brain regions. Using diverse integrative data analysis techniques we characterized the complex and multifaceted effects of fluoxetine on region-specific and cell-type-specific gene regulatory networks and pathways. Remarkably, we observed profound molecular changes across the brain (>4,000 differentially expressed genes and differentially acetylated ChIP-seq peaks each) that were highly region-dependent. We leveraged this atlas to identify fluoxetine-moduated genes and gene-regulatory loci, predict enriched motifs that suggest potential upstream regulators, and validate global mechanisms of fluoxetine action.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36056172" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193194" }, "primaryId" : "GEO:GSE193194", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193194" } ] }, "title" : "Gene expression profiling of neural stem cells in 3D hydrogels with different stiffness", "dateAssigned" : "2022-01-07T00:00:00.000-06:00", "summary" : "We report a transcriptome sequencing to identify 3D hydrogel stiffness-dependent genes", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35427160" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193284" }, "primaryId" : "GEO:GSE193284", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193284" } ] }, "title" : "Analysis of changes in transcriptomes of the rat medial prefrontal cortex tissues (mPFC) in vehicle group, chronic mild stress (CMS) group, and CMS+Phloretin group", "dateAssigned" : "2022-01-08T00:00:00.000-06:00", "summary" : "Results: We found that Phloretin treatment changed some gene expression, especially in neuronal plasticity, compared with CMS group.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36793870" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193408" }, "primaryId" : "GEO:GSE193408", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193408" } ] }, "title" : "Regional transcriptomics and mechanical properties of rat Achilles tendons", "dateAssigned" : "2022-01-10T00:00:00.000-06:00", "summary" : "The transcriptome of different tendons varies based on anatomical location and is likely influenced by the biomechanical loading environment. While differences in biologic and mechanical properties of whole tendons have been assessed, less is understood about differences within a tendon along its proximal-distal axis. Therefore, our objective was to determine the characteristics of and relationship between the transcriptomes and mechanical properties of a single tendon.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36305762" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193432" }, "primaryId" : "GEO:GSE193432", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193432" } ] }, "title" : "Exercise-generated β-aminoisobutyric acid (BAIBA) reduces cardiomyocytes metabolic stress and apoptosis caused by mitochondrial dysfunction through the miR-208b/AMPK pathway", "dateAssigned" : "2022-01-11T00:00:00.000-06:00", "summary" : "Conclusion: Exercise-induced BAIBA can reduce the metabolic stress and apoptosis induced by mitochondrial dysfunction through the miR-208b/AMPK pathway.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35282369" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193466" }, "primaryId" : "GEO:GSE193466", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193466" } ] }, "title" : "Time-dependent Effects of BRAF-V600E on Cell Cycling, Metabolism, and Function in Engineered Myocardium ", "dateAssigned" : "2022-01-11T00:00:00.000-06:00", "summary" : "Candidate cardiomyocyte (CM) mitogens such as those affecting ERK signaling pathway represent potential targets for functional heart regeneration. We explored whether activating ERK via a constitutively active mutant of BRAF, BRAF-V600E (caBRAF), can induce pro-proliferative effects in neonatal rat engineered cardiac tissues (ECTs). Sustained CM-specific caBRAF expression induced chronic ERK activation, significant tissue growth, deficit in sarcomeres and contractile function, and tissue stiffening, all of which persisted for at least 4 weeks of culture. CaBRAF-expressing CMs in ECTs exhibited broad transcriptomic changes, shift to glycolytic metabolism, loss of connexin-43, and a pro-migratory phenotype. Transient, doxycycline-controlled caBRAF expression revealed that the induction of CM cycling is rapid, precedes functional decline, and the effects are reversible only with a short-lived ERK activation. Together, direct activation of the BRAF kinase is sufficient to modulate CM cycling and functional phenotype, offering mechanistic insights into roles of ERK signaling in the context of cardiac development and regeneration.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:38266090" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193521" }, "primaryId" : "GEO:GSE193521", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193521" } ] }, "title" : "Comprehensive analysis of circRNA expression profiles in rat cerebral cortex after moderate traumatic brain injury", "dateAssigned" : "2022-01-12T00:00:00.000-06:00", "summary" : "Conclusion: This study showed that differentially expressed circular RNAs existed between rat cerebral cortex after moderate traumatic brain injury and control. And this will provide valuable information for circular RNA research in the field of traumatic brain injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193545" }, "primaryId" : "GEO:GSE193545", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193545" } ] }, "title" : "Investigation of differential microRNAs in the exosomes of alcohol-induced H9c2 myocardial cells", "dateAssigned" : "2022-01-12T00:00:00.000-06:00", "summary" : "We use the illumina high-throughput sequencing technology to identify miRNAs between the exosomes of H9c2 cells with or without alcohol-induced.The H9c2 cells were cultured in serum-free medium and stimulated with ethanol (100mmol/L) or PBS for 24h, then collected the exosomes samples from serum-free medium. Exosomes were isolated and extracted by differential centrifugation and detected by electron microscopy, particle size and related marker proteins.In total, 123 differentially expressed miRNAs (12 upregulated and 111 downregulated) were screened by miRNA sequence.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193564" }, "primaryId" : "GEO:GSE193564", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193564" } ] }, "title" : "Single-cell analysis reveals the progress in skin repair after radiation in rats.", "dateAssigned" : "2022-01-12T00:00:00.000-06:00", "summary" : "This study aims to compare the cell heterogeneity and mRNA expression between irradiated and non-irradiated rat skin tissues at the single cell level. In this study, the skin was isolated from rats with radiation or non-irradiated rats. Male Sprague Dawley (SD) rats (6 weeks of age) were used. For irradiation, the hair on the gluteal region of the rats was shaved using a razor. The animals were immobilized using adhesive tape on a plastic plate to minimize motion during radiation exposure. A 3-cm-thick piece of lead was used to shield the animals and localize the radiation field (3-4 cm). Irradiation was performed on the treatment area at a dose rate of 1000 cGy/min using a 6-MeV electron beam accelerator. Irradiated skin was taken on day 7, 14, 28 and 60 for RNA-seq, respectively. The control group of skin were collected from four rats without radiation and mixed for RNA-seq.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193580" }, "primaryId" : "GEO:GSE193580", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193580" } ] }, "title" : "Hippocampus RNA-sequencing of Q808 against PTZ-induced seizure model", "dateAssigned" : "2022-01-12T00:00:00.000-06:00", "summary" : "The present study aimed to use RNA sequencing to reveal the gene transcriptomic profile of PTZ-induced seizure rats and the difference of the PTZ model rat before and after treatment with Q808.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193653" }, "primaryId" : "GEO:GSE193653", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193653" } ] }, "title" : "Gene expression profiling of total rat epididymal cells during postnatal development.", "dateAssigned" : "2022-01-13T00:00:00.000-06:00", "summary" : "Our goal was to assess the gene expression profiles at different time points in the developping epididymis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35590013" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193757" }, "primaryId" : "GEO:GSE193757", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193757" } ] }, "title" : "Glucocorticoid receptor-regulated enhancers play a central role in the gene regulatory networks underlying drug addiction", "dateAssigned" : "2022-01-15T00:00:00.000-06:00", "summary" : "Substance abuse and addiction represent a major public health problem that impacts multiple dimensions of society, including healthcare, economy, and workforce. In 2021, over 100,000 drug overdose deaths have been reported in the US with an alarming increase in fatalities related to opioids and psychostimulants. Understanding of the fundamental gene regulatory mechanisms underlying addiction and related behaviors could facilitate more effective treatments. To explore how repeated drug exposure alters gene regulatory networks in the brain, we combined capped small (cs)RNA-seq, which accurately captures nascent-like initiating transcripts from total RNA, with Hi-C and single nuclei (sn)ATAC-seq. We profiled initiating transcripts in two addiction-related brain regions, the prefrontal cortex (PFC) and the nucleus accumbens (NAc), from rats that were never exposed to drugs or were subjected to prolonged abstinence after oxycodone or cocaine intravenous self-administration (IVSA). Interrogating in total over 100,000 active transcription start regions (TSRs) revealed that most TSRs had hallmarks of bona-fide enhancers and highlighted the KLF/SP1, RFX and AP1 transcription factors families as central to establishing brain-specific gene regulatory programs. Analysis of rats with addiction-like behaviors versus controls, identified addiction-associated repression of transcription at regulatory enhancers recognized by nuclear receptor subfamily 3 group C (NR3C) factors, which include glucocorticoid receptors. Cell-type deconvolution analysis using snATAC-seq uncovered a potential role of glial cells in driving the gene regulatory programs associated with addiction-related phenotypes. These findings highlight the power of advanced transcriptomics methods to provide insight into how addiction perturbs gene regulatory programs in the brain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35651629" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193764" }, "primaryId" : "GEO:GSE193764", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193764" } ] }, "title" : "Next Generation Sequencing Analysis on Grafts with Macrosteatosis for Liver Transplantation in rats", "dateAssigned" : "2022-01-15T00:00:00.000-06:00", "summary" : "We reported the transcriptomic expression profile of the MaS/non-MaS graft samples from rats before/after liver transplantation and long-term surviving rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193773" }, "primaryId" : "GEO:GSE193773", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193773" } ] }, "title" : "Estrogen Modulation of the Pronociceptive Effects of Serotonin on Female Rat Trigeminal Sensory Neurons is Timing- and Dosage-Dependent and Requires Estrogen Receptor Alpha", "dateAssigned" : "2022-01-16T00:00:00.000-06:00", "summary" : "Since estrogen is a major hormone involved in multiple gene expression pathways in the cell, we wanted to determine the corresponding changes in trigeminal ganglia transcriptome of the E2-treated rats. Adult ovariectomized female rats were subcutaneneously implanted with either 5% (physiological level comparable to diestrus; 15-20 pg/ml; one capsule), 20% (physiological level comparable to proestrus; 40-60 pg/ml; 2 capsules of 10%), 40% (supraphysiological level; 2 capsules of 20%) E2, or control (2 capsules of 100% cholesterol) capsules. One week after implantation, nocifensive behaviors were recorded and trigeminal ganglia tissue was extracted.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35121697" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193857" }, "primaryId" : "GEO:GSE193857", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE193857" } ] }, "title" : "Single-cell RNA sequencing reveals a role for reactive oxygen species and peroxiredoxins in fatty-acid-induced rat ß-cell proliferation", "dateAssigned" : "2022-01-18T00:00:00.000-06:00", "summary" : "The functional mass of insulin-secreting pancreatic β cells expands to maintain glucose homeostasis in the face of nutrient excess, in part via replication of existing β cells. To decipher the underlying molecular mechanisms, we assessed β-cell proliferation in isolated rat islets exposed to glucose and oleate or palmitate for 48 h and analyzed the transcriptional response by single-cell RNA sequencing. Unsupervised clustering of pooled β cells identified subpopulations, including proliferating β cells. β-cell proliferation increased in response to oleate but not palmitate. Both fatty acids enhanced the expression of genes involved energy metabolism and mitochondrial activity. Comparison of proliferating vs. non-proliferating β cells and pseudotime ordering suggested the involvement of reactive oxygen species (ROS) and peroxiredoxin signaling. Accordingly, the antioxidant N-acetyl cysteine and the peroxiredoxin inhibitor Conoidin A both blocked oleate-induced β-cell proliferation. Our data reveal a key role for ROS signaling in β-cell proliferation in response to nutrients.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36191509" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194015" }, "primaryId" : "GEO:GSE194015", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194015" } ] }, "title" : "RNA-seq of rat nucleus pulposus cells after stabilizing G-Quadruplexes", "dateAssigned" : "2022-01-19T00:00:00.000-06:00", "summary" : "We report the RNA-seq data for rat nucleus pulposus cells after stabilizing G-Quadruplexes (G4). We sequenced rat nucleus pulposus cells treated with PDS, Braco-19 and Phen-DC3 separately and untreated with these G4 stabilizers, which could stabilize G4 structure in cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36304116" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194063" }, "primaryId" : "GEO:GSE194063", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194063" } ] }, "title" : "Transcriptomic analysis of the spiral ganglion from hearing and aminoglycoside deafened rats", "dateAssigned" : "2022-01-20T00:00:00.000-06:00", "summary" : "We used RNAseq to assess transcriptomic changes in the spiral ganglion of rats deafened with kanamycin compared to hearing control rats to gain a better understanding of the deafening-induced changes that occur in the spiral ganglion. Transcriptomic profiles were obtained from whole spiral ganglion from hearing and deafened rats at P32 and P60. We observed significant changes in gene expression in not only deafened compared to hearing ganglia, but also from P32 to P60 in normal hearing animals. The most prominent change after deafening was an increase in immune response-related gene expression, indicating that immune response activation occurs in the deafened spiral ganglion.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194067" }, "primaryId" : "GEO:GSE194067", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194067" } ] }, "title" : "Epigenome-wide profiling uncovers novel pathway networks in human pulmonary arterial hypertension [pul31]", "dateAssigned" : "2022-01-20T00:00:00.000-06:00", "summary" : "Pulmonary arterial hypertension (PAH) is a progressive pulmonary vascular disease that culminates in right heart failure. Vascular pathology in PH is characterized by pulmonary vasoconstriction and progressive vascular remodeling processes that affects all layers of the vascular wall (intima, media and adventitia). Our objective was to profile and analyze the differential gene expression signatures between the cells isolated from normal and idiopathic PAH patients. We generated vascular cell-specific transcriptome profiles from the adventitial fibroblasts (PAAF) isolated ex vivo from the dissected human pulmonary arteries of normal donor and PAH lungs using paired-end RNA-sequencing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35675437" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194074" }, "primaryId" : "GEO:GSE194074", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194074" } ] }, "title" : "Effect of Atm Inhibitor on Galactose-Induced Cataract in Rat Lens", "dateAssigned" : "2022-01-20T00:00:00.000-06:00", "summary" : "A total of six samples were analyzed: a sample without induced turbidity (control), three samples in which turbidity was induced by galactose (galactose), and a sample with ATM inhibitor added (KU55933 or AZD0156).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36149903" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194205" }, "primaryId" : "GEO:GSE194205", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194205" } ] }, "title" : "mRNA profiling of schwann cells cultured with monocytes derived macrophages and PDAC cell lines supernants-induced tumor-associated macrophages (TAMs)", "dateAssigned" : "2022-01-22T00:00:00.000-06:00", "summary" : "Tumor associated macrophages(TAMs) have been demonstrated to promote tumor progression and perineural invasion in PDAC, however the underlying machanism of TAMs interacting with Schwann cells is still unclear. We found the gene expression of Schwann cell is different from TAMs-induced Schwann cells by comparing mRNA profiling.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194236" }, "primaryId" : "GEO:GSE194236", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194236" } ] }, "title" : "Transcriptional profiling of transport mechanisms and regulatory pathways in rat choroid plexus", "dateAssigned" : "2022-01-23T00:00:00.000-06:00", "summary" : "Transcriptomic profile of rat choroid plexus (whole tissue) of both male and female sex, epithelial cells captured by fluorescence-activated cell sorting (FACS), and compared to proximal tubules of the kidneys. The transcriptomic profile of choroid plexus displays high similarity between sex and choroid plexus epithelial cells, and lesser similarity to another secretory epithelium, the proximal tubules. The analysis provides an insight into transport mechanisms that could participate in CSF secretion and suggest regulatory candidates.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35659263" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194240" }, "primaryId" : "GEO:GSE194240", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194240" } ] }, "title" : "Circulating MicroRNA: Myocardium-Derived Prenatal Biomarker of Ventricular Septal Defects", "dateAssigned" : "2022-01-24T00:00:00.000-06:00", "summary" : "MicroRNAs (miRNAs) regulate transcription factors and relate to ventricular septal defect (VSD) occurrence, progression and outcome. Recently, circulating miRNAs from maternal blood and amniotic fluid have been used as biomarkers for congenital heart defect (CHD) diagnosis. However, whether circulating miRNAs are associated with foetal heart tissue remains unknown. Dimethadione (DMO) induced a VSD rat model and the miRNA expression profiles of the myocardium, amniotic fluid and maternal serum were analysed. MiRNAs were differentially expressed in the myocardium, amniotic fluid or maternal serum of VSD foetal rats and might be involved in cardiomyocyte differentiation and apoptosis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36035156" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194289" }, "primaryId" : "GEO:GSE194289", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194289" } ] }, "title" : "Integrative multi-omics landscape of fluoxetine action across 27 brain regions [bulk RNA-seq]", "dateAssigned" : "2022-01-24T00:00:00.000-06:00", "summary" : "We constructed a comprehensive multi-omics map of the molecular effects of fluoxetine (an SSRI antidepressant), in 27 rat brain regions. We profiled gene expression (bulk RNA-seq, 210 datasets) and chromatin state (bulk chromatin immunoprecipitation sequencing (ChIP-seq) for the histone marker H3K27ac, 100 datasets) in a broad, unbiased panel of 27 brain regions across the entire rodent brain, in naive and fluoxetine-treated animals. We complemented this approach with single-cell RNA-seq (scRNA-seq) analysis of two brain regions. Using diverse integrative data analysis techniques we characterized the complex and multifaceted effects of fluoxetine on region-specific and cell-type-specific gene regulatory networks and pathways. Remarkably, we observed profound molecular changes across the brain (>4,000 differentially expressed genes and differentially acetylated ChIP-seq peaks each) that were highly region-dependent. We leveraged this atlas to identify fluoxetine-moduated genes and gene-regulatory loci, predict enriched motifs that suggest potential upstream regulators, and validate global mechanisms of fluoxetine action.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36056172" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194317" }, "primaryId" : "GEO:GSE194317", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194317" } ] }, "title" : "Rat ex vivo cataract model using DNA damage inducer", "dateAssigned" : "2022-01-25T00:00:00.000-06:00", "summary" : "To investigate genes whose expression fluctuates when DNA damage is inflicted and causes lens opacity, microarray analysis was performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36477544" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194325" }, "primaryId" : "GEO:GSE194325", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194325" } ] }, "title" : "Expression data from RVLM of Wistar-Kyoko (WKY) rats and spontaneously hypertensive rats (SHR)", "dateAssigned" : "2022-01-25T00:00:00.000-06:00", "summary" : "We used microarrays to identified distinct classes of genes involved in the central regulation of blood pressure.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194367" }, "primaryId" : "GEO:GSE194367", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194367" } ] }, "title" : "Transcriptomic changes in response to 5/6 or 1/3 nephrectomy", "dateAssigned" : "2022-01-25T00:00:00.000-06:00", "summary" : "We report the changes in kidney mRNA abundance in response to 5/6 nephrectomy or 1/3 nephrectomy surgery when compared to sham operated controls.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194390" }, "primaryId" : "GEO:GSE194390", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194390" } ] }, "title" : "Angioplasty induces epigenomic remodeling in injured arteries", "dateAssigned" : "2022-01-25T00:00:00.000-06:00", "summary" : "Neointimal hyperplasia (IH) is a primary etiology of stenotic vascular diseases. It is perpetuated principally by smooth muscle cell proliferation. Epigenome-scale studies concerning IH have been confined to in vitro models, and the IH-underlying epigenetic mechanisms remain poorly understood. The current study has integrated information from in vivo epigenomic mapping, conditional knockout, gene transfer and pharmacology in rodent models of IH. The data from injured (IH-prone) rat arteries revealed a surge of genomewide occupancy by H3K27me3, a gene repression mark. This was unexpected in the traditional view of prevailing post-injury gene activation rather than repression. Further analysis illustrated a shift of H3K27me3 enrichment to anti-proliferative genes, from pro-proliferative genes where gene activation mark H3K27ac instead accumulated. In accordance, H3K27ac and its reader BRD4 co-enriched at Ezh2 governing its expression. Moreover, H3K27me3 writer EZH2 positively regulated another recently identified pro-IH chromatin modulator UHRF1. Thus, results unravel injury-induced loci-specific H3K27me3 redistribution in the epigenomic landscape entailing BRD4->EZH2->UHRF1 hierarchical regulations, and may guide translation to treat IH given that these players are pharmaceutical targets.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35169042" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194398" }, "primaryId" : "GEO:GSE194398", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE194398" } ] }, "title" : "Mogrosisde V improves follicular development and ovulation in PCOS rats induced by letrozole and high-fat diet through promoting glycolysis", "dateAssigned" : "2022-01-25T00:00:00.000-06:00", "summary" : "Methods: Ovarian mRNA profiles of 15-week-old Control, PCOS and PCOS-MV group rats (4 rats per group) were generated by deep sequencing,using Illumina PE150.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35418943" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE195702" }, "primaryId" : "GEO:GSE195702", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE195702" } ] }, "title" : "Pseudo-temporal analysis of Single-cell RNA sequencing reveals trans-differentiation potential of Greater Epithelial Ridge cells into hair cells during postnatal development of cochlea in Rats", "dateAssigned" : "2022-01-29T00:00:00.000-06:00", "summary" : "The hair cells of the cochlea play a decisive role in the process of hearing damage and recovery, yet knowledge of their regeneration process is still limited. Greater epithelial ridge (GER) cells, a type of cell present during cochlear development that has the characteristics of a precursor sensory cell, disappear at the time of maturation of hearing development. Its development and evolution remain mysterious for many years. Here, we performed single-cell RNA sequencing to profile the gene expression landscapes of rats' cochlear duct from P1, P7, and P14 and identified eight major subtypes of GER cells. Furthermore, single-cell trajectory analysis for GER cells and hair cells indicated that among the different subtypes of GER, four subtypes had transient cell proliferation after birth and could transdifferentiate into inner and outer hair cells, and two of them mainly transdifferentiated into inner hair cells. The other two subtypes eventually transdifferentiate into outer hair cells. Our study lays the groundwork for elucidating the mechanisms of the key regulatory genes and signaling pathways in the trans-differentiation of GER cell subtypes into hair cells and provides potential clues to understand hair cell regeneration.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35370544" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE195733" }, "primaryId" : "GEO:GSE195733", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE195733" } ] }, "title" : "RNA-Seq in HG-challenged H9C2 cells with or without FGFR1 knockdown", "dateAssigned" : "2022-01-30T00:00:00.000-06:00", "summary" : "RNA-seq is a powerful tool to analyze differential expression of cellular pathways under different conditions. The goals of this study is to analyze the potential pathways involved in cellular defense against high glucose with or without FGFR1 knowdown.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE195833" }, "primaryId" : "GEO:GSE195833", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE195833" } ] }, "title" : "Postoperative pain and dorsal root ganglia transcriptomic signatures in a novel rat model of total knee arthroplasty", "dateAssigned" : "2022-01-31T00:00:00.000-06:00", "summary" : "These data are from a preclinical model of total knee arthroplasty (TKA) performed in healthy rats. One day after surgery, ipsilateral dorsal root ganglia (DRG) from L3 and L4 were collected for RNA extraction and sequencing.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36473007" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE195869" }, "primaryId" : "GEO:GSE195869", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE195869" } ] }, "title" : "Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species", "dateAssigned" : "2022-02-01T00:00:00.000-06:00", "summary" : "We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale, base-resolution DNA methylation profiles of primary tissue samples from various organs. Reference-genome independent analysis of this comprehensive dataset defined a “genomic code” of DNA methylation, which allowed us to predict global and locus-specific DNA methylation from the DNA sequence within and across species. This code appears broadly conserved throughout vertebrate evolution, with two major transitions – once in the first vertebrates and again with the emergence of reptiles. Beyond the central role of species-specific DNA sequence composition, our dataset identified the tissue type and the individual as two main sources of DNA methylation variability within species. Tissue type was the dominant factor in fish, birds, and mammals, while in invertebrates, reptiles, and amphibians both factors were similarly strong. Cross-species comparisons focusing on heart and liver tissues supported a highly conserved role of DNA methylation for tissue type and identity and cross-mapping based promoter methylation analysis revealed divergence at specific genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36646694" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE195913" }, "primaryId" : "GEO:GSE195913", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE195913" } ] }, "title" : "Metabolomic and Transcriptomic Signatures of Chemnogenetic Heart Failure", "dateAssigned" : "2022-02-01T00:00:00.000-06:00", "summary" : "In our chemogenetic rat heart failure model, LV and RV transcriptomic analysis was performed by RNA-seq", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE195978" }, "primaryId" : "GEO:GSE195978", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE195978" } ] }, "title" : "RNA sequencing analysis of WT and Dusp6-/- rat cardiac infiltrated macrophages transcriptomes", "dateAssigned" : "2022-02-02T00:00:00.000-06:00", "summary" : "Dual-specificity phosphatase 6 (DUSP6), a member of MAPK phosphatase, serves a specific and conserved function on the dephosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2) in multiple species. Utilizing a rat strain harboring nonsense mutation of Dusp6, we found that Dusp6 deficiency improves cardiac function by attenuating cardiomyocyte death and fibrosis in acute inflammatory phase after MI. To investigate the effect of DUSP6 on macrophages in acute inflammatory phase of MI, we performed RNA-seq analysis using CD45+HIS36+ macrophages isolated from Dusp6-deficient and WT infarcted LV tissues 72 h after MI by fluorescent activated cell sorting (FACS).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36335128" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196133" }, "primaryId" : "GEO:GSE196133", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196133" } ] }, "title" : "BRB-seq analysis of PFOS-induced thyroid hormone system disrupted rats reveal organ-specific effects", "dateAssigned" : "2022-02-04T00:00:00.000-06:00", "summary" : "Perfluorooctanesulfonic acid (PFOS) is a persistent anthropogenic chemical that can affect the thyroid hormone system in humans. In experimental animals, PFOS exposure decreases thyroxine (T4) and triiodothyronine (T3) levels, without a compensatory upregulation of thyroid stimulating hormone (TSH). In adults, THs are regulated by the hypothalamus-pituitary-thyroid (HPT) axis, but also organs such as the liver and potentially the gut microbiota. PFOS and other xenobiotics can therefore potentially disrupt the TH system through various entry points of disruption. To start addressing this issue, we performed a PFOS exposure study to identify effects in multiple organs and pathways simultaneously.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35460815" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196147" }, "primaryId" : "GEO:GSE196147", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196147" } ] }, "title" : "Temporal gene expression with 30 days 'spillover' resistance training in the rat tibialis anterior muscle delivered with implantable pulse generators.", "dateAssigned" : "2022-02-04T00:00:00.000-06:00", "summary" : "Global gene expression patterns were determined from NGS on hypertrophying tibialis anterior muscles after 2, 10, 20 and 30 days resistance training (1 hour post exercise) and control muscles.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36468768" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196153" }, "primaryId" : "GEO:GSE196153", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196153" } ] }, "title" : "PCBP-1 regulates the transcription and alternative splicing of inflammation and ubiquitination-related genes in Parkinson’s disease model", "dateAssigned" : "2022-02-04T00:00:00.000-06:00", "summary" : "In this study, we cloned and constitutively overexpressed PCBP-1 in rat PC12 cells. RNA-seq was performed to analyze PCBP-1-regulated differentially expressed genes (DEGs) and alternative splicing events (ASEs) between control and PCBP1-overexpressed cells. GO and KEGG pathway analyses were performed to identify functional DEGs and alternatively spliced genes. Consequently, we validated PCBP-1-regulated genes using RT-qPCR.Overexpression of PCBP-1 widely regulated the ASE and expression of genes enriched in neuroinflammation and protein ubiquitination, which were also associated with PD pathogenesis. Moreover, RT-qPCR assay verified the PCBP-1-modulated expression of neuroinflammatory genes, like LCN-2, and alternative splicing (AS) of ubiquitination-related gene WWP-2", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35795237" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196242" }, "primaryId" : "GEO:GSE196242", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196242" } ] }, "title" : "Pregestational Diabetes Alters Cardiac changes", "dateAssigned" : "2022-02-07T00:00:00.000-06:00", "summary" : "Conclusions: Transcriptomic profiling of the RNA-seq data revealed that several of the altered genes were associated with cardiac pathogenesis in neonatal heart during PGDM.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36176990" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196313" }, "primaryId" : "GEO:GSE196313", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196313" } ] }, "title" : "Single cell transcriptomic profiling of microvascular endothelial cell heterogeneity in congenital diaphragmatic hernia", "dateAssigned" : "2022-02-07T00:00:00.000-06:00", "summary" : "Congenital diaphragmatic hernia (CDH) is a neonatal anomaly that includes pulmonary hypoplasia and hypertension. We hypothesized that differences in microvascular endothelial cell (EC) heterogeneity may be present during CDH lung development and contribute to nderdevelopment and remodeling of the lungs. Time mated rats were gavaged nitrofen to induce CDH. Left lungs were harvested from healthy control (2HC), nitrofen exposed (NC) and nitrofen-exposed with CDH (CDH) fetuses at E21.5. Transcriptomic analysis was performed using single-cell RNA sequencing, and unbiased clustering revealed 3 distinct microvascular EC clusters. The general microvascular EC cluster (mvEC) had a transcriptomic signature suggestive of increased inflammation in CDH. mvEC differential gene expression (DGE) between NC and CDH revealed downregulation of Ca4, Apln and Ednrb, which define a subpopulation of microvascular ECs important to lung development, gas exchange and repair of alveolar injury (mvCa4+). mvCa4+ ECs were significantly reduced between 2HC (22.6%), NC (13.1%) and CDH (5.3%), demonstrating an impact from lung compression. Gene ontology and Ingenuity Pathway Analysis demonstrated that mvCa4+ ECs are primed for vasculogenesis but have DGE suggestive of impaired cell division. These data suggest that inflammation driven by mvECs and absence of mvCa4+ ECs may contribute to CDH pathogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37330615" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196332" }, "primaryId" : "GEO:GSE196332", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196332" } ] }, "title" : "Melanoma-secreted Amyloid Beta Suppresses Neuroinflammation and Promotes Brain Metastasis", "dateAssigned" : "2022-02-08T00:00:00.000-06:00", "summary" : "Brain metastasis is a significant cause of morbidity and mortality in multiple cancer types and represents an unmet clinical need. The mechanisms that mediate metastatic cancer growth in the brain parenchyma are largely unknown. Melanoma, which has the highest rate of brain metastasis among common cancer types, is an ideal model to study how cancer cells adapt to the brain parenchyma. Our unbiased proteomics analysis of melanoma short-term cultures revealed that proteins implicated in neurodegenerative pathologies are differentially expressed in melanoma cells explanted from brain metastases compared to those derived from extracranial metastases. We showed that melanoma cells require amyloid beta (Ab) for growth and survival in the brain parenchyma. Melanoma-secreted Ab activates surrounding astrocytes to a prometastatic, anti-inflammatory phenotype and prevents phagocytosis of melanoma by microglia. Finally, we demonstrate that pharmacological inhibition of Ab decreases brain metastatic burden.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35262173" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196374" }, "primaryId" : "GEO:GSE196374", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196374" } ] }, "title" : "Heightened Cocaine-Seeking in Male Rats Associates with a Distinct Transcriptomic Profile in the Medial Prefrontal Cortex", "dateAssigned" : "2022-02-08T00:00:00.000-06:00", "summary" : "Drug overdose deaths involving cocaine have skyrocketed, an outcome attributable in part to the lack of FDA-approved medications for the treatment of cocaine use disorder (CUD), highlighting the need to identify new pharmacotherapeutic targets. Vulnerability to cocaine-associated environmental contexts and stimuli serves as a risk factor for relapse in CUD recovery, with individual differences evident in the motivational aspects of these cues. The medial prefrontal cortex (mPFC) provides top-down control of striatal circuitry to regulate the incentive-motivational properties of cocaine-associated stimuli. Clinical and preclinical studies have identified genetic variations that impact the degree of executive restraint over drug-motivated behaviors, and we designed the present study to employ next-generation sequencing to identify specific genes associated with heightened cue-evoked cocaine-seeking in the mPFC of male, outbred rats. Rats were trained to stably self-administer cocaine, and baseline cue-reinforced cocaine-seeking was established. Rats were phenotyped as either high cue (HC) or low cue (LC) responders based upon lever pressing for previously associated cocaine cues and allowed 10 days of abstinence in their home cages prior to mPFC collection for RNA-sequencing. The expression of 309 genes in the mPFC was significantly different in HC vs. LC rats. Functional gene enrichment analyses identified ten biological processes that were overrepresented in the mPFC of HC vs. LC rats. The present study identifies distinctions in mPFC mRNA transcripts that characterizes individual differences in relapse-like behavior and provides prioritized candidates (i.e., Htr2c, Adora2a, Drd2) for future pharmacotherapeutics aimed to help maintain abstinence in CUD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36588704" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196437" }, "primaryId" : "GEO:GSE196437", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196437" } ] }, "title" : "Alkaline nucleoplasm facilitates contractile gene expression in the mammalian heart [RNA-seq]", "dateAssigned" : "2022-02-09T00:00:00.000-06:00", "summary" : "Cardiac contractile strength is recognised as highly pH-sensitive, but less is known about the influence of pH on cardiac gene expression, which may be relevant during changes in myocardial metabolism or vascularization in development or disease. We sought evidence for pH-responsive cardiac genes and a context in which this has physiological relevance. pHLIP, a peptide-based reporter of acidity, revealed a non-uniform pH landscape in early-postnatal myocardium, dissipating in later life. pH-responsive differentially-expressed genes (pH-DEGs) were identified by transcriptomics of neonatal cardiomyocytes cultured over a range of pH. Enrichment analysis indicated “striated muscle contraction” as a pH-responsive biological process. Label-free proteomics verified fifty-four pH-responsive gene-products, including contractile elements and the adaptor protein CRIP2. Using transcriptional assays, acidity was found to inhibit p300/CBP acetylase activity and, as its functional readout, negatively affect myocardin, a co-activator of cardiac gene expression. In cultured myocytes, acid-inhibition of p300/CBP reduced H3K27 acetylation, as demonstrated by chromatin immunoprecipitation. H3K27ac levels were more strongly reduced at promoters of acid-downregulated DEGs, suggesting an epigenetic mechanism of pH-sensitive gene expression. By tandem cytoplasmic/nuclear pH imaging, the cardiac nucleus was found to exercise a degree of control over its pH through Na+/H+ exchangers at the nuclear envelope. Thus, we describe how extracellular pH signals gain access to the nucleus and regulate the expression of a subset of cardiac genes, notably those coding for contractile proteins and Crip2. Acting as a proxy of a well-perfused myocardium, alkaline conditions are permissive for expressing genes related to the contractile apparatus.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35357563" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196438" }, "primaryId" : "GEO:GSE196438", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196438" } ] }, "title" : "Alkaline nucleoplasm facilitates contractile gene expression in the mammalian heart [ChIP-seq]", "dateAssigned" : "2022-02-09T00:00:00.000-06:00", "summary" : "Cardiac contractile strength is recognised as highly pH-sensitive, but less is known about the influence of pH on cardiac gene expression, which may be relevant during changes in myocardial metabolism or vascularization in development or disease. We sought evidence for pH-responsive cardiac genes and a context in which this has physiological relevance. pHLIP, a peptide-based reporter of acidity, revealed a non-uniform pH landscape in early-postnatal myocardium, dissipating in later life. pH-responsive differentially-expressed genes (pH-DEGs) were identified by transcriptomics of neonatal cardiomyocytes cultured over a range of pH. Enrichment analysis indicated “striated muscle contraction” as a pH-responsive biological process. Label-free proteomics verified fifty-four pH-responsive gene-products, including contractile elements and the adaptor protein CRIP2. Using transcriptional assays, acidity was found to inhibit p300/CBP acetylase activity and, as its functional readout, negatively affect myocardin, a co-activator of cardiac gene expression. In cultured myocytes, acid-inhibition of p300/CBP reduced H3K27 acetylation, as demonstrated by chromatin immunoprecipitation. H3K27ac levels were more strongly reduced at promoters of acid-downregulated DEGs, suggesting an epigenetic mechanism of pH-sensitive gene expression. By tandem cytoplasmic/nuclear pH imaging, the cardiac nucleus was found to exercise a degree of control over its pH through Na+/H+ exchangers at the nuclear envelope. Thus, we describe how extracellular pH signals gain access to the nucleus and regulate the expression of a subset of cardiac genes, notably those coding for contractile proteins and Crip2. Acting as a proxy of a well-perfused myocardium, alkaline conditions are permissive for expressing genes related to the contractile apparatus.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35357563" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196469" }, "primaryId" : "GEO:GSE196469", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196469" } ] }, "title" : "Knockdown of miR-192 and miR-432 in progenitor cell-derived small extracellular vesicles enhances tissue repair in myocardial infarction", "dateAssigned" : "2022-02-10T00:00:00.000-06:00", "summary" : "Small extracellular vesicles (sEVs) play a critical role in cardiac cell therapy by delivering molecular cargo and mediating cellular signaling. Among sEV cargo molecule types, microRNA (miRNA) is particularly potent and highly heterogenous. However, not all miRNAs in sEV are beneficial. Two previous studies utilizing computational modeling identified miR-192-5p and miR-432-5p as potentially deleterious in cardiac function and repair. Here, we show that knocking down miR-192-5p and miR-432-5p in cardiac c-kit+ cell-derived sEVs enhances the therapeutic capabilities of sEVs in vitro and in a rat in vivo model of cardiac ischemia reperfusion. miR-192-5p and miR-432-5p depleted CPC-sEVs enhance cardiac function by reducing fibrosis, enhancing mesenchymal stromal cell-like cell mobilization, and inducing macrophage polarization to the M2 phenotype. Knocking down deleterious miRNAs from sEV could be a promising therapeutic strategy for treatment of chronic myocardial infarction.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36867699" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196498" }, "primaryId" : "GEO:GSE196498", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196498" } ] }, "title" : "Thrombin exerts an inflammatory role in chondrocytes through activating the MEK-Erk1/2-Stat3 signaling pathway.", "dateAssigned" : "2022-02-10T00:00:00.000-06:00", "summary" : "Rat chondrocytes were divided into control group (RP), thrombin group (RPT), and thrombin plus inhibitor group (RPTi). The differential genes were identified by RNA-sequencing, and verified by western blot (WB), quantitative polymerase chain reaction (qPCR), cell immunofluorescence (IF), endoplasmic reticulum (ER) staining, functional enrichment analysis, and Gene Ontology (GO).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196500" }, "primaryId" : "GEO:GSE196500", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196500" } ] }, "title" : "Gene expression data from the hippocampus of rats with prenatal valproic acid exposure", "dateAssigned" : "2022-02-10T00:00:00.000-06:00", "summary" : "Comparative analyses revealed that prenatal VPA exposure altered gene expression, a part of which is involved in key features including memory, developmental process, and epilepsy. Oxytocin partly improved these gene expression, which were predicted to interact with those involved in social behaviors and hippocampal-dependent memory. The present study documented molecular profiling in the hippocampus related to ASD and improvement by chronic treatment of oxytocin.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35432011" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196572" }, "primaryId" : "GEO:GSE196572", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196572" } ] }, "title" : "Genetic mapping of multiple metabolic traits identifies novel genes for adiposity, lipids and insulin secretory capacity in outbred rats", "dateAssigned" : "2022-02-11T00:00:00.000-06:00", "summary" : "RNA-Seq was used in an attempt to identify candidate genes regulating metabolic and physiological traits", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196660" }, "primaryId" : "GEO:GSE196660", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196660" } ] }, "title" : "Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Rat]", "dateAssigned" : "2022-02-14T00:00:00.000-06:00", "summary" : "Conclusions: Seven cell types were identified in rat ileum based on reported markers, including enterocytes, transient-amplifying (TA) cells, goblet cells, goblet progenitor cells, stem cells, enteroendorcine cells and tuft cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35511361" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196664" }, "primaryId" : "GEO:GSE196664", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196664" } ] }, "title" : "Next Generation Sequencing to examine common set of transcripts induced in spinal cord neurons by polyPL and mutSOD1-ACM common set of transcripts", "dateAssigned" : "2022-02-14T00:00:00.000-06:00", "summary" : "Next Generation Sequencing shows that synthetic polyPL and mutSOD1-ACM alter a large and common set of transcripts in primary ventral spinal cord cultures", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196704" }, "primaryId" : "GEO:GSE196704", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196704" } ] }, "title" : "Transcriptome sequencing for exploring the mechanism of islet cell protection by anthocyanin.", "dateAssigned" : "2022-02-14T00:00:00.000-06:00", "summary" : "We applied GSIS, immunofluorescence staining, WB, and flow cytometry to observe the protective effects of C3G on palmitate-induced beta cell apoptosis and insulin deficiency, after which we explored the mechanism using RNA sequencing (RNA-seq) and quantitative real-time PCR (qPCR), and finally validated the mechanism using Western Blot (WB) and small interfering RNA (siRNA).The results of GSIS on both INS-1E cells and mouse primary islets plus a series of experiments related to cell apoptosis showed that C3G could restore the damage caused by lipotoxicity through promoting insulin secretion and alleviating cell apoptosis. RNA-seq and qPCR results indicated that the protective effect of C3G was most likely mediated by repressing ER stress pathways, especially the PERK pathway, while partly due to elevated expression of insulin secretion-related genes. Finally, the results of knockdown of the pro-apoptotic marker CHOP in PERK pathway further confirmed the above findings.Conclusion: C3G may act though reducing ER stress to exert its protective impact on pancreatic beta cells under lipotoxicity. This research provides favorable evidence for the therapeutic application of C3G in T2DM.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35565803" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196818" }, "primaryId" : "GEO:GSE196818", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196818" } ] }, "title" : "Adrenal stress hormone regulation of hepatic homeostatic function after an acute ozone exposure", "dateAssigned" : "2022-02-15T00:00:00.000-06:00", "summary" : "Ozone-induced lung injury/inflammation and pulmonary/hypothalamus gene expression are diminished in adrenalectomized (ADREX) rats. Acute ozone exposure induces metabolic alterations concomitant with increases in epinephrine and corticosterone. We hypothesized that adrenal hormones are responsible for observed hepatic ozone effects, and in ADREX rats, these changes would be diminished. Five-seven days after sham or ADREX surgeries, male Wistar-Kyoto rats were exposed to air or 0.8-ppm ozone for 4-hrs. Serum samples were analyzed for metabolites and liver for transcriptional changes immediately post-exposure. Ozone increased circulating triglycerides, cholesterol, free fatty acids, and leptin in sham but not ADREX rats. Ozone-induced inhibition of glucose-mediated insulin release was reversed in ADREX rats. Unlike diminution of hypothalamus and lung mRNA expression changes, ADREX in air-exposed rats (ADREX-air/sham-air) caused differential expression of ~1000 genes in liver. Likewise, ~1000 genes were differentially expressed in ozone-exposed ADREX rats (ADREX-ozone/ADREX-air). Ozone-induced hepatic changes in sham rats reflected enrichment for pathways involving metabolic processes, including acetyl-CoA biosynthesis, TCA cycle, and sirtuins. Upstream predictor analysis identified significant similarity to glucocorticoids and pathways involving CREBBP. These changes were absent in ADREX rats exposed to ozone. However, ozone caused unique changes in ADREX liver mRNA reflecting activation of synaptogenesis, neurovascular coupling, neuroinflammation, and insulin signaling with inhibition of senescence pathways. In these rats, upstream predictor analysis identified numerous microRNAs involved under glucocorticoid insufficiency. These data demonstrate the critical role of adrenal stress hormones in ozone-induced hepatic homeostasis and the need for further research elucidating their role in propagating environmentally driven diseases.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35737395" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196930" }, "primaryId" : "GEO:GSE196930", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196930" } ] }, "title" : "Monocytes transition to monocyte-macrophages within the inflamed vasculature via CCR2 on monocytes and endothelial TNFR2", "dateAssigned" : "2022-02-16T00:00:00.000-06:00", "summary" : "Our study reports the CCR2 dependent functional specialization of monocytes into immature macrophages occurs within the TNF-TNFR2 activated vasculature and establishes a chemokine-based autocrine, feed-forward loop that may aplify the inflammation and renal injury.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35404389" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196983" }, "primaryId" : "GEO:GSE196983", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE196983" } ] }, "title" : "Gene expression of hCG-treated rat mammosphere culture", "dateAssigned" : "2022-02-18T00:00:00.000-06:00", "summary" : "We performed microarray analysis of RNA isolated from mammospheres formed by normal mammary epithelial cells extracted from rats treated for 21 days either with r-hCG or vehicle (control).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197043" }, "primaryId" : "GEO:GSE197043", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197043" } ] }, "title" : "An intersectional analysis of LncRNAs and mRNAs reveals the potential therapeutic targets of Bi Zhong Xiao Decoction in collagen-induced arthritis rats", "dateAssigned" : "2022-02-19T00:00:00.000-06:00", "summary" : "Rheumatoid arthritis (RA) is a chronic progressive autoimmune disease of unknown etiology. Both clinical and experimental studies have revealed the effects of the traditional Chinese formula Bi Zhong Xiao Decoction (BZXD) in treating RA. However, the multifaceted mechanisms of BZXD in RA treatment are not comprehensively understood. In this study, we aimed to explore therapeutic targets of BZXD by using lncRNA and mRNA transcriptomics.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197074" }, "primaryId" : "GEO:GSE197074", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197074" } ] }, "title" : "Macrophage extracellular traps originated from the vascular smooth muscle cells play key roles in atherosclerosis progression [RNA-seq]", "dateAssigned" : "2022-02-20T00:00:00.000-06:00", "summary" : "Smooth muscle cells (SMC) play significant roles in atherosclerosis via phenotypic switching, a pathological process in which SMC transdifferentiation into macrophage-like SMCs. Furthermore, during transdifferentiation, the SMCs' expression of PADI4 upregulating and SMC generated extracellular trap, a web-like structure, which plays key role in the development of atherosclerosis plaque. To reveal the potential mechanism of the SMC derived macrophages generated ETs surducing surrounding SMCs within the media of artery during the process of atherosclerosis plaque development, we utilized the dsDNA and H3CIT protein to stimuli the SMCs, the SMC stimulated with 0.2%BSA as coontrol group, we collect the cells and did RNA-sequencing between two groups to find the potential signaling pathway participating in the process", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36473863" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197085" }, "primaryId" : "GEO:GSE197085", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197085" } ] }, "title" : "BMSC-derived exosomal miR-27a-3p and miR-196b-5p regulate bone remodeling in ovariectomized rats", "dateAssigned" : "2022-02-21T00:00:00.000-06:00", "summary" : "BMSC-derived exosomes from ovariectomized rats (OVX-Exo) and sham-operated rats (Sham-Exo) were co-cultured with bone marrow-derived macrophages to study their effects on osteoclast differentiation. Next-generation sequencing was utilized to identify the differentially expressed miRNAs (DE-miRNAs) in OVX-Exo and Sham-Exo, while target genes were analyzed using bioinformatics. The regulatory effects of miR-27a-3p and miR-196b-5p on osteogenic differentiation of BMSCs and osteoclast differentiation were verified by gain-of-function and loss-of-function analyses.Osteoclast differentiation was significantly enhanced in the OVX-Exo treatment group compared to the Sham-Exo group. Twenty DE-miRNAs were identified in OVX-Exo and Sham-Exo, among which miR-27a-3p and miR-196b-5p promoted the expressions of osteogenic genes in BMSCs. Incontrast, knockdown of miR-27a-3p and miR-196b-5p increased the expressions of osteoclastic genes in osteoclasts. These 20 DE-miRNAs were found to target 11435 mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that these target genes were involved in several biological processes and osteoporosis-related signaling pathways.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197089" }, "primaryId" : "GEO:GSE197089", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197089" } ] }, "title" : "RNA Sequencing Facilitates Quantitative Analysis of rat pancreas islet beta cell Transcriptomes in uric acid treat", "dateAssigned" : "2022-02-21T00:00:00.000-06:00", "summary" : "The effect of uric acid on islet function remains to be confirmed,We applied GSIS, immunofluorescence staining, WB, and flow cytometry to observe the protective effects of uric acid on beta cell apoptosis and insulin deficiency.To further explore the molecular mechanisms involved in this,we found UA could directly suppressed GSIS in both INS-1E cells and primary isolated islets in a dose- and time-dependent manner. RNAseq suggested that CHOP/NLRP3 is critical in the UA-induced beta cell dysfunction. These data suggest that UA might be an independent risk factor for beta cell function which induced beta cell dysfunction via OAT2/chop/ NLRP3 pathway. which provided new insight into the diabetogenic effect of UA.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197097" }, "primaryId" : "GEO:GSE197097", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197097" } ] }, "title" : "Transcriptomic profiling of diabetic rats treated with peripherical focused ultrasound (pFUS)", "dateAssigned" : "2022-02-21T00:00:00.000-06:00", "summary" : "To better characterize the systemic response of diabetic rats to daily hepatoportal pFUS stimulation, we conducted transcriptomic profiling of different metabolic tissues by RNAseq. For this purpose, we included samples from liver, intestines, kidney, adipose, muscle, pancreas, hypothalamus and blood in the Zucker diabetic fatty (ZDF) and diet induced obese (DIO) rodent models. ZDF rats spontaneously develop type 2 diabetes (T2D) as a result of a missense mutation (fatty, fa) in the leptin receptor gene and develop moderate hyperglycemia spontaneously as a result of the insulin resistance and pancreatic insufficiency. DIO model uses a high fat/high carbohydrate diet to induce obesity and insulin resistance. Following development of obesity low dose streptozotocin (STZ) is used to induce a moderate level of pancreatic beta cell death which impairs insulin secretion similar to that seen in later stage T2D. Tissue samples were processed and analyzed after 3 days, 4 weeks, and 7 weeks of 3 minute per day pFUS treatments. All procedures performed were done in accordance with the National Institutes of Health (NIH) Guidelines under protocols approved by the Institutional Animal Care and Use Committee (IACUC) of GE Global Research.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35361935" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197241" }, "primaryId" : "GEO:GSE197241", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197241" } ] }, "title" : "Understanding the underlying molecular mechanisms of meiotic arrest in organotypic culture of prepubertal rat testicular tissues", "dateAssigned" : "2022-02-22T00:00:00.000-06:00", "summary" : "We report the use of the Bulk RNA-sequencing technology on in vivo and in vitro cultured prepubertal testicular tissues. The goal of this study is to identify the origin of the maturation arrest observed in rat prepubertal testicular tissue cultured with the organ culture system with a transcriptomic approach. We compared the gene expression of 14.5 dpp rat testicular tissues cultured up to 6, 16, 22 and 28 days. The statistical filtration revealed 600 differentially expressed genes showing significant differential abundances in all three comparisons. This study uncovered for the first time several mechanisms that could explain the meiotic arrest observed in cultures of rat prepubertal testicular tissues.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35682573" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197403" }, "primaryId" : "GEO:GSE197403", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197403" } ] }, "title" : "ROLE OF ENDOPLASMIC RETICULUM STRESS IN IMPAIRED NEONATAL LUNG GROWTH AND BRONCHOPULMONARY DYSPLASIA", "dateAssigned" : "2022-02-24T00:00:00.000-06:00", "summary" : "Using multiomic data to investigate the role of endoplasmic reticulum stress in the development of BPD in rat model.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36018859" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197449" }, "primaryId" : "GEO:GSE197449", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197449" } ] }, "title" : "A critical role of the mechanosensor PIEZO1 in glucose-induced insulin secretion in pancreatic β-cells", "dateAssigned" : "2022-02-25T00:00:00.000-06:00", "summary" : "PIEZO1 is a mechanosensitive ion channel involved in the regulation of a diverse range of physiological responses. We examined the role of the mechanosensor ion channel PIEZO1 in glucose-induced insulin secretion in pancreatic β-cells. PIEZO1 expression is elevated in β-cells from human donors with type-2 diabetes (T2D) and a rodent T2D model (db/db 48 mouse). Silencing of Piezo1 inhibits glucose-induced Ca2+ signaling and insulin secretion. PIEZO1 translocates from the cytosol and plasmalemma into the nucleus in cells cultured at high glucose, experimental conditions emulating diabetes. The translocation of PIEZO1 into the nucleus in response to hyperglycemia suggests that PIEZO1 might be involved in transcriptional control in addition to serving as a mechanosensor in the plasma membrane. To address this, we performed mRNA sequencing in INS-1 832/13 cells to determine which genes are regulated by Piezo channels. Overall, we found 3292, 1656, and 1920 genes were significantly differentially expressed after silencing Piezo1, Piezo2, or both genes (adj.p-value < 0.05). Among these, the expression of the gene encoding cocaine- and amphetamine-regulated transcript (Cartpt) was increased >15-fold. We confirmed this effect by qPCR, which indicated a corresponding stimulation of expression. In insulin-secreting INS-1 832/13 cells, Cart has been reported to influence the expression and release of insulin. Thus, the impact of PIEZO1 on β-cell function may not be limited to electrical excitability but these changes are likely to operate on a slower timescale than the acute/electrical effects.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35869052" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197466" }, "primaryId" : "GEO:GSE197466", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197466" } ] }, "title" : "Cholinergic Anti-inflammatory Pathway (CAP) Activation in a Model of Acute Lung Infection", "dateAssigned" : "2022-02-25T00:00:00.000-06:00", "summary" : "The cholinergic anti-inflammatory pathway (CAP), has been well-studied and shown to control peripheral cytokine levels and inflammation. This nerve pathway has been activated pharmacologically or by nerve stimulators and studied in animal models and clinical studies. However, these CAP investigations have typically been performed in models or study populations of severe systemic or pathological inflammation. This transcriptomic profiling study was conducted in rats to understand CAP in a model of actue lung infeaction. Splenic ultrasound stimulation was used to activate CAP in both healthy animals and animals with an acute lung infection.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35784337" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197544" }, "primaryId" : "GEO:GSE197544", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197544" } ] }, "title" : "Expression profiles of long non-coding RNAs in neurogenic bladder of spinal cord injured rats: A transcriptomic analysis", "dateAssigned" : "2022-02-27T00:00:00.000-06:00", "summary" : "Conclusions: The results revealed the expression profiles and possible roles of lncRNAs in SCI rat NB.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197622" }, "primaryId" : "GEO:GSE197622", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197622" } ] }, "title" : "Integrative multi-omics landscape of fluoxetine action across 27 brain regions (single cell profiling for 2 regions)", "dateAssigned" : "2022-02-28T00:00:00.000-06:00", "summary" : "We constructed a comprehensive multi-omics map of the molecular effects of fluoxetine (an SSRI antidepressant) in 27 rat brain regions. We profiled gene expression (bulk RNA-seq, 210 datasets) and chromatin state (bulk chromatin immunoprecipitation sequencing (ChIP-seq) for the histone marker H3K27ac, 100 datasets) in a broad, unbiased panel of 27 brain regions across the entire rodent brain, in naive and fluoxetine-treated animals. We complemented this approach with single-cell RNA-seq (scRNA-seq) analysis of two brain regions (20 datasets). Remarkably, in the single-cell RNA-seq profiling we observed profound changes in the transcripts of hippocampal dorDG and venDG (~500 DEGs in specific cell types). Using diverse integrative data analysis techniques we characterized the complex and multifaceted effects of fluoxetine on region-specific and cell-type-specific gene regulatory networks and pathways. We leveraged this atlas to identify fluoxetine-modulated genes and gene-regulatory loci, predict enriched motifs that suggest potential upstream regulators, and validate global mechanisms of fluoxetine action.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36056172" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197664" }, "primaryId" : "GEO:GSE197664", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197664" } ] }, "title" : "The transcription factor, α1ACT, acts through a microRNA network to regulate neurogenesis and cell death during neonatal cerebellar development", "dateAssigned" : "2022-03-01T00:00:00.000-06:00", "summary" : "To investigate whether α1ACT acts through a microRNA network, we studied α1ACT-associated simultaneous miRNA:mRNA expression transcriptome profiles during cerebellar development in a context-dependent manner, using miRNA-seq paired with previously reported RNA-seq.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197736" }, "primaryId" : "GEO:GSE197736", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197736" } ] }, "title" : "Recruitment of transcriptional effectors by Cas9 creates cis regulatory elements and demonstrates distance-dependent transcriptional regulation", "dateAssigned" : "2022-03-02T00:00:00.000-06:00", "summary" : "It is essential to regulate the expression of genes, such as those encoding the proteins of the cardiac sarcomere. This regulation is often mediated by cis regulatory elements termed enhancers and repressors that recruit transcription factors to gene-distal sites. However, the relationship between transcription factors recruitment to gene-distant sites and the regulation of gene expression is not fully understood. Specifically, it is unclear if such recruitment to any genomic site is sufficient to form an enhancer or repressor at the site, and what is the relationship between the cis regulatory element’s position and its ability to control the transcription of distant genes. Using dead Cas9 to recruit either viral or endogenous transcription factor activation domains, we demonstrate that targeting 'naïve' genomic sites lacking open chromatin or active enhancer marks is sufficient to alter the chromatin signature of the target site, the distant gene promoter, and significantly induce the distant gene expression, even across chromatin insulating loci. The magnitude of induction is affected by the distance between the activation site and the cognate gene in a non-linear manner. Dead Cas9 mediated recruitment of repression domains behaves similarly to activation in that targeting of non-regulatory regions could repress gene expression with a nonlinear distance dependence and across chromatin insulating loci. These findings expand the models of enhancer generation and function by showing that an arbitrary genomic site can become a regulatory element and interact epigenetically and transcriptionally with a distant promoter. They also provide new fundamental insights into the rules governing gene expression.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197864" }, "primaryId" : "GEO:GSE197864", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197864" } ] }, "title" : "Maladaptive Positive Feedback Production of ChREBPβ Drives Glucotoxic β-Cell Failure", "dateAssigned" : "2022-03-03T00:00:00.000-06:00", "summary" : "Conclusions: ChREBPbeta is necessary for adaptive beta cell expansion, but drives glucose toxicity when overexpressed, mimicking the graded effect of Myc overexpression in beta cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35908073" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197926" }, "primaryId" : "GEO:GSE197926", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197926" } ] }, "title" : "TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function", "dateAssigned" : "2022-03-04T00:00:00.000-06:00", "summary" : "Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species, and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find 14% of all human TAD boundaries to be shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons, compared to species-specific boundaries. CRISPR-Cas9 knockouts of two ultraconserved boundaries in mouse models leads to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations, and showcase the functional importance of TAD evolution.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:38062027" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197930" }, "primaryId" : "GEO:GSE197930", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197930" } ] }, "title" : "Effect of monoacylglycerol lipase inhibition on intestinal permeability of rats with severe acute pancreatitis", "dateAssigned" : "2022-03-04T00:00:00.000-06:00", "summary" : "Endocannabinoid 2-arachidonoylglycerol (2-AG) is an anti-nociceptive lipid that is inactivated through cellular uptake and subsequent catabolism by monoacylglycerol lipase (MAGL). In this study, we investigated the effects of MAGL inhibition on intestinal permeability and explored the possible mechanism. A rat model of severe acute pancreatitis (SAP) was established. Rats were divided into three groups according to treatment. We analyzed intestinal permeability to fluorescein isothiocyanate-dextran and the levels of inflammatory factors interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) and 2-AG. Hematoxylin and eosin staining was used to assess histological tissue changes. In vivo intestinal permeability was evaluated by transmission electron microscopy. We obtained ileum tissues, extracted total RNA, and applied RNA-sequencing. Sequencing data were analyzed by bioinformatics. Inflammatory factor levels were higher, while 2-AG levels were lower in the SAP group compared with the control group. Administration of JZL184 to rats with SAP increased the levels of 2-AG and lowered the levels of IL-6 and TNF-α. Notably, intestinal permeability was improved by JZL184 as demonstrated by fluorescein isothiocyanate-dextran measurement, hematoxylin and eosin staining, and transmission electron microscopy. RNA-sequencing showed significant transcriptional differences in SAP and JZL184 groups compared with the control group. KEGG analysis showed that the up- or downregulated genes in multiple comparison groups were enriched in two pathways, focal adhesion and PI3K-Akt signaling pathways. Differential alternative splicing (AS) genes, such as Myo9b, Lsp1, and Git2, have major functions in intestinal diseases. A total of 132 RNA-binding proteins (RBPs) were screened by crossing the identified abnormally expressed genes with the reported RBP genes. Among them, Hnrnpdl coexpressed the most AS events as the main RBP. MAGL inhibition improved intestinal mucosal barrier injury in SAP rats and induced a large number of differentially expressed genes and alternative splicing events. Hnrnpdl might play an important role in improving intestinal mucosal barrier injury by affecting alternative splicing events.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35496266" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197999" }, "primaryId" : "GEO:GSE197999", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE197999" } ] }, "title" : "RNA Sequencing of Cardiac in STZ-induced Rat model Uncovers Potential Target of Diabetic cardiomyopathy", "dateAssigned" : "2022-03-06T00:00:00.000-06:00", "summary" : "Diabetic cardiomyopathy (DCM) is one of the major causes of heart failure in diabetic patients, but its pathogenesis remains unclear. Long non-coding RNAs (lncRNAs) are involved in the development of various cardiovascular diseases, but is little known in DCM. We build diabetic cardiomyopathy (DCM) rat model and investigated the genome-wide expression profiling of cardiac lncRNAs and mRNAs in rat model with and without DCM by RNA sequencing, to uncovers potential path mechanisms target of DCM.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35495145" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198008" }, "primaryId" : "GEO:GSE198008", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198008" } ] }, "title" : "Young CSF restores oligodendrogenesis and memory in aged mice via Fgf17", "dateAssigned" : "2022-03-06T00:00:00.000-06:00", "summary" : "Recent understanding of how the systemic environment shapes the brain throughout life has led to numerous intervention strategies to slow brain ageing. Cerebrospinal fluid (CSF) makes up the immediate environment of brain cells, providing them with nourishing compounds. We discovered that infusing young CSF directly into aged brains improves memory function. Unbiased transcriptome analysis of the hippocampus identified oligodendrocytes to be most responsive to this rejuvenated CSF environment. We further showed that young CSF boosts oligodendrocyte progenitor cell (OPC) proliferation and differentiation in the aged hippocampus and in primary OPC cultures. Using SLAMseq to metabolically label nascent mRNA, we identified serum response factor (SRF), a transcription factor that drives actin cytoskeleton rearrangement, as a mediator of OPC proliferation following exposure to young CSF. With age, SRF expression decreases in hippocampal OPCs, and the pathway is induced by acute injection with young CSF. We screened for potential SRF activators in CSF and found that fibroblast growth factor 17 (Fgf17) infusion is sufficient to induce OPC proliferation and long-term memory consolidation in aged mice while Fgf17 blockade impairs cognition in young mice. These findings demonstrate the rejuvenating power of young CSF and identify Fgf17 as a key target to restore oligodendrocyte function in the ageing brain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35545674" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198020" }, "primaryId" : "GEO:GSE198020", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198020" } ] }, "title" : "Metabolomic and transcriptomic profiling of DRG in SNI rat reveal a common pattern of changes in metabolites and signaling pathways in Neuropathic Pain", "dateAssigned" : "2022-03-07T00:00:00.000-06:00", "summary" : "Neuropathic Pain (NP) is a clinically common chronic refractory pain syndrome which threat to approximately 7–10% of the global population physical and mental health. However, the mechanism of metabolism alteration in NP remains unclear. This study is intended to figure out the relationship between the alternation of metabolism and the progression of NP.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198021" }, "primaryId" : "GEO:GSE198021", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198021" } ] }, "title" : "The effect of Bailing Capsule on gene expression in rat kidney", "dateAssigned" : "2022-03-07T00:00:00.000-06:00", "summary" : "The effect of Bailing Capsule on gene expression in rat kidney", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198151" }, "primaryId" : "GEO:GSE198151", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198151" } ] }, "title" : "Expression data of quaternary clones from rat lung CD117+ endothelial cells vs. non-clonal control endothelial cells", "dateAssigned" : "2022-03-08T00:00:00.000-06:00", "summary" : "We used microarrays to identify the steady state gene expression profile of quaternary clones derived from CD117+ rat lung ECs vs control ECs derived from rat lung CD117- cells.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36438452" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198219" }, "primaryId" : "GEO:GSE198219", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198219" } ] }, "title" : "RNA-sequencing analysis of SD rat abdominal wall treated with adhesive or non-adhesive implant", "dateAssigned" : "2022-03-09T00:00:00.000-06:00", "summary" : "We utilize bulk RNA-seq to profile the mRNA expression in day 3 and day 14 post-implantation of SD rat abdminal wall treated with adhesive or non-adhesive implants", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198237" }, "primaryId" : "GEO:GSE198237", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198237" } ] }, "title" : "scRNAseq RAT DIA WT and DMD 12months", "dateAssigned" : "2022-03-09T00:00:00.000-06:00", "summary" : "Duchenne muscular dystrophy (DMD) is a fatal muscle-wasting disorder caused by mutations in the Dystrophin gene with no therapeutic option. To bridge the gap between preclinical and therapeutic evaluation studies, we have generated a rat model for DMD that carries an exon 52 deletion (R DMDdel52) causing a complete lack of dystrophin protein. Here we show that R DMDdel52 animals recapitulated human DMD pathophysiological trajectory more faithfully than the mdx mouse model. We report that R DMDdel52 rats displayed progressive and severe skeletal muscle loss associated with fibrotic deposition, fat infiltration and fibre type switch. Early fibrosis was also apparent in the cardiac muscle. These histological modifications led to severe muscle, respiratory and cardiac functional impairments leading to premature death around one year. Moreover, DMD muscle exhibited systemic inflammation with a mixed M1/M2 phenotype. A comparative single cell RNAseq analysis of the diaphragm muscle was performed, revealing cellular populations alteration and molecular modifications in all muscle cell types. We show that DMD fibroadipogenic progenitors produced elevated levels of cartilage oligomeric matrix protein (COMP), a glycoprotein responsible for modulating homeostasis of extracellular matrix, and whose increased concentration correlated with muscle fibrosis both in R DMDdel52 rats and human patients. Fibrosis is a component of tissue remodelling impacting the whole musculature of DMD patients, at the tissue level but most importantly at the functional level. We therefore propose that this specific biomarker can optimize the prognostic monitoring of functional improvement of patients included in clinical trials.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35468843" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198250" }, "primaryId" : "GEO:GSE198250", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198250" } ] }, "title" : "High depth profiling of miRNA targets with chimeric eCLIP [eCLIPseq]", "dateAssigned" : "2022-03-09T00:00:00.000-06:00", "summary" : "Growing demand in RNA-targeted therapies and promise of miRNA-based drugs creates a need for tools that can accurately identify and quantify miRNA:target interactions at scale. The experimental capture of miRNA:mRNA interactions by ligation into chimeric RNA fragments provides a direct read out of miRNA targets by enabling profiling of miRNA targets with high-throughput sequencing. However, integration of chimeric CLIP-seq into wide practical use has been limited because the inefficiency of the miRNA:mRNA ligation step (resulting in a low rate of chimeric reads in final libraries) combined with the technical complexity of the method makes it challenging to apply to miRNAs of interest at scale. Here we describe chimeric eCLIP, in which we integrate a chimeric ligation step into AGO2 eCLIP to enable chimeric read recovery, and show that removal of the cumbersome polyacrylamide gel and nitrocellulose membrane transfer step common to CLIP techniques can be omitted for chimeric AGO2 eCLIP to create a simplified high throughput version of the assay that maintains high signal-to-noise. With the increased yield of recovered miRNA:mRNA interactions in no-gel chimeric eCLIP, we show that simple enrichment steps using either PCR or on-bead probe capture can be added to chimeric eCLIP in order to target and enrich libraries for chimeric reads specific to one or more miRNAs of interest in both cell lines and tissue samples, resulting in 30- to 175-fold increases in recovery of chimeric reads for miRNAs of interest. We further show that the same probe-capture approach can be used to recover miRNA interactions for a targeted gene of interest, revealing both distinct miRNA targeting as well as co-targeted by several miRNAs from the same seed family. RNA-seq analysis of gene expression following miRNA overexpression confirmed miRNA-mediated repression of chimeric eCLIP identified targets, and indicated that chimeric eCLIP can provide additional sensitivity to detect regulated targets among genes that either contain or lack computationally predicted miRNA target sites. Thus, we believe that chimeric eCLIP will be a useful tool for quantitative profiling of miRNA targets in varied sample types at scale, and revealing a deeper picture for regulatory networks for miRNAs of biological interest.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198452" }, "primaryId" : "GEO:GSE198452", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198452" } ] }, "title" : "Environmental Induced Epigenetic Transgenerational Inheritance of Pathology: Systems Epigenetics in Disease Etiology and Generational Toxicology", "dateAssigned" : "2022-03-11T00:00:00.000-06:00", "summary" : "Several epigenome-wide association studies (EWAS) have been shown to identify epigenetic alterations (i.e., epimutations) associated with diseases. The sperm epimutations potentially involved in the transgenerational inheritance of specific pathologies have been identified. Transgenerational sperm epimutations associated with kidney, prostate, puberty, testis, obesity, and multiple pathologies have been identified for a variety of environmental toxicants including dioxin, plastics, pesticides, glyphosate, methoxychlor, atrazine, and jet fuel. The transgenerational sperm epimutations for exposure and disease-specific epimutations have been identified in these EWAS studies. The current study used the information from these previous toxicant-induced epigenetic transgenerational inheritance EWAS rat studies and adds a comparable control group, rats that have not been exposed to any particular toxicant. Two additional control groups were collected and are presented here.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35440735" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198507" }, "primaryId" : "GEO:GSE198507", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198507" } ] }, "title" : "Transcriptome analysis of subacute injured kidney by intraperitoneal injections of Fe-NTA in wildtype and BRCA1+/- rats", "dateAssigned" : "2022-03-12T00:00:00.000-06:00", "summary" : "Fenton reaction-based repeated oxidative stress via ferric nitrilotriacetate (Fe-NTA) causes renal cell carcinoma (RCC), which was found to be promoted in BRCA1 haploinsufficiency rats.To elucidate the molecular mechanism, we performed a subacute study of repeated ip administration of Fe-NTA for 1 or 3 weeks to understand the early events. We compared the microarray gene expression profiles of rat kidney cortex tissues of wild-type and BRCA1+/- rats from the study.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35667247" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198508" }, "primaryId" : "GEO:GSE198508", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198508" } ] }, "title" : "Genomic profiles of oxidative stress-induced renal cell carcinomas developed in wild-type and BRCA1+/- SD rats", "dateAssigned" : "2022-03-12T00:00:00.000-06:00", "summary" : "Fenton reaction-based repeated oxidative stress via ferric nitrilotriacetate (Fe-NTA) causes renal cell carcinoma (RCC) with genetic alterations similar to those in humans. We conducted high-resolution microarray comparative genomic hybridization with Fe-NTA induced RCC obtained from both wild-type and BRCA1+/- rats to evaluate the involvement of BRCA1 haploinsufficiency in carcinogenesis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35667247" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198608" }, "primaryId" : "GEO:GSE198608", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198608" } ] }, "title" : "Single-cell RNA sequencing reveals the link between axonal regeneration and neuropathic pain by modified analysis of a novel peripheral nerve injury rat model", "dateAssigned" : "2022-03-14T00:00:00.000-05:00", "summary" : "Severe peripheral nerve injury (PNI) often causes significant movement disorders and intractable pain. Therefore, promoting nerve regeneration while avoiding neuropathic pain, a problem that remains unsolved, is key to the clinical treatment of PNI patients. Here, we establish a novel spared nerve crush (SNC) rat model that successfully reproduces axonal regeneration and neuropathic pain after PNI. Subsequently, we obtained single-cell RNA sequencing (scRNA-seq) data from rat directly injured and indirectly injured rat dorsal root ganglion (DRG) neurons at various time points after SNC and found that the PEP1 neuronal subtype in directly injured DRG is of particular interest. Through experimental design, sc-RNA sequence processing (EDSSP) and functional verification, we identified a potential key gene, Adcyap1, that encodes a key molecule linking nerve regeneration and pain after PNI. Our study sheds new light on the intrinsic link between axonal regeneration and neuropathic pain following PNI and provides new molecular targets and ideas for therapeutic intervention.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198617" }, "primaryId" : "GEO:GSE198617", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198617" } ] }, "title" : "Probiotic supplementation with Lactiplantibacillus plantarum 299v modulates ER and oxidative stress pathways in ?-cells and prevents Type 1 diabetes in gluten-free BioBreeding Rats", "dateAssigned" : "2022-03-14T00:00:00.000-05:00", "summary" : "Here we investigated the effect of Lp299v supplement on T1D progression and inflammatory phenotypes in diabetes prone BB DRlyp/lyp rats. Rats were weaned at 21 days onto a normal cereal diet (ND) or a gluten-free hydrolyzed casein diet (HCD), with and without daily Lp299v supplementation. All DRlyp/lyp ND rats developed T1D by day 83 (mean time to onset of 62.8+/-7.9 days). DRlyp/lyp ND+Lp299v rats exhibited an insignificant delay in T1D onset (62.6+/-6.5 days), however 8% remained diabetes-free to day 130. Providing DRlyp/lyp rats HCD prevented T1D in 17% of rats (to age 130 days) and significantly delayed onset (mean time to onset 72.8+/-7.3 days, p<0.001). Providing DRlyp/lyp rats HCD+Lp299v prevented T1D in 25% of rats and more robustly delayed onset (mean time to onset 84.9 +/-14.3 days, p<0.001). While multiplex ELISA failed to detect significantly altered plasma cytokine/chemokine levels at 40 days of life, plasma induced transcription revealed greatest normalization of systemic inflammation in the HCD+Lp299v group. Plasma SCFA levels (propionate and butyrate, p<0.01) were elevated in the HCD+Lp299v group compared to the ND group. Global gene expression analysis of pancreatic islets was conducted at 40 days, prior to insulitis. Endoplasmic reticulum (ER) stress has been implicated in the formation of islet neoantigens that may underlie the initial loss of immune tolerance in T1D. Under one or both diets, Lp299v favorably modulated islet expression levels of pathways and transcripts related to inflammation and innate immunity (Cxcl9, Cxcl10), oxidative stress (Gsta1, Gsta4, Gstp1, Gstk1), as well as ER stress and unfolded protein response (Cirbp, Edem1, Hspa1a, Atf4). These ongoing studies add to a growing understanding that inherited susceptibility can be modulated by diet and microbiota.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36261888" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198642" }, "primaryId" : "GEO:GSE198642", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198642" } ] }, "title" : "Lack of xanthine dehydrogenase leads to a remarkable renal decline in a novel hypouricemic rat model", "dateAssigned" : "2022-03-14T00:00:00.000-05:00", "summary" : "The SSXdh-/- rat (SS-Xdhem1Mcwi, Rat Genome Database ID:14398479), created on the Dahl SS background, resulted in severe hypouricemia in the tissues. With the Xdh project, the overall hypothesis is that the Xdh gene ablation will result in kidney damage and perturbation of blood pressure control. We were interested in finding out if the gene ablation alternates the kidney development process. The deletion of Xdh protein produced dramatic changes in proteins related to the salvage pathway. The novel Xdh knockout rat model exhibited profound hypouricemia, which increased oxidative stress and crystal formation, leading to inflammation, renal cell proliferation, severe kidney damage, and a subsequent decline in renal function.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36039296" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198737" }, "primaryId" : "GEO:GSE198737", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198737" } ] }, "title" : "Characterization of 5-hmC DNA Methylation Patterns in the Hippocampus of an Experimental Model of Epilepsy", "dateAssigned" : "2022-03-16T00:00:00.000-05:00", "summary" : "Temporal lobe epilepsy is one of the most common refractory epilepsies in the world. Epilepsy progression is controlled through the expression of epilepsy permissive genes, ultimately resulting in a hyperexcitable network and spontaneous seizures. DNA methylation has been explored as a potential epigenetic regulatory mechanism of gene expression in epilepsy, however, the role of 5-hydroxymethylcytosine (5-hmC) has been underexplored to date. 5-hmC is a stable epigenetic mark most abundantly expressed in the brain. In this study, we show that 5-hmC but not 5-methylcytosine (5-mC) is lost in temporal lobe epilepsy. Using 5-hmC meDIP-sequencing, we characterized epileptic 5-hmC distribution in the rat kainic acid model of temporal lobe epilepsy. We identified the correlation of 5-hmC loss and gain with epilepsy-associated gene ontology pathways and implicate the potential involvement of multiple cell types with 5-hmC regulation of temporal lobe epilepsy. Overall, we show that 5-hmC has the potential to be a crucial regulator of epilepsy and epileptic gene expression and are the first to characterize the genomic distribution of 5-hmC in a model of epilepsy.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198747" }, "primaryId" : "GEO:GSE198747", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198747" } ] }, "title" : "Expression data from plasma exosomal microRNA of rats with remote ischemic conditioning and normal controls", "dateAssigned" : "2022-03-16T00:00:00.000-05:00", "summary" : "Five RIC rats and 5 control rats were enrolled in this study. We used microarray analysis to identify miRNA expression in their plasma exosomes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198756" }, "primaryId" : "GEO:GSE198756", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198756" } ] }, "title" : "Integrative genomics reveals pathogenic mediator of valproate-induced neurodevelopmental outcomes.", "dateAssigned" : "2022-03-16T00:00:00.000-05:00", "summary" : "Prenatal exposure to the anti-seizure drug sodium valproate (VPA) is associated with an increased risk of adverse postnatal neurodevelopmental outcomes, including lowered intellectual ability, autism spectrum disorder and attention-deficit hyperactivity disorder. In this study, we aimed to clarify the molecular mechanisms underpinning the neurodevelopmental consequences of gestational VPA exposure using integrative genomics. First, we assessed the effect of gestational VPA on fetal brain gene expression using a validated rat model of valproate teratogenicity that mimics the human scenario of chronic oral valproate treatment during pregnancy at doses which are therapeutically relevant to the treatment of epilepsy. Two different rat strains were studied - inbred Genetic Absence Epilepsy Rats from Strasbourg (GAERS), a model of genetic generalized epilepsy, and inbred Non-Epileptic Control (NEC) rats. Female rats were fed standard chow or VPA mixed in standard chow for 2 weeks prior to conception and then mated with same-strain males. In the VPA-exposed rats maternal oral treatment was continued throughout pregnancy. Fetuses were extracted via C-section on gestational day 21 (one day prior to birth) and fetal brains were snap frozen and genome-wide gene expression data generated. We found that gestational VPA exposure via chronic maternal oral dosing was associated with substantial drug-induced differential gene expression in the pup brains, including dysregulated splicing, and observed that this occurred in the absence of evidence for significant neuronal gain or loss. The set of genes down-regulated by VPA in the pup brains were significantly enriched for pathways related to neurodevelopment and synaptic function, and significantly enriched for heritability to human intelligence, schizophrenia and bipolar disorder. Our results provide a mechanistic link between chronic fetal VPA exposure and adverse neurodevelopmental outcomes mediated by VPA-induced transcriptional dysregulation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36071595" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198803" }, "primaryId" : "GEO:GSE198803", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198803" } ] }, "title" : "small-RNA sequencing after controlled cortical impact model of repeated mild traumatic brain injury in male rats", "dateAssigned" : "2022-03-16T00:00:00.000-05:00", "summary" : "We report the miRNAs differentially expressed in the orbitofrontal cortex of adult male rats 5 weeks after a controlled cortical injury model of traumatic brain injury (TBI). Animals underwent 3 repeated mild injuries on days 1, 4 and 7. Tissue was collected on day 42.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198807" }, "primaryId" : "GEO:GSE198807", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198807" } ] }, "title" : "RNA sequencing after heroin or immune challenge in male rats", "dateAssigned" : "2022-03-16T00:00:00.000-05:00", "summary" : "We report the miRNAs differentially expressed in the nucleus accumbens of adult male rats after either heroin self-administration, experimenter administered heroin, lipopolysaccharide (LPS) or LPS and experimenter administered heroin", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:39702361" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198906" }, "primaryId" : "GEO:GSE198906", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198906" } ] }, "title" : "Control of pancreatic islet function and glucose homeostasis by a novel microexon program misregulated in type 2 diabetes", "dateAssigned" : "2022-03-17T00:00:00.000-05:00", "summary" : "Pancreatic islets control glucose homeostasis by the balanced secretion of insulin and other hormones, and its abnormal function causes diabetes or hypoglycemia. Here, we uncover a conserved program of alternative microexons included in mRNAs of islet cells, particularly in genes involved in vesicle transport and exocytosis. Islet microexons (IsletMICs) are regulated by the RNA binding protein SRRM3 and represent a subset of the larger neural program that are particularly sensitive to the levels of this protein. Both SRRM3 and IsletMICs are induced by elevated glucose levels, and depletion of SRRM3 in beta cell lines and mouse islets, or repression of particular IsletMICs using antisense oligonucleotides, leads to inappropriate insulin secretion. Consistently, SRRM3 mutant mice display defects in islet cell identity and function, leading to hyperinsulinemic hypoglycemia. Importantly, human genetic variants that influence SRRM3 expression and microexon inclusion in islets are associated with fasting glucose variation and type 2 diabetes risk.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36759540" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198994" }, "primaryId" : "GEO:GSE198994", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE198994" } ] }, "title" : "Cortical and hippocampal gene expression after transcranial focal stimulation in healthy rats", "dateAssigned" : "2022-03-19T00:00:00.000-05:00", "summary" : "We aimed to screen genetic expression in the cerebral cortex and the hippocampus of healthy rats to identify potential targets of therapeutic or adverse effects of TFS.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199066" }, "primaryId" : "GEO:GSE199066", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199066" } ] }, "title" : "mRNA Seqeuencing of MCAO and trat pons after stroke [bulk RNA-seq]", "dateAssigned" : "2022-03-21T00:00:00.000-05:00", "summary" : "We report the result of mRNA-seq of MCAO and pontine infarction in rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199067" }, "primaryId" : "GEO:GSE199067", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199067" } ] }, "title" : "Single cell Seqeuencing of trat pons after stroke [scRNA-seq]", "dateAssigned" : "2022-03-21T00:00:00.000-05:00", "summary" : "We report the result of scRNA-seq of pontine infarction in rats.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199117" }, "primaryId" : "GEO:GSE199117", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199117" } ] }, "title" : "Antibiotics-induced depletion of rat microbiota induces changes in the expression of host drug-processing genes and pharmacokinetic behaviors of CYPs probe drugs", "dateAssigned" : "2022-03-22T00:00:00.000-05:00", "summary" : "This study aimed to quantify and compare the mRNA abundance of drug-processing genes (DPGs) in liver and jejunum between wild-type rats and antibiotics-treated rats by using an unbiased quantitative RNA-Seq method. Our results show that antibiotics treatments altered the mRNA expressions of 112 DPGs in the liver and jejunum of rats. The mRNA levels of CYP2A1, CYP2C11, CYP2C13, CYP2D, CYP2E1, and CYP3A of CYP family members were significantly downregulated in antibiotics-treated rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36623881" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199183" }, "primaryId" : "GEO:GSE199183", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199183" } ] }, "title" : "Cortical and hippocampal gene expression after transcranial focal stimulation and a single seizure in rats", "dateAssigned" : "2022-03-22T00:00:00.000-05:00", "summary" : "Nevertheless, the mechanisms and therapeutic targets that induced these effects remain ellusive. We aimed to screen the genetic expression in the cerebral cortex and the hippocampus of rats after a single seizure and TFS to identify potential targets.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199221" }, "primaryId" : "GEO:GSE199221", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199221" } ] }, "title" : "Late transcriptional changes in blood, neural, and colon tissues in rat stress alone and comorbid pain model compared with naïve have regulatory roles in neurological disease", "dateAssigned" : "2022-03-23T00:00:00.000-05:00", "summary" : "Conclusions: Our study highlights an increased inflammatory response in CPH compared to SIH rats in the blood and colon. DRG and spinal transcriptomic profiles of both CPH and SIH rats showed inhibition of synaptic activity along with activation of angiogenesis. Targeting these biological processes may lead to more profound understanding of the mechanisms underlying IBS-TMD comorbidities and new diagnostic and therapeutic strategies", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35655748" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199231" }, "primaryId" : "GEO:GSE199231", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199231" } ] }, "title" : "Effect of disturbance of vagal- or COX- dependent route of neuroimmune communication on the hypotalamic transcriptome", "dateAssigned" : "2022-03-23T00:00:00.000-05:00", "summary" : "This is data from studies on mechanisms compensating for disturbances in the activity of neuronal or humoral neuroimmune communication pathways in the model of intraperitoneal inflammation.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35874650" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199234" }, "primaryId" : "GEO:GSE199234", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199234" } ] }, "title" : "The anti-androgenic fungicide triticonazole induces region-specific transcriptional changes in the developing rat perineum and phallus", "dateAssigned" : "2022-03-23T00:00:00.000-05:00", "summary" : "Intrauterine exposure to endocrine disrupting chemicals can interfere with male reproductive development. This can lead to male reproductive disorders such as hypospadias, cryptorchidism and reduced fertility, as well as shorter anogenital distance (AGD) – a biomarker for incomplete androgen-dependent fetal masculinization. However, it remains challenging to predict adverse in vivo outcomes based on in vitro effect patterns for many chemicals. This is a challenge for modern toxicology, which aims to reduce animal testing for chemical safety assessments. To enable the transition towards higher reliance on alternative test methods, we need to better map underlying mechanisms leading to adverse effects. Herein, we have analyzed the transcriptome of the perineum and phallus of male fetal rats and defined the impacts of exposure to an anti-androgenic fungicide, triticonazole. Previously we have shown that developmental exposure to triticonazole can induce short male AGD, but without a marked effect on the transcriptome of the fetal testes. In contrast, we report here significant changes to the transcriptional landscape of the perineum and phallus, including regional differences between these adjacent tissues. This highlights the importance of analyzing the correct tissue when characterizing mechanisms of complex in vivo effect outcomes. Our results provide a rich resource for the spatiotemporal gene networks that are involved in the development of male external genitalia, and that can be disrupted upon exposure to chemicals that prevent normal masculinization of the perineum and phallus. Such data will be critical in the development of novel alternative test methods to determine the endocrine disrupting potential of existing and emerging chemicals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199260" }, "primaryId" : "GEO:GSE199260", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199260" } ] }, "title" : "Methamphetamine induced regional-specific transcriptomic and epigenetic changes in rat brain [ATAC-seq]", "dateAssigned" : "2022-03-23T00:00:00.000-05:00", "summary" : "We investigated the transcriptomic and epigenetic responses to a METH overdose in four regions of rat brain, including the nucleus accumbens, dentate gyrus, Ammon’s horn, and subventricular zone. We found that 24 hours after the METH overdose, 15.6% of genes changed expression and 27.6% of open-chromatin regions altered chromatin accessibility in all four rat brain regions. Interestingly, only a few of those differentially expressed genes (DEGs) and differentially accessible regions (DARs) were simultaneously affected. Among the four rat brain regions analyzed, 149 transcription factors (TFs) and 31 epigenetic factors were significantly affected by the METH overdose. The METH overdose also resulted in reversed regulation patterns of both gene and chromatin accessibility in the dentate gyrus and Ammon’s horn. About 70% of METH-induced chromatin accessibility alterations are highly enriched in neurological processes and shared conserved sequences to the human genome. Many of these conserved regions were active brain-specific enhancers and harbored the SNPs associated with human neurological functions and diseases. Our results indicate strong region-specific transcriptomic and epigenetic responses to a METH overdose in distinct rat brain regions. We describe the conservation of region-specific gene regulatory networks associated with a METH overdose. Overall, our study provides clues to a better understanding of the molecular responses to METH overdose in the human brain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199363" }, "primaryId" : "GEO:GSE199363", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199363" } ] }, "title" : "Methamphetamine induced regional-specific transcriptomic and epigenetic changes in rat brain [RNA-seq]", "dateAssigned" : "2022-03-24T00:00:00.000-05:00", "summary" : "We investigated the transcriptomic and epigenetic responses to a METH overdose in four regions of rat brain, including the nucleus accumbens, dentate gyrus, Ammon’s horn, and subventricular zone. We found that 24 hours after the METH overdose, 15.6% of genes changed expression and 27.6% of open-chromatin regions altered chromatin accessibility in all four rat brain regions. Interestingly, only a few of those differentially expressed genes (DEGs) and differentially accessible regions (DARs) were simultaneously affected. Among the four rat brain regions analyzed, 149 transcription factors (TFs) and 31 epigenetic factors were significantly affected by the METH overdose. The METH overdose also resulted in reversed regulation patterns of both gene and chromatin accessibility in the dentate gyrus and Ammon’s horn. About 70% of METH-induced chromatin accessibility alterations are highly enriched in neurological processes and shared conserved sequences to the human genome. Many of these conserved regions were active brain-specific enhancers and harbored the SNPs associated with human neurological functions and diseases. Our results indicate strong region-specific transcriptomic and epigenetic responses to a METH overdose in distinct rat brain regions. We describe the conservation of region-specific gene regulatory networks associated with a METH overdose. Overall, our study provides clues to a better understanding of the molecular responses to METH overdose in the human brain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199443" }, "primaryId" : "GEO:GSE199443", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199443" } ] }, "title" : "Epigenetic aberrations of gene expression in a rat model of hepatocellular carcinoma", "dateAssigned" : "2022-03-25T00:00:00.000-05:00", "summary" : "Hepatocellular carcinoma (HCC) is mostly triggered by environmental and life-style factors and may involve epigenetic aberrations. However, a comprehensive documentation of the link between the dysregulated epigenome, transcriptome, and liver carcinogenesis is lacking. In the present study, Fischer-344 rats were fed a choline-deficient (CDAA, cancer group) or choline-sufficient (CSAA, healthy group) L-amino acid-defined diet. At the end of 52 weeks, transcriptomic alterations in livers of rats with HCC tumors and healthy livers were investigated by RNA sequencing. DNA methylation and gene expression were assessed by pyrosequencing and quantitative reverse-transcription PCR (qRT-PCR), respectively. We discovered 1,848 genes that were significantly differentially expressed in livers of rats with HCC tumors (CDAA) as compared with healthy livers (CSAA). Upregulated genes in the CDAA group were associated with cancer-related functions, whereas macronutrient metabolic processes were enriched by downregulated genes. Changes of highest magnitude were detected in numerous upregulated genes that govern key oncogenic signaling pathways, including Notch, Wnt, Hedgehog, and extracellular matrix degradation. We further detected perturbations in DNA methylating and demethylating enzymes, which was reflected in decreased global DNA methylation and increased global DNA hydroxymethylation. Four selected upregulated candidates, Mmp12, Jag1, Wnt4, and Smo, demonstrated promoter hypomethylation with the most profound decrease in Mmp12. MMP12 was also strongly overexpressed and hypomethylated in human HCC HepG2 cells as compared with primary hepatocytes, which coincided with binding of Ten-eleven translocation 1 (TET1). Our findings provide comprehensive evidence for gene expression changes and dysregulated epigenome in HCC pathogenesis, potentially revealing novel targets for HCC prevention/treatment.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35502615" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199458" }, "primaryId" : "GEO:GSE199458", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199458" } ] }, "title" : "Candidate master microRNA regulator of arsenic-induced pancreatic beta cell impairment revealed by multi-omics analysis", "dateAssigned" : "2022-03-25T00:00:00.000-05:00", "summary" : "Arsenic is a pervasive environmental toxin that is ranked as the number one investigative priority by the Agency for Toxic Substance and Disease Registry. Chronic exposure to arsenic has been associated with type 2 diabetes (T2D). However, the underlying mechanisms remain largely unknown. We have recently demonstrated that arsenic treatment of INS-1 832/13 pancreatic beta-cells impairs glucose stimulated insulin secretion (GSIS), a hallmark of T2D. We have also shown that arsenic alters the microRNA (miRNA) profile in beta-cells more dramatically than other metals. miRNAs have a well-established regulatory role in both normal beta-cell function and T2D pathogenesis. We hypothesized that there are miRNA master regulators that mediate arsenic-associated GSIS defects. To test this hypothesis, we first treated INS-1 832/13 beta-cells with either 1 μM of inorganic arsenic (iAsIII) or 0.5 μM of monomethylarsenite (MAsIII) and confirmed that GSIS is significantly reduced. We then performed multi-omic analysis using chromatin run-on sequencing (ChRO-seq), RNA-sequencing (RNA-seq), and small RNA-seq in order to define arsenic-associated chromatin and transcriptional activity, gene expression, and miRNA profiles, respectively. Integrating across these data sets we first showed that genes downregulated by iAsIII treatment are enriched in insulin secretion, T2D, and maturity onset diabetes of the young (MODY) pathways, whereas genes downregulated by MAsIII treatment are enriched in cell cycle and include genes that encode the critical beta cell maintenance factors Neurod1 and Rfx6. Secondly, we also identified those genes that are subject primarily to post-transcriptional regulation in response to arsenicals. Finally, we demonstrated that miR-29a is the top candidate master regulator of these genes. Our study is the first multi-omic analysis of beta cells after exposure to arsenicals, and the results strongly suggest that arsenicals lead to aberrant miR-29 expression and activity in beta-cells, which in turn leads to the repression of critical genes for beta-cell function, ultimately predisposing to diabetes.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199508" }, "primaryId" : "GEO:GSE199508", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199508" } ] }, "title" : "Transcriptome profiling of miRNA and mRNA of the cortex in a rat model of Vascular dementia by RNA-sequencing", "dateAssigned" : "2022-03-27T00:00:00.000-05:00", "summary" : "In this study, we investigated the miRNA and mRNA profiling of the cortex of rat model of vascular dementia (VaD) to analyze the regulatory mechanism in the pathology of VaD involved by miRNAs, transcription factors (TFs), and corresponding target genes. As a validated model of VaD, rats suffering from bilateral common carotid artery occlusion (2VO) were used in the present study and the reliability of this model was examined by the Morris water maze (MWM) test and the Nissl staining. Overall, results showed that rats with 2VO presented declined learning and memory capabilities in the MWM test and neuronal loss in the hippocampus and cortex indicated by Nissl-staining compared to sham rats. DEGs, DEMs, and DETFs were discriminated between rats with 2VO and sham rats in the cortex, illustrated by 13 aberrantly-expressed miRNAs, 805 mRNAs, and 63 TFs. Further network analysis revealed that 7 target genes, 5 miRNAs, and 10 TFs were the key molecule in the miRNA-TF-gene network related to VaD. Gene Ontology (GO) and pathway enrichment analyses of these VaD-related transcripts showed that these differently changed genes mostly got involved in PI3K-Akt signaling pathway, neuroactive ligand-receptor interaction, calcium signaling pathway, and Wnt signaling pathway, along with central locations around cell membrane, exerting function such as growth factor binding, integrin binding, and extracellular matrix structural constituent, with representative biological processes like vasculature development, cell-substrate adhesion, cellular response to growth factor stimulus, and synaptic transmission. In conclusion, these results will help us understand the underlying regulatory mechanisms of miRNA-TF-genes in pathogenesis and provide potential therapeutic targets for the treatment of VaD.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36203804" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199558" }, "primaryId" : "GEO:GSE199558", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199558" } ] }, "title" : "MANF relieves cerebral infarction injury by enhancing the pyroptosis inhibition of BMSCs", "dateAssigned" : "2022-03-28T00:00:00.000-05:00", "summary" : "Cerebral infarction is a common disease characterized by high mortality, narrow therapeutic window and limited therapeutic avenue.We constructed animal model of Middle Cerebral Artery Occlusion (MCAO), compared different expression genes (DEGs) between Sham and MCAO group by single-cell RNA sequencing (scRNA-seq) to explore the potential cell death-related pathways involved in cerebral infarction.We found that the DEGs up-regulated in four major cellclusters after MCAO were enriched for not only apoptosis, ferroptosis and necroptosis, but also pyroptosis-related pathways and functions. Surprisingly, our protein-protein interaction (PPI) networks analysis showed indirect correlation between MANF and pyroptosis-related proteins.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199661" }, "primaryId" : "GEO:GSE199661", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199661" } ] }, "title" : "Effects of paternal nicotine taking on gene expression in dorsal hippocampus of drug naïve male offspring", "dateAssigned" : "2022-03-29T00:00:00.000-05:00", "summary" : "To characterize the molecular changes associated with the heritable effects of paternal nicotine taking, an unbiased, whole-genome analysis was used to characterize the hippocampal transcriptome of drug-naïve F1 males", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35595980" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199753" }, "primaryId" : "GEO:GSE199753", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199753" } ] }, "title" : "Next Generation Sequencing Analysis of primary rat lung fibroblast transcriptomes", "dateAssigned" : "2022-03-30T00:00:00.000-05:00", "summary" : "Purpose: We report the application of single-molecule-based sequencing technology for high-throughput profiling of primary rat lung fibroblast cultured on 3-5 kPa PDMS compared to plastic over a 14-day timecourse.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199790" }, "primaryId" : "GEO:GSE199790", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199790" } ] }, "title" : "Transcriptome analysis of rMSCs cultured for 4 hours in differerent substrate (TCP, PCL film, ISB-P fIlm)", "dateAssigned" : "2022-03-30T00:00:00.000-05:00", "summary" : "We developed new isosorbide derivatives (propoxylated or ethoxylated isosorbide) which have more reactivity in PCL-PU copolymer synthesis than the original isosorbide. PCL-PU copolymer incorporated propoxylated isosorbide (ISB-P) exhibited notable mechanical performance (50 MPa tensile strength and 1150% elongation with hyperelasticity under cyclic load), ultra-cell-adhesive property, and enhanced osteogenic differentiation. There was no significant difference in surface characteristics between ISB-P and PCL), however, mRNA profiles showed higher expressions of heat shock proteins which have been reported to promote osteogenic differentiation at 4 h after cell seeding in rMSC cultured on ISB-P compared to PCL. In conclusion, the engagement of heat shock protein to the ISB-P surface during cell attachment may promote osteogenic differentiation in ISB-P.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36176615" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199846" }, "primaryId" : "GEO:GSE199846", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199846" } ] }, "title" : "A bioengineered tridimensional substrate designed for mesenchymal stem cells culture: whole transcriptomic analysis", "dateAssigned" : "2022-03-31T00:00:00.000-05:00", "summary" : "In this work we aimed to evaluate how the three-dimensionality of an engineered scaffold, concieved to emulate the stem cell niche, can influence the whole gene expression profile of mesenchymal stem cells. We performed a differential expression analysis, comparing the transcriptome of MSCs grown in 3D Nichoids with that of MSCs grown on 2D Nichoids, a structure with the same grid geometry, except for the overall tickness which allows a spreading expansion of cells. We found a total of 603 differentially expressed genes that were used also for functional enrichment analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36686258" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199848" }, "primaryId" : "GEO:GSE199848", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199848" } ] }, "title" : "Acute ethanol challenge differentially regulates expression of Growth Factors and miRNA expression profile of whole tissue of the dorsal hippocampus", "dateAssigned" : "2022-03-31T00:00:00.000-05:00", "summary" : "Acute ethanol exposure produces rapid alterations in neuroimmune gene expression that are both time- and cytokine-dependent. Interestingly, adolescent rats, who often consume binge-like quantities of alcohol, displayed reduced neuroimmune responses to acute ethanol challenge. However, it is not known whether growth factors, a related group of signaling factors, respond to ethanol similarly in adults and adolescents. To test this, adolescent and adult Sprague Dawley rats of both sexes were injected with either ethanol or saline, and brains were harvested 3 hr post-injection for assessment of growth factor, cytokine, or miRNA expression. RNASeq revealed a rapid suppression of 12 miRNA species. Of the miRNA affected by ethanol, the majority were related to inflammation or cell survival and proliferation factors, including FGF2, MAPK, NFκB, and VEGF.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35706690" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199892" }, "primaryId" : "GEO:GSE199892", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199892" } ] }, "title" : "Epitranscriptomic map of N6-methyladenosine circular RNAs in the spinal cord of morphine-tolerant rats", "dateAssigned" : "2022-03-31T00:00:00.000-05:00", "summary" : "Morphine tolerance is a tricky problem, the mechanism of it is still unclear. Circular RNAs (CircRNAs) play important roles in biological process of central nervous system. N6-methyladenosine (m6A) as a key post-transcriptional modification of RNA can regulate the metabolism and functions of circRNAs. Here we conducted this research to explore the patterns of m6A-methylation of circRNAs in the spinal cords of 4 morphine tolerated rats and 4 normal rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35992914" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199970" }, "primaryId" : "GEO:GSE199970", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199970" } ] }, "title" : "Sequencing and Quantitative Analysis of Skin Transcriptomes from Rats with EGFR Inhibitors Induced Rash", "dateAssigned" : "2022-04-01T00:00:00.000-05:00", "summary" : "Skin mRNA profiles of wild-type (WT) and EGFR Inhibitors (Gefitinib and Afatinib) induced rash rats were generated by deep sequencing, in triplicate, using Illumina GAIIx. Raw sequences were mapped to the rat reference sequence by Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis was performed using the DESeq2 R package (1.16.1).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35618045" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199976" }, "primaryId" : "GEO:GSE199976", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199976" } ] }, "title" : "Kidney RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org)", "dateAssigned" : "2022-04-01T00:00:00.000-05:00", "summary" : "As part of the PhenoGen Project (https://phenogen.org), kidney RNA-Seq data has been collected from the HXB/BXH recombinant inbred rat panel, which is part of the Hybrid Rat Diversity Panel (HRDP). RNA expression levels were estimated using high throughput RNA sequencing (RNA-Seq) on long (>200 nucleotides) RNAs, i.e., total RNA where ribosomal RNA was depleted. These data can be used to examine predisposition phenotypes in the HRDP. Processed data and interactive graphics are also available through the PhenoGen website.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36186443" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199984" }, "primaryId" : "GEO:GSE199984", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199984" } ] }, "title" : "Whole brain RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org)", "dateAssigned" : "2022-04-01T00:00:00.000-05:00", "summary" : "As part of the PhenoGen Project (https://phenogen.org), whole brain RNA-Seq data has been collected from strains of the Hybrid Rat Diversity Panel (HRDP). RNA expression levels were estimated using high throughput RNA sequencing (RNA-Seq) on long (>200 nucleotides) RNAs, i.e., total RNA where ribosomal RNA was depleted. These data can be used to examine predisposition phenotypes in the HRDP. Processed data and interactive graphics are also available through the PhenoGen website. Additional data from additional strains will be added as they become available.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36186443" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199985" }, "primaryId" : "GEO:GSE199985", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199985" } ] }, "title" : "Epigenetic function during heroin self-administration controls future relapse-like behaviors in a cell type-specific manner", "dateAssigned" : "2022-04-01T00:00:00.000-05:00", "summary" : "We used microarrays to define genes differentially expressed in the presence or absence of AAV2-DIO-HDAC5-3SA in both D1 and D2 cell-types derived from Nucleus accumbens following vTRAP.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36745812" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199986" }, "primaryId" : "GEO:GSE199986", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE199986" } ] }, "title" : "Liver RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org)", "dateAssigned" : "2022-04-01T00:00:00.000-05:00", "summary" : "As part of the PhenoGen Project (https://phenogen.org), liver RNA-Seq data has been collected from strains of the Hybrid Rat Diversity Panel (HRDP). RNA expression levels were estimated using high throughput RNA sequencing (RNA-Seq) on long (>200 nucleotides) RNAs, i.e., total RNA where ribosomal RNA was depleted. These data can be used to examine predisposition phenotypes in the HRDP. Processed data and interactive graphics are also available through the PhenoGen website. Additional data from additional strains will be added as they become available.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200055" }, "primaryId" : "GEO:GSE200055", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200055" } ] }, "title" : "Comparison of oligodendrocyte mRNAs in normal and differentiated conditions in culture", "dateAssigned" : "2022-04-03T00:00:00.000-05:00", "summary" : "Oligodendrocyte mRNAs in control and differentiated conditions are compared.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200057" }, "primaryId" : "GEO:GSE200057", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200057" } ] }, "title" : "Depletion of CRAT in cardiomyocyte results in DCM", "dateAssigned" : "2022-04-03T00:00:00.000-05:00", "summary" : "Carnitine acetyltransferase (CRAT) is a mitochondrial enzyme and catalyzes the conversion of acetyl-CoA to acetyl-Carnitine, which enables its export from mitochondria. It was reported that CRAT played a central role in regulating metabolic flexibility and promoting substrate switching from fatty acid to glucose in skeletal myocytes5. Interestingly, CRAT is most abundantly expressed in the heart and its activity is dramatically decreased in the mouse model of HF5,9. However, the specific contribution of this enzyme in the pathogenesis of HF remains largely uncharacterized.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200058" }, "primaryId" : "GEO:GSE200058", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200058" } ] }, "title" : "Gene expression alteration in rat primary TNF-α-induced chondrocytes and the treatment of Nanofat lysate", "dateAssigned" : "2022-04-03T00:00:00.000-05:00", "summary" : "Therefore, to investigate the effects of the stimulation of TNF-α on primary chondrocytes and the effect of NFL, we can speculate that unique genetic profiles in vitro might exist with different interventions.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37050907" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200127" }, "primaryId" : "GEO:GSE200127", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200127" } ] }, "title" : "Contraction band necrosis and dephosphorylated cardiac connexin 43 in rat myocardium after 14 days cocaine administration", "dateAssigned" : "2022-04-04T00:00:00.000-05:00", "summary" : "Total RNAs from the control and cocaine groups (day 14) were subjected to DNA microarray analysis.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36233284" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200175" }, "primaryId" : "GEO:GSE200175", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200175" } ] }, "title" : "Transcriptomic effects of medical treatment on gene expression of growth hormone secreting pituitary neruoendocrine tumour biology", "dateAssigned" : "2022-04-05T00:00:00.000-05:00", "summary" : "Pituitary neuroendocrine tumours (PitNET) are rare neoplasms of the pituitary gland that can overproduce pituitary hormones or cause headaches and visual impairment due to mass effect. Growth hormone overproducing somatotroph PitNETs cause acromegaly leading to wide range of connective tissue, metabolic and oncologic disorders. The medical treamment of acromegaly is somatostin analogues (SSA) in specific cases combined with dopamine agnoists (DA), but almost half of patients excert SSA resistence and potential causes of this is unknown. The aim of this study was to characterize transcriptomic patterns of somatotroph PitNETs specifically assessing impact of SSA treatment effects. We investigated gene expession on several levels and functional models of GH PitNETs - tumour tissue of patients with and without SSA preoperative treamtment, tumour derived pituisphere model and classically used GH3 cell line treated with SSA.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200184" }, "primaryId" : "GEO:GSE200184", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200184" } ] }, "title" : "mRNA and microRNA Transcriptional Profiling of Gestation Day 21 Female Rat Liver and Placenta following Gestation Day 6 - 20 Ketoconazole Exposure", "dateAssigned" : "2022-04-05T00:00:00.000-05:00", "summary" : "We report the RNAseq-based mRNA and microRNA transcriptome profiles of gestation day 21 female rat liver and placenta following oral ketoconazole exposure from gestation day 6 to 20. A treatment-related change in mRNA and microRNA levels was observed in both liver and placenta.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35596682" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200221" }, "primaryId" : "GEO:GSE200221", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200221" } ] }, "title" : "Integrated multi-omics and bioinformatic methods to reveal the mechanisms of sinomenine against diabetic nephropathy", "dateAssigned" : "2022-04-05T00:00:00.000-05:00", "summary" : "To investigate the function and the molecular mechanism of sinomenine in treating diabetic nephropathy via transcriptomics study.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200249" }, "primaryId" : "GEO:GSE200249", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200249" } ] }, "title" : "The effects of environmental enrichment on maternal nurturance, lactation quality, and offspring social behavior", "dateAssigned" : "2022-04-05T00:00:00.000-05:00", "summary" : "It was our goal to discern the effects of environemental enrichement on quality of mRNA in milk from Sprague-Dawley rat mothers.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35995560" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200307" }, "primaryId" : "GEO:GSE200307", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200307" } ] }, "title" : "MicroRNA Expression Profiling of Lumbar Spinal Cord in a Rat Model of Bone Cancer Pain", "dateAssigned" : "2022-04-06T00:00:00.000-05:00", "summary" : "Bone cancer pain (BCP), in which the majority is caused by metastasis from other cancer sites, is the most common type of chronic cancer pain. Bone cancer pain is developed accompanied by changes of numerous genes expression, from peripheral to central nervous system, which may account for this dysfunctional nociceptive perception. Although the pivotal role of lncRNA in neuropathic pain are well acknowledged, the involvement of lncRNA in bone cancer pain development are remain to be clarified. Thus, in the present study we performed transcriptome sequencing to explore changes in expression profiles of lncRNA and mRNA to provide a landscape of dysregulated miRNA in spinal cord of bone cancer pain.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36143385" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200400" }, "primaryId" : "GEO:GSE200400", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200400" } ] }, "title" : "Transcription factor Creb3l1 maintains proteostasis in neuroendocrine cells [ChiP-seq]", "dateAssigned" : "2022-04-07T00:00:00.000-05:00", "summary" : "We have shown that the expression of the endoplasmic reticulum stress sensor Creb3l1 increases in magnocellular neurones (MCNs) in the rat hypothalamus in response to increased physiological demands for protein synthesis. Here we adopted a multiomic strategy to investigate specific roles of Creb3l1 in MCN homeostasis. We first performed chromatin immunoprecipitation followed by genome sequencing (ChIP-seq) to identify Creb3l1 genomic targets in the water deprived MCN enriched hypothalamic preparation. We then compared ChIP-seq gene targets with water deprived and Creb3l1 knockdown supraoptic nucleus RNA sequencing transcriptome datasets. This has provided an integrated signalling-gene regulation network for this transcription factor illuminating changes to cell pathways and function, an approach that has led us to understand the physiological changes that occur in MCNs to cope with excessive protein demands.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35803572" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200401" }, "primaryId" : "GEO:GSE200401", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200401" } ] }, "title" : "Transcription factor Creb3l1 maintains proteostasis in neuroendocrine cells [RNA-seq]", "dateAssigned" : "2022-04-07T00:00:00.000-05:00", "summary" : "We have shown that the expression of the endoplasmic reticulum stress sensor Creb3l1 increases in magnocellular neurones (MCNs) in the rat hypothalamus in response to increased physiological demands for protein synthesis. Here we adopted a multiomic strategy to investigate specific roles of Creb3l1 in MCN homeostasis. We first performed chromatin immunoprecipitation followed by genome sequencing (ChIP-seq) to identify Creb3l1 genomic targets in the water deprived MCN enriched hypothalamic preparation. We then compared ChIP-seq gene targets with water deprived and Creb3l1 knockdown supraoptic nucleus RNA sequencing transcriptome datasets. This has provided an integrated signalling-gene regulation network for this transcription factor illuminating changes to cell pathways and function, an approach that has led us to understand the physiological changes that occur in MCNs to cope with excessive protein demands.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35803572" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200428" }, "primaryId" : "GEO:GSE200428", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200428" } ] }, "title" : "Genomic analysis of kidneys from male and female F1 Fischer F344 rats following dietary ochratoxin A exposure in utero and throughout development.", "dateAssigned" : "2022-04-07T00:00:00.000-05:00", "summary" : "A toxicogenomic approach was used to assess the sex-specific transcriptomic changes in kidney tissue of rats from a one generation reproductive toxicity study. Transcriptomic data from both F0 and F1, male and female rats were assessed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200453" }, "primaryId" : "GEO:GSE200453", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200453" } ] }, "title" : "Genetic mapping of multiple metabolic traits identifies novel genes for adiposity, lipids and insulin secretory capacity in outbred rats II", "dateAssigned" : "2022-04-07T00:00:00.000-05:00", "summary" : "RNA-Seq was used in an attempt to identify candidate genes regulating metabolic and physiological traits", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200463" }, "primaryId" : "GEO:GSE200463", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200463" } ] }, "title" : "tendon mRNA seq after particulate matter inhalation", "dateAssigned" : "2022-04-08T00:00:00.000-05:00", "summary" : "Open tenotomy of the Achilles tendon of 6 rats was performed. The animals were divided into two groups according to exposure of PM2.5 (particulate matter less than 2.5 µm): control group (Non-PM group) or PM exposure group (PM group). After 6 weeks of PM exposure, the tendon RNA was extracted and anlyzed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35897746" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200470" }, "primaryId" : "GEO:GSE200470", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200470" } ] }, "title" : "Divergent composition and transposon-silencing activity of small RNAs in mammalian oocytes", "dateAssigned" : "2022-04-08T00:00:00.000-05:00", "summary" : "We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species, except mouse. We found endo-siRNAs resulted from the truncated Dicer isoform were mouse-specific, and os-piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2’-3’-O-methylation. The sequences of many highly expressed piRNA clusters are fast-evolving compared with their syntenic genomic locations, and the TE families distributing in the conserved piRNA clusters are various between species.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200518" }, "primaryId" : "GEO:GSE200518", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200518" } ] }, "title" : "Osteoinductive biodegradable intramedullary implant accelerates bone healing and mitigates complications in a rat bone transport model", "dateAssigned" : "2022-04-08T00:00:00.000-05:00", "summary" : "Bone transport distraction osteogenesis (DO) is one of the most successful surgery-driven endogenous tissue regeneration approaches for the treatment of large bone defects. However, prolonged consolidation, docking site nonunion, and pin tract infection remain challenging complications. Here, we engineered an osteoinductive, biodegradable intramedullary (IM) implant for sustained release of bone morphogenetic protein-2 (BMP-2) as an adjunctive therapy of bone transport to address the clinical challenges. A hybrid tissue engineering construct (HyTEC) technique was developed to enable sustained release of BMP-2 in a broad range. 100% bony fusion was achieved in the IM implants incorporating with 2 μg and 6 μg BMP-2 as early as 34 days after bone transport surgeries in the management of 8-mm femoral defect. Load bearing was restored 55 days after surgeries when the fixator was removed. Eluting BMP-2 from the IM implants accelerates bone formation and angiogenesis at early phase, and increase mineralization at late phase, especially at the docking sites, leading to early bony bridging. Moreover, no pin tract infection but seamless integration could be found in the 2 μg and 6 μg BMP-2 treated groups. Surgical control and IM implant showed high proportion of non-union and pin tract infections. 2 μg BMP-2 delivered by collagen sponge or 0.5 μg BMP-2-laden IM implant did not induce bone regeneration effectively, resulting in some non-unions and infections. A presence of bacteria of fecal origin in the infection sites was identified. In conclusion, this osteoinductive IM implant holds great promise in revolutionizing bone transport DO technique in the management of bone defect by accelerating bone regeneration and mitigating complications.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200550" }, "primaryId" : "GEO:GSE200550", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200550" } ] }, "title" : "Hepatocyte-derived liver progenitor-like cells attenuate liver cirrhosis via induction of apoptosis in hepatic stellate cells", "dateAssigned" : "2022-04-10T00:00:00.000-05:00", "summary" : "Cell therapy shows great promise as an alternative therapy for the cirrhotic liver. We have previously developed an approach for efficient expansion of both murine and human hepatocyte-derived liver progenitor-like cells (HepLPCs) in vitro without genetic modification. The current study aimed to apply HepLPCs to treatment of liver cirrhosis. The effects of allogeneic HepLPCs transplantation were studied in rat models of liver cirrhosis induced by carbon tetrachloride (CCl4) . Liver tissues were collected and analyzed by RNA sequencing array to analyze changes in histology or gene expression patterns. Transplantation of HepLPCs reduced active fibrogenesis and net fibrosis in model of liver cirrhosis. Apoptosis of hepatic stellate cells (HSCs) was observed in vivo after HepLPCs treatment.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200564" }, "primaryId" : "GEO:GSE200564", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200564" } ] }, "title" : "Transcriptional profile of brain region involved in habitual learning following methamphetamine self-administration and dopamine receptor antagonist", "dateAssigned" : "2022-04-11T00:00:00.000-05:00", "summary" : "Methamphetamine (METH) is a powerful stimulant that has caused addiction (compulsive drug seeking and taking behavior) in millions of people world-wide. METH abuse is also associated with negative impact on the brain. One feature of addiction is uncontrollable drug seeking despite adverse consequences and becomes habitual. To mimic this in a rat model, rats with a history of METH use are given the opportunity to earn METH accompanied by aversive shocks on their feet. Rats that continue to take METH are shock-resistant (SR) and rats that reduce their METH intake are shock-sensitive (SS ).Rats that self-administered saline are controls (CT). Thereafter, rats were injected intraperitoneally with the dopamine D1 receptor antagonist, SCH23390. SCH23390 caused substantial reduction of METH taking in a dose-dependent fashion. Stopping SCH23390 administration led to re-emergence of compulsive METH taking in the shock-resistant rats.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:40141377" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200598" }, "primaryId" : "GEO:GSE200598", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200598" } ] }, "title" : "RNA-seq of cardiomyocytes exposed to glucose deprivation with or without empagliflozin treatment", "dateAssigned" : "2022-04-11T00:00:00.000-05:00", "summary" : "Glucose-lowering drugs sodium-glucose cotransporter 2 (SGLT2) inhibitors reduce the risk of serious heart failure events, regardless of diabetes status, but the underling mechanism of this cardioprotective benefit is unknown. Here, we performed RNA-seq screening in cardiomyocytes to determine the potential cardioprotective mechanism of empagliflozin (EMPA). ", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200666" }, "primaryId" : "GEO:GSE200666", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200666" } ] }, "title" : "Wnt5a-YAP signaling axis mediates mechanotransduction in cardiac myocytes and contributes to the transition to heart failure (rat sample)", "dateAssigned" : "2022-04-12T00:00:00.000-05:00", "summary" : "Non-canonical Wnt signaling activated by Wnt5a and Wnt11 is required for the development of second heart field cardiac progenitor cells in mice. However, the pathophysiological role of non-canonical Wnt signaling in the adult heart has not been fully elucidated. Here we show that cardiomyocyte-specific Wnt5a knockout mice exhibit improved systolic function and reduced expression of mechanosensitive genes including Nppb compared to control mice when subjected to pressure overload. In cultured cardiac myocytes, Wnt5a knockdown reduces the upregulation of Nppb gene expression and YAP nuclear translocation induced by cyclic cell stretch. Wnt5a knockdown-induced Nppb downregulation in response to cell stretch is rescued by inhibition of Hippo pathway, and the rescue effect of Hippo inhibition is canceled by YAP knockdown. These results collectively suggest that Wnt5a-YAP signaling axis mediates mechanotransduction in cardiac myocytes and contributes to the transition to heart failure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:37456848" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200709" }, "primaryId" : "GEO:GSE200709", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200709" } ] }, "title" : "Tendon methylation microarray after particulate matter inhalation", "dateAssigned" : "2022-04-12T00:00:00.000-05:00", "summary" : "Genome-wide DNA methylation profiles were determinen. DNA amplicons were prepared using Differential Methylation Hybridization (DMH) method, subsequently hybridized on to the Customized Agilent Rat CpG island Microarray. The goal was to unravel the DNA methylation patterns in different subgropus of tendon tissue according to partciulate matter exposure.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35897746" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200928" }, "primaryId" : "GEO:GSE200928", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE200928" } ] }, "title" : "Transcriptomic Changes in Microdissected CCDs after Three Hours Lipopolysaccharide (LPS) Administration in Rats", "dateAssigned" : "2022-04-17T00:00:00.000-05:00", "summary" : "Ureteral obstruction is marked by disappearance of the vasopressin-dependent water channel aquaporin-2 (AQP2) in the renal collecting duct and polyuria upon reversal. Most studies of unilateral ureteral obstruction (UUO) models have examined late time points, obscuring the early signals that trigger loss of AQP2. Here, we performed RNA-Seq on microdissected rat cortical collecting ducts (CCDs) to identify early signaling pathways post-UUO. To address whether the induction of inflammatory signaling is a cause of loss of AQP2 expression, we directly induced inflammatory signaling in rats with lipopolysaccharide (LPS) administration", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35918145" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201025" }, "primaryId" : "GEO:GSE201025", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201025" } ] }, "title" : "Analysis of gene expression patterns in denervated muscle atrophy", "dateAssigned" : "2022-04-19T00:00:00.000-05:00", "summary" : "To further analyze the gene expression patterns in denervated muscle atrophy, we have employed whole genome microarray.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35812340" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201117" }, "primaryId" : "GEO:GSE201117", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201117" } ] }, "title" : "Increased risk of mammary cancer recurrence in socially isolated rats is linked to upregulation of IL6/JAK/STAT3 and inhibition of oxidative phosphorylation signaling, activities blocked by the herbal mixture Jaeumganghwa-tang", "dateAssigned" : "2022-04-20T00:00:00.000-05:00", "summary" : "While multifactorial in origin, one of the most prevalent and impactful consequences of social isolation is an increase in cancer mortality. Using a preclinical model in Sprague Dawley rats, we found that social isolation increased the risk of mammary tumor recurrence after completion of antiestrogen therapy. The increased recurrence risk was associated with an upregulation of IL6/JAK/STAT3 signaling in the mammary glands and tumors and suppression of mitochondrial oxidative phosphorylation (OXPHOS) pathway. Also inhibited were genes involved in mitochondrial pyruvate transport and the conversion of pyruvate to acetyl CoA but lactate levels were not altered. In addition, social isolation increased the expression of receptor for advanced glycation end-products (RAGE), consistent with the impaired insulin sensitivity and weight gain linked to social isolation. All these changes are commonly associated with aging. In socially isolated animals consumption of the anti-inflammatory 12 herb mixture Jaeumganghwa-tang (JGT) inhibited IL6/JAK/STAT3 signaling, upregulated OXPHOS signaling, suppressed expression of the RAGE ligands S100a8 and S100a9, and prevented the increased risk of mammary cancer recurrence. In summary, increased breast cancer mortality among socially isolated survivors may be most effectively prevented by focusing on the period following the completion of endocrine therapy using tools that inhibit IL6/JAK/STAT3 inflammatory cytokine signaling and reverse disrupted OXPHOS.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36980301" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201161" }, "primaryId" : "GEO:GSE201161", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201161" } ] }, "title" : "Screening for crucial biomarkers of tendon injury and repair in a rat model", "dateAssigned" : "2022-04-20T00:00:00.000-05:00", "summary" : "The rat tendon injury models were established and divided into three groups: normal control group, injury model group, and celecoxib + lactoferrin treatment group. Then, RNA sequencing and differential expression analysis were performed for samples from injury model group and celecoxib + lactoferrin treatment group on day 14. Next, autophagy/hypoxia/ferroptosis/pyroptosis-related genes retrieved from the corresponding databases and related literatures were downloaded to obtain the genes associated with autophagy/hypoxia/ferroptosis/pyroptosis. Subsequently, functional annotation, protein-protein interaction (PPI) network and transcriptional regulatory network construction for these genes were performed.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201163" }, "primaryId" : "GEO:GSE201163", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201163" } ] }, "title" : "GPER/β-alanine Positive Interaction in the Dorsal Root Ganglion Uncovers Potential Mechanisms: Mediating Continuous Neuronal Sensitization and Neuroinflammation Responses in Neuropathic Pain", "dateAssigned" : "2022-04-20T00:00:00.000-05:00", "summary" : "Background: The pathogenesis of neuropathic pain and the reasons for the prolonged unhealing are still unknown. Increasing evidence suggests that oestrogen sex differences play a role in pain sensitivity, but few studies focused on the role of oestrogen receptor which maybe an important molecular component contributing to peripheral pain transduction. We aimed to investigate the impact of ooestrogen receptors in nociceptive neuronal response in the dorsal root ganglion (DRG) and spinal dorsal horn using a spared nerve injury (SNI) rat model of chronic pain. Methods: We used a class of oestrogen receptors antagonists and agonists intrathecal (i.t.) administrated to male rats with SNI or normal rats to identify the main receptor. Moreover, we applied genes identified through genomic metabolic analysis to determine the key metabolism point and elucidate potential mechanisms mediating continuous neuronal sensitisation and neuroinflammation responses in neuropathic pain. The excitability of DRG neurons was detected using the patch clamp technique. Primary culture was used to extract microglia and DRG neurons, and siRNA transfection was used to silence receptor protein expression. Immunofluorescence, Western blotting, qPCR and behavioral testing were used to assess the expressions, cellular distributions, and actions of main receptor and its related signaling molecules. Results: Increasing the expression and function of G protein-coupled oestrogen receptor (GPER), but not oestrogen receptor-α (ERα) and oestrogen receptor-β (ERβ), in the DRG neuron and microglia, but not the dorsal spinal cord, contributed to SNI-induced neuronal sensitisation. Inhibiting GPER expression in the DRG alleviated SNI-induced pain behaviours and neuroinflammation by downregulating iNOS, IL-1β and IL-6 expression as well as restoring GABAα2 expression simultaneously. Additionally, the positive interaction between GPER and β-alanine, β-alanine accumulation enhances pain sensation and promotes chronic pain development. Conclusion: GPER activation in the DRG causes a positive interaction of β-alanine with iNOS, IL-1β and IL-6 expression and represses GABAα2 involved in post-SNI neuropathic pain development. Blocking GPER and eliminating β-alanine in the DRG neuron and microglia may prevent neuropathic pain development.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35729568" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201196" }, "primaryId" : "GEO:GSE201196", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201196" } ] }, "title" : "A honeybee stinger inspired self-interlocking microneedle patch and its application in myocardial infarction treatment", "dateAssigned" : "2022-04-20T00:00:00.000-05:00", "summary" : "Microneedle patches are widely employed in pain-free drug delivery, biosensing, and cosmetic applications. However, weak tissue adhesion remains a major challenge in clinical translation of microneedle patches. Here, mimicking the structural features of honeybee stingers, stiff polymeric microneedles with unidirectionally backward facing barbs were fabricated and embedded into various elastomer films to produce self-interlocking microneedle patches. The spirality of the barbing pattern was adjusted to increase interlocking efficiency. In the challenging working condition of animal hearts beat with large cyclic strains, the barbs provided 0.4 N interlocking force, which resulted in firm fixation of the bioinspired microneedle patch. In addition, the minimal bleeding caused by microneedle puncturing adhered the porous surface of the patch substrate between microneedles to the epicardium via coagulation. In the demonstrative application of myocardial infarction treatment, the microneedle patches significantly reduced cardiac wall stress and strain in the infarct and border zone, maintaining left ventricular function and morphology. In addition, the microneedle patch was minimally invasively implanted onto beating porcine heart free of sutures and adhesives, and the fixation step only took 2 minutes. Therefore, the honeybee stinger inspired microneedles could provide an adaptive and convenient means to adhere patches for various medical applications.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201231" }, "primaryId" : "GEO:GSE201231", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201231" } ] }, "title" : "Effect of anti-osteoporotic treatments on circulating and bone microRNA patterns in osteopenic ZDF ratsEffect of anti-osteoporotic treatments on circulating and bone microRNA patterns in osteopenic ZDF rats", "dateAssigned" : "2022-04-21T00:00:00.000-05:00", "summary" : "We studied microRNA expression levels from serum and ulna bone in an in vivo model of type II diabetes (ZDF rats) by investigating different anti-osteoporotic treatments (anti-sclerostin, PTH and insulin). Serum and ulna bone RNA were extracted and subject to small RNA sequencing on an Illumina NextSeq550 SR75 High using 75bp, single end reads. After mapping against Rnor.6.0 provided by Ensembl and miRBase v22.1 differential expression analysis was undertaken with edgeRv3.32 using a quasi-likelihood negative binomial generalized log-linear model. We identified a panel of altered small non-coding RNAs.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35742976" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201236" }, "primaryId" : "GEO:GSE201236", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201236" } ] }, "title" : "Genome-wide association study finds multiple loci associated with intraocular pressure in HS rats", "dateAssigned" : "2022-04-21T00:00:00.000-05:00", "summary" : "Elevated intraocular pressure (IOP) is influenced by environmental and genetic factors. It is associated with 23 multiple disease processes with primary open angle glaucoma (POAG) being the most prevalent. Due to its 24 complex, multifactorial nature, genetic predisposition is not completely understood thus, there is an urgent 25 need for additional investigations into the genetic regulation of IOP. Heterogenous stock (HS) outbred rats are 26 a multigenerational outbred population derived from eight inbred strains that have been fully sequenced. This 27 population is ideal for genome-wide association studies (GWAS) due to the accumulated recombinations 28 among well-defined haplotypes, the relatively high allele frequencies, access to a large collection of tissue 29 samples, and the large allelic effect size compared to human studies. The purpose of this study was to identify 30 genetic loci underlying elevated IOP using HS rats. Both male and female HS rats (N=1,812) were used in the 31 study. Genotyping-by-sequencing was used to obtain ~3.5M single nucleotide polymorphisms from each 32 individual. We performed a GWAS for the IOP phenotype using a linear mixed model and used permutation to 33 determine a genome-wide significance threshold. We also estimated SNP heritabilities. Our GWAS results 34 identified three genome-wide significant loci for elevated IOP on chromosomes 1, 5, and 16. These loci 35 contained 7 genes in total including Tyr, Grm5, Ctsc, Rab38, MGC94199, Plekhf2, and Csmd1. We also 36 mapped expression quantitative trait loci (eQTLs) in HS rat eye tissue and discovered a cis-eQTL for Ctsc 37 among our significant loci. Tyr is the only gene that has been previously associated with human IOP. This 38 study highlights the efficacy of HS rats for investigating the genetics of elevated IOP and identifying potential 39 candidate genes for future functional testing. In summary, GWAS using HS rats is a powerful method for 40 identifying genome regions that harbor variants responsible for the variation in quantitative traits, such as IOP. 41 Additional studies are ongoing to further narrow the list of candidate genes in these intervals.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201258" }, "primaryId" : "GEO:GSE201258", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201258" } ] }, "title" : "Genome-wide identification of m6A-related transcriptional profiles in cortex of rats with cerebral ischemia-reperfusion and intervention of Buyang Huanwu Decoction", "dateAssigned" : "2022-04-21T00:00:00.000-05:00", "summary" : "To reveal the effect of Buyang Huanwu Decoction on m6A related transcriptional profiles of cortex in rats with cerebral ischemia-reperfusion injury", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36479246" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201263" }, "primaryId" : "GEO:GSE201263", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201263" } ] }, "title" : "Dual RNA-seq reveals a type 6 secretion system-dependent blockage of TNF-alpha signaling and BicA as a Burkholderia pseudomallei virulence factor important during gastrointestinal infection", "dateAssigned" : "2022-04-21T00:00:00.000-05:00", "summary" : "Melioidosis is a disease caused by the Gram-negative bacillus Burkholderia pseudomallei (Bpm), commonly found in soil and water of endemic areas. Naturally acquired human melioidosis infections can result from either exposure through percutaneous inoculation, inhalation, or ingestion of soil-contaminated food or water. Our prior studies recognized Bpm as an effective enteric pathogen, capable of establishing acute or chronic gastrointestinal infections following oral inoculation (Sanchez-Villamil, Tapia et al. 2020). However, the specific mechanisms and virulence factors involved in the pathogenesis of Bpm during intestinal infection are unknown. In our current study, we standardized an in vitro intestinal infection model using mouse primary intestinal epithelial cells (mIECs) and demonstrated that Bpm requires a functional T6SS for full virulence. Further, we performed dual RNA-seq analysis on Bpm-infected mIECs to evaluate differentially expressed host and bacterial genes in the presence or absence of a T6SS. Our results showed a dysregulation in the TNF- signaling via NF-B pathway in the absence of the T6SS, with some of the genes involved in inflammatory processes and cell death also affected. Analysis of the bacterial transcriptome identified virulence factors and regulatory proteins playing a role during infection, with association to the T6SS. By using a Bpm transposon mutant library and isogenic mutants, we showed that deletion of the bicA gene, encoding a putative T3SS/T6SS regulator, ablated intracellular survival and plaque formation by Bpm and impacted survival and virulence when using murine models of acute and chronic gastrointestinal infection. Overall, these results highlight the importance of the type 6 secretion system in the gastrointestinal pathogenesis of Bpm.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35984745" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201281" }, "primaryId" : "GEO:GSE201281", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201281" } ] }, "title" : "Skeletal muscle unloading affects muscle progenitor cells functional activity", "dateAssigned" : "2022-04-22T00:00:00.000-05:00", "summary" : "In this work we employed classic skeletal muscle unloading rat model to determine how hindlimb suspension (HS) affects functional activity of skeletal muscle progenitor cells (SMPC). We have purified SMPC from m. soleus from control rats and after 1, 3, 7 and 14 days of exposure (HS1, HS3, HS7, HS14).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201312" }, "primaryId" : "GEO:GSE201312", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201312" } ] }, "title" : "6-Gingerol attenuates subarachnoid hemorrhage-induced early brain injury via GBP2/PI3K/AKT pathway in the rat model", "dateAssigned" : "2022-04-22T00:00:00.000-05:00", "summary" : "Numerous studies have elucidated the neuroprotective effect of 6-gingerol in central nervous system diseases. However, the potential role and mechanism of 6-gingerol on early brain injury (EBI) after subarachnoid hemorrhage (SAH) remains poorly understood. Here, we report that 6-gingerol exerts a neuroprotective effect on SAH-induced EBI through the GBP2/PI3K/AKT pathway. A SAH rat model was established by injecting femoral artery blood into the cisterna magna. 6-gingerol or vehicle was injected intraperitoneally one hour post-SAH induction. We found that the neurological function score and brain edema of SAH rats were significantly improved after 6-gingerol treatment, as well as neuronal apoptosis was attenuated in SAH rats by Nissl staining assay and TUNEL assay. To further explore potential molecular mechanisms associated with 6-gingerol, RNA sequencing was implemented to investigate the differences in transcriptomes between SAH rats with and without 6-gingerol treatment; and found that the expression of guanylate-binding protein 2 (GBP2) evidently was suppressed with 6-gingerol treatment compared to vehicle group. In addition, dual immunofluorescence was also employed to investigate changes in neurons, astrocytes, and microglia after 6-gingerol treatment. The results showed that GBP2 was expressed in neurons but not astrocytes or microglia. Western blotting analysis results demonstrated that the PI3K/AKT pathway was activated in the SAH rats treated with 6-gingerol. Furthermore, recombinant GBP2 protein and LY294002 (PI3K inhibitor) treatment reversed the effects of 6-gingerol treatment in SAH rats. These results indicate that 6-gingerol suppressed the expression of GBP2 to activate the PI3K/AKT pathway, improve neurologic outcomes, reduce brain edema and neuronal apoptosis. In summary, our findings suggest that 6-gingerol could attenuate EBI post-SAH in rats, and 6-gingerol may serve as a novel candidate neuroprotective drug for SAH-induced EBI.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36091803" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201504" }, "primaryId" : "GEO:GSE201504", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201504" } ] }, "title" : "A promising clinical treatment for EGFRI-induced rash by targeting the early pathological alteration revealed by transcriptome analysis", "dateAssigned" : "2022-04-25T00:00:00.000-05:00", "summary" : "In order to investigate the early pathological alteration of EGFRI-induced rash, we treated rat with vehicle or afatinib for 3 days. We then performed gene expression profiling analysis using data obtained from RNA-Seq of 3 different rat skins in each group", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201522" }, "primaryId" : "GEO:GSE201522", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201522" } ] }, "title" : "Congenital heart disease associated bronchopulmonary dysplasia and its underlying mechanisms", "dateAssigned" : "2022-04-26T00:00:00.000-05:00", "summary" : "We reported the RNAseq analyses of lungs tissues in neonatal SD rats with or without reduced pulmonary blood flow(RPF). RPF was induced by causing the supravalvular pulmonary stenosis through pulmonary artery banding within 24 hours postnatally (P1). RNAseq analyses of the upper lobe of the right lung tissues was generated at P14 from 5 sham-operated rats and 5 PAB rats. The results revealed that there were 2013 differentially expressed genes between PAB and sham group at P7, among which 936 were upregulated and 1077 were downregulated. GO and KEGG pathway analysis of downregulation of DEGs indicated that abundantly enriched terms of cell migration and metabolism.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36472329" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201565" }, "primaryId" : "GEO:GSE201565", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201565" } ] }, "title" : "Sirtuin 3 is a common target of non-steroidal anti-inflammatory drugs to induce gastric cancer cell death and gastric mucosal injury.", "dateAssigned" : "2022-04-26T00:00:00.000-05:00", "summary" : "Nonsteroidal anti-inflammatory drugs (NSAIDs), the quintessential medicines to treat pain and inflammatory conditions, induce cell death in human cancer cells, as repurposed anticancer agents, and in normal gastric mucosa, as a major side effect. The subcellular target/s of NSAIDs that leads to the cell death remained elusive so far. Here, by venturing transcriptomics followed by functional validation, we, for the first time, identified mitochondrial deacetylase Sirtuin 3 (Sirt3) as a non-canonical target of NSAIDs whose depletion induced the hyperacetylation of mitochondrial proteome, OGG1 depletion, mtDNA damage, electron transport chain defect associated mitochondrial dysfunction and finally cell death. Silencing of Sirt3 in AGS cells (a human gastric adenocarcinoma cell line) significantly aggravated NSAID-induced cytopathology. Whereas, honokiol mediated induction of Sirt3 corrected the NSAID-induced transcriptome alteration and gastropathy in rodent model. Together, the results identify Sirt3 as a common target used by NSAIDs to induce gastric carcinoma cell death and gastric mucosal injury.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201623" }, "primaryId" : "GEO:GSE201623", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201623" } ] }, "title" : "Egr2 promoter antisense RNA as coordinator of chromatin remodeling and genome reorganization in Schwann cells [RNA-seq]", "dateAssigned" : "2022-04-26T00:00:00.000-05:00", "summary" : "The Egr2 promoter antisense RNA (Egr2-AS-RNA) recruits chromatin remodeling complexes to inhibit Egr2 transcription following peripheral nerve injury. Here we show that the Egr2-AS-RNA modulates chromatin accessibility and serves as scaffold for two distinct histone modification complexes. The Egr2-AS-RNA binds to Ezh2 and Wdr5 and enables coordinate targeting of H3K27me3 and H3K4me3 to promoters of Egr2 and c-Jun. Expression of the AS-RNA results in reorganization of the global chromatin landscape and quantitative changes in loop formation and in contact frequency at domain boundaries exhibiting enrichment for AP-1 binding events. Our results show for the first time that the Egr2 promoter AS-RNA may serve as a regulator of coordinate chromatin remodeling and genome organization to regulate transcription, with a significant role in phenotypic plasticity of SCs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201624" }, "primaryId" : "GEO:GSE201624", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201624" } ] }, "title" : "Egr2 promoter antisense RNA as coordinator of chromatin remodeling and genome reorganization in Schwann cells [ATAC-seq]", "dateAssigned" : "2022-04-26T00:00:00.000-05:00", "summary" : "The Egr2 promoter antisense RNA (Egr2-AS-RNA) recruits chromatin remodeling complexes to inhibit Egr2 transcription following peripheral nerve injury. Here we show that the Egr2-AS-RNA modulates chromatin accessibility and serves as scaffold for two distinct histone modification complexes. The Egr2-AS-RNA binds to Ezh2 and Wdr5 and enables coordinate targeting of H3K27me3 and H3K4me3 to promoters of Egr2 and c-Jun. Expression of the AS-RNA results in reorganization of the global chromatin landscape and quantitative changes in loop formation and in contact frequency at domain boundaries exhibiting enrichment for AP-1 binding events. Our results show for the first time that the Egr2 promoter AS-RNA may serve as a regulator of coordinate chromatin remodeling and genome organization to regulate transcription, with a significant role in phenotypic plasticity of SCs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201625" }, "primaryId" : "GEO:GSE201625", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201625" } ] }, "title" : "Egr2 promoter antisense RNA as coordinator of chromatin remodeling and genome reorganization in Schwann cells [Hi-C]", "dateAssigned" : "2022-04-26T00:00:00.000-05:00", "summary" : "The Egr2 promoter antisense RNA (Egr2-AS-RNA) recruits chromatin remodeling complexes to inhibit Egr2 transcription following peripheral nerve injury. Here we show that the Egr2-AS-RNA modulates chromatin accessibility and serves as scaffold for two distinct histone modification complexes. The Egr2-AS-RNA binds to Ezh2 and Wdr5 and enables coordinate targeting of H3K27me3 and H3K4me3 to promoters of Egr2 and c-Jun. Expression of the AS-RNA results in reorganization of the global chromatin landscape and quantitative changes in loop formation and in contact frequency at domain boundaries exhibiting enrichment for AP-1 binding events. Our results show for the first time that the Egr2 promoter AS-RNA may serve as a regulator of coordinate chromatin remodeling and genome organization to regulate transcription, with a significant role in phenotypic plasticity of SCs.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201674" }, "primaryId" : "GEO:GSE201674", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201674" } ] }, "title" : "Gene expression changes in femur tissues of ovariectomy-induced osteoporosis rats", "dateAssigned" : "2022-04-27T00:00:00.000-05:00", "summary" : "We then performed gene expression profiling analysis using data obtained from RNA-seq of the rat femur tissues.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35680981" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201686" }, "primaryId" : "GEO:GSE201686", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201686" } ] }, "title" : "Transcription regulation of SNCA by dystonia type 6 gene product THAP1 [Rat_ChIP-seq]", "dateAssigned" : "2022-04-27T00:00:00.000-05:00", "summary" : "The predominantly function of THAP1 has been defined as a transcription factor, but how it regulates gene expression in human neurons is not well understood. Here, we found that THAP1 is able to regulate the expression of alpha-synuclein (SNCA), a key protein in Parkinson’s disease (PD).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35015830" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201717" }, "primaryId" : "GEO:GSE201717", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201717" } ] }, "title" : "Molecular and Functional Remodeling of the Superior and Inferior Sinoatrial Nodes in a Rat Model of Hypertrophic Cardiomyopathy", "dateAssigned" : "2022-04-27T00:00:00.000-05:00", "summary" : "Conclusions: Pressure-overload-induced heart failure resulted in significant downregulation of critical transcription factors, ion channels, and structural transcripts of the iSAN, which could explain the functional silencing of the iSAN in failing rat hearts.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201757" }, "primaryId" : "GEO:GSE201757", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201757" } ] }, "title" : "Long-Term Persistence of Fetal Hepatocyte Gene Expression and Histone Modification Signatures Following Transplantation to Adult Liver", "dateAssigned" : "2022-04-28T00:00:00.000-05:00", "summary" : "Introduction: Hepatic cell transplantation offers an alternative to orthotopic liver transplantation for chronic liver disease. We previously demonstrated that fetal rat hepatocytes durably persist and proliferate when transplanted to an injured adult liver. To identify mechanisms underlying fetal hepatocyte repopulation, we profiled gene expression and histone post-translational modifications (hPTM) of post-transplantation fetal colonies and surrounding liver, as well as those of primary fetal and adult hepatocytes. Methods: Using the DPPIV rat model, we transplanted and traced fetal hepatocytes into adult hosts. At 10 months after transplantation, we used laser capture microscopy to isolate fetal-derived colonies and surrounding adult host tissue. RNA and histones were extracted from laser captured tissue and isolated hepatocytes for RNA-seq and quantitation of hPTM. Results: Principal component analysis of RNA-seq results discriminated between fetal-derived colonies and surrounding adult host tissue. We identified 953 differentially expressed genes, many of which were significantly overexpressed in pre-transplant fetal hepatocytes relative to adult hepatocytes. This gene set included a disproportionate number of genes encoding ion transmembrane transporters. Proteomic analyses identified 13 distinct marks on Histone H3 whose relative abundance differed significantly between fetal-derived colonies and adult host tissue. Of these 13 marks, 11 had abundance profiles similar to those of fetal hepatocytes. Conclusions: A distinct gene expression and epigenetic profile seen in pre-transplant fetal cells is retained for at least 10 months following transplantation. Ontological and pathway analysis indicates activation of ion transporters, which may relate to the growth advantage of transplanted fetal cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201888" }, "primaryId" : "GEO:GSE201888", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201888" } ] }, "title" : "Activation of NOTCH and BMP signaling pathways during acute hypoxic stress in cardiac mesenchymal cells", "dateAssigned" : "2022-04-29T00:00:00.000-05:00", "summary" : "We then performed a gene expression profile analysis using data obtained from RNA sequencing of 3 different postinfarction tissues and cells. Healthy tissues and cells of the left ventricle of the heart of sham-operated rats were used as controls.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35740305" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201900" }, "primaryId" : "GEO:GSE201900", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE201900" } ] }, "title" : "Long-term high-fat high-fructose diet induces type 2 diabetes in rats through oxidative stress", "dateAssigned" : "2022-04-29T00:00:00.000-05:00", "summary" : "Long-term consumption of a western diet is a major cause of type 2 diabetes mellitus (T2DM). However, the effects of diet on pancreatic structure and function remain unclear. Rats fed a high-fat, high-fructose (HFHF) diet were compared with rats fed a normal diet for 3 and 18 months. Plasma biochemical parameters and inflammatory factors were used to reflect metabolic profile and in-flammatory status. The rats developed metabolic disorders, and the size of the islets in the pancreas increased after three months of HFHF treatment but decreased and became irregular after 18 months. Fasting insulin, C-peptide, proinsulin, and intact proinsulin levels were significantly higher in the HFHF group than those in the age-matched controls. Plasma oxidative parameters and nucleic acid oxidation markers (8-oxo-Gsn and 8-oxo-dGsn) elevated before inflammatory factors, suggesting that the HFHF diet increased the degree of oxidative stress before affecting in-flammation. Single-cell RNA sequencing also verified that the transcriptional level of oxidoreduc-tase changed differently in islet sub-populations with aging and long-term HFHF diet. We demonstrated that long-term HFHF diet and aging-associated structural and transcriptomic changes that underlie pancreatic islet functional decay is a possible underlying mechanism of T2DM, and our study could provide new insights to prevent the development of diet-induced T2DM", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35683981" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202031" }, "primaryId" : "GEO:GSE202031", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202031" } ] }, "title" : "Gene expression profiles in ethylene glycol-induced renal stone formation and phlorizin treatment", "dateAssigned" : "2022-05-02T00:00:00.000-05:00", "summary" : "Nephrolithiasis is a disorder with a poor quality of life due to severe pain and no effective medication. Sodium-glucose cotransporter-2 (SGLT2) inhibitors, an anti-diabetic agent, have diuretic and anti-inflammatory effects, suggesting their benefit in treating nephrolithiasis. However, the effects of SGLT2 inhibition against renal stone formation have not been elucidated. To check gene expression profiles, microarray analysis was performed.", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:36349594" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202111" }, "primaryId" : "GEO:GSE202111", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202111" } ] }, "title" : "Major differences in transcriptional alterations in dorsal root ganglia between spinal cord injury and peripheral neuropathic pain models", "dateAssigned" : "2022-05-03T00:00:00.000-05:00", "summary" : "Chronic, often intractable pain is caused by neuropathic conditions such as peripheral nerve injury (PNI) and spinal cord injury (SCI). These conditions are associated with alterations in gene and protein expression correlated with functional changes in somatosensory neurons having cell bodies in dorsal root ganglia (DRGs). Most studies of DRG transcriptional alterations have utilized PNI models where axotomy-induced changes important for regeneration may overshadow changes that drive neuropathic pain. Both PNI and SCI produce DRG neuron hyperexcitability linked to pain, but contusive SCI produces little peripheral axotomy or peripheral nerve inflammation. Thus, comparison of transcriptional signatures of DRGs across PNI and SCI models may highlight pain-associated transcriptional alterations that don’t depend on peripheral axotomy and associated effects such as peripheral Wallerian degeneration. Data from our rat thoracic SCI experiments were combined with meta-analysis of whole-DRG RNA-seq datasets from prominent rat PNI models. Striking differences were found between transcriptional responses to PNI and SCI, especially in regeneration-associated genes and long noncoding RNAs. Many transcriptomic changes after SCI were also found after corresponding sham surgery, indicating they were caused by injury to surrounding tissue rather than to the spinal cord itself. Another unexpected finding was of few transcriptomic similarities between any rat neuropathic pain model and the only reported transcriptional analysis of human DRGs linked to neuropathic pain. These findings show that DRGs exhibit complex transcriptional responses to central and peripheral neural and tissue injury. Although few genes in DRG cells show similar changes in gene expression across all these painful conditions, the few widely shared transcriptional alterations promise novel insights into fundamental mechanisms within DRGs that can drive neuropathic pain.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202138" }, "primaryId" : "GEO:GSE202138", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202138" } ] }, "title" : "Analysis of miRNA expression profiles in reactivated neurons from latent PRV infection", "dateAssigned" : "2022-05-03T00:00:00.000-05:00", "summary" : "To examine the effects of glucocorticoids on latently infected PRV neurons, we constructed gene expression profiles of RNA-seq data for miRNA expression from PC-12 cell with a PRV latent infection model group (PRV group), a reactivation model group (DEX group) and a blank control group (CON group).", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:40259414" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202139" }, "primaryId" : "GEO:GSE202139", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202139" } ] }, "title" : "Analysis of mRNA expression profiles in reactivated neurons from latent PRV infection", "dateAssigned" : "2022-05-03T00:00:00.000-05:00", "summary" : "To examine the effects of glucocorticoids on latently infected PRV neurons, we constructed gene expression profiles of RNA-seq data from PC-12 cell with a PRV latent infection model group (PRV group), a reactivation model group (DEX group) and a blank control group (CON group).", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202168" }, "primaryId" : "GEO:GSE202168", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202168" } ] }, "title" : "Inhibition of DYRK1A, via histone modification, promotes cardiomyocyte proliferation and heart repair after myocardial infarction [ChIP-Seq]", "dateAssigned" : "2022-05-03T00:00:00.000-05:00", "summary" : "To explore effect of DYRK1A silencing on H3K4me3 and H3K27ac modification of primary cultured cardiomyocytes isolated from 1-day-old SD rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35810562" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202169" }, "primaryId" : "GEO:GSE202169", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202169" } ] }, "title" : "Inhibition of DYRK1A promotes cardiomyocyte proliferation and heart repair after myocardial infarction [RNA-Seq]", "dateAssigned" : "2022-05-03T00:00:00.000-05:00", "summary" : "To explore effect of DYRK1A silencing on gene expression of primary cultured cardiomyocytes isolated from 1-day-old SD rats", "categoryTags" : [ "unclassified" ], "publications" : [ { "publicationId" : "PMID:35810562" } ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202185" }, "primaryId" : "GEO:GSE202185", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202185" } ] }, "title" : "Effect of PPAR γ agonist on gene expression changes in RBL-2H3 cells", "dateAssigned" : "2022-05-04T00:00:00.000-05:00", "summary" : "To identify the key genes participating in the regulation of mast cell activation, we profiled the expression patterns of mRNAs associated with PPAR γ agonist,pioglitazone (PIO), treatment in RBL-2H3 cells.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202228" }, "primaryId" : "GEO:GSE202228", "crossReferences" : [ { "pages" : [ "htp/dataset" ], "id" : "GEO:GSE202228" } ] }, "title" : "Cardiac patch treatment alleviates ischemic cardiomyopathy correlated with unloading pathological stretch and reverting Piezo1/2 expression in left ventricular myocardium", "dateAssigned" : "2022-05-04T00:00:00.000-05:00", "summary" : "Pathologically elevated mechanical load promotes the adverse remodeling of left ventricle (LV) post myocardial infarction, which results in the progression from ischemic cardiomyopathy to heart failure. Cardiac patches could attenuate adverse LV remodeling by providing mechanical support to infarcted and border zone myocardium. However, the mechanism of the translation from mechanical effects to favorable therapeutic outcome is still not clear. This study aims to strengthen the foundation of the theory of cardiac patch treatment. By transcriptome analysis, we found that the myocardial transcription levels of mechanosensitive ion channel proteins Piezo1 and Piezo2 significantly increased in patients with ischemic cardiomyopathy. In vitro tensile tests with local tissue information and finite element modeling revealed a significant decrease in local strain and mechanical load in rat infarcts and sheep LV. Cardiac function and geometry were preserved compared to non-treated control. Further, in LV myocardium of the patch-treated group, MI induced expression levels of Piezo1/2 were significantly reverted to the similar levels of the control group, indicating that Piezo1/2 are key contributors as mechanosensor which initiated the signaling cascade and translated the beneficial mechanical support to therapeutic effects. These findings demonstrated the potential of cardiac patches in treating ICM patients with remodeling risks, and could provide guidance for improvement in next generation of patch devices.", "categoryTags" : [ "unclassified" ] }, { "datasetId" : { "preferredCrossReference" : { "pages" : [ "htp/dataset" ],